PDB 1pkn A proteindomain is a part of protein sequence and tertiary structure structure that can biological ... domain forms a compact three dimensional structure and often can be independently stable and protein ... protein chimeric proteins . Background The concept of the domain was first proposed in 1973 by Wetlaufer ... protein, each domain may fulfill its own function independently, or in a concerted manner with its ... 11 pages 871 9 year 2002 author George RA, Heringa J. title An analysis of proteindomain linkers ... figure, right . Each domain in this protein occurs in diverse sets of protein families. The central ... JM. title CATH a hierarchic classification of proteindomain structures pmid 9309224 doi 10.1016 S0969 ... to be the result of the insertion of one domain into another during the protein s evolution. It has ... S, Stewart M, Michie A, Swindells MB, Orengo C, Thornton JM. title Domain assignment for protein structures ... function by domain swapping pmid 11050932 doi ref Domains are units of protein structure Main ... pmc 2143041 ref In domain swapping, a secondary or tertiary element of a monomeric protein is replaced by the same element of another protein. Domain swapping can range from secondary structure ... CA, Jones DT, Thornton JM. title Protein superfamilies and domain superfolds pmid 7990952 doi 10.1038 ... of an animal proteindomain by bacteria2 pmid 1409594 doi 10.1073 pnas.89.19.8990 issue 19 pmc 50050 ... 1994 author Russell, R. B title Domain insertion pmid 7716150 doi 10.1093 protein 7.12.1407 issue ... domain. Domains are autonomous folding units Folding Further2 Protein folding date August 2010 Protein ... by structural domains represents an advantage for protein folding, with each domain being able .....911W ref domain formation appears to be the optimal solution for a large protein to bury its hydrophobic ... However, the role of inter domain interactions in protein folding and in energetics of stabilisation ... of water from the domain interface. Domains and protein flexibility The presence of multiple ... more details
1nkl 88 122 PDB3 1l9l A 104 136 In molecular biology a saposin proteindomain is a region of the saposin protein that has a certain conserved sequence or structure that defines a Proteindomaindomain ... doi 10.1002 pro.5560030219 author Ponting CP title Acid sphingomyelinase possesses a domain homologous to its activator proteins saposins B and D journal Protein Sci. volume 3 issue 2 pages 359 361 ... 91 94 year 1996 pmid 8868085 doi 10.1016 0966 842X 96 81522 8 ref Domain organization Below is a schematic diagram of the Protein primary structure primary structure of the prosaposin protein depicting .... Proteolysis Proteolytic cleavage of the protein precursor proprotein occurs in the grey regions ... 600px Human proteins containing this domain AOAH GNLY Prosaposin PSAPL1 SFTPB References reflist ... External links http www.expasy.org cgi bin nicedoc.pl?PDOC50015 Saposin B type domain in PROSITE Category Protein domains Category Protein families Category Peripheral membrane proteins membrane protein ... more details
Pfam box Symbol Pkinase Name Protein kinase domain image PDB 1apm EBI.jpg width caption Structure of the catalytic subunit of cAMP dependent protein kinase. ref name pmid15299526 Cite journal author Knighton ... 1apm TCDB OPM family 417 OPM protein 2w5a CDD cd00180 PDB The protein kinase domain is a structurally conserved sequence conserved proteindomain containing the catalytic function of protein kinase s. ref name pmid1956325 Cite journal author Hanks SK, Quinn AM title Protein kinase catalytic domain ... 0076 6879 91 00126 H url chapter 2 Protein kinase catalytic domain sequence database Identification ... isbn 9780121821012 ref ref name pmid7768349 Cite journal author Hanks SK, Hunter T title Protein kinases 6. The eukaryotic protein kinase superfamily kinase catalytic domain structure and classification ... in the catalytic domain of protein kinases. In the N terminal extremity of the catalytic domain ... TYR DYR Use dmy dates date September 2010 DEFAULTSORT Protein Kinase Domain Category Protein domains ... dependent protein kinase complexed with a peptide inhibitor and detergent journal Acta Crystallogr ... Scheeff ED, Bourne PE title Structural evolution of the protein kinase like superfamily journal PLoS ... journal.pcbi.0010049 url ref Protein kinases are a group of enzyme s that move a phosphate group ..., S. Sudarsanam, The Protein Kinase Complement of the Human Genome , Science 6 December 2002, 298 1912 1934 DOI 10.1126 science.1075762 ref Protein kinases possess a catalytic subunit which transfers ... amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. These enzymes fall into two broad classes, characterised with respect to substrate specificity serine threonine specific protein kinase serine threonine specific and tyrosine ... The protein kinase family conserved features and deduced phylogeny of the catalytic domains journal ... Function Protein kinase function has been evolutionarily conserved from Escherichia coli to Homo sapiens ... more details
protein Name LEM domain containing protein 3 caption image width HGNCid 28887 Symbol LEMD3 AltSymbols MAN1 EntrezGene 23592 OMIM 607844 RefSeq NM 014319 UniProt Q9Y2U8 PDB ECnumber Chromosome 12 Arm q Band 14 LocusSupplementaryData LEM domain containing protein 3 LEMD3 , also known as MAN1 , is an integral Inner nuclear membrane proteins protein in the inner nuclear membrane INM of the nuclear envelope . It is encoded by the LEMD3 gene ref name Worman Cite pmid 19587457 ref and was first identified after it was isolated from the serum of a patient with a collagen vascular disease. ref name PL Cite pmid 8575249 ref Structure The protein is 82.3 kDa and has a 40 amino acid long LEM domain LEM proteindomaindomain located at its amino terminal region. In its carboxyl end it has a RNA recognition motif . The LEM domain is also common to two other integral proteins of the INM lamina associated polypeptide 2 LAP2 and emerin . ref name Lin Cite pmid 10671519 ref The LEM segment enables LEMD3 to attach to the barrier to autointegration factor BAF , and therefore, indirectly interact with the chromatin . LEMD3 also has several implications in regulating the cytokine family such as the transforming growth factor beta TGF and bone morphogenic protein BMPs . The RRM domain in its carboxylic region attaches to the Smads proteins, the mediators of the cytokine family cellular signalling , and consequently, regulates the downstream genes. LEMD3 seems to play an important role in regulating the expression of several fundamental genes. LEMD3 and disease LEMD3 has been associated with laminopathies ref name Worman ref as well as osteopoikilosis . ref name Mumm Cite pmid 17087626 ref Mutations in the LEMD3 gene have been linked to several genetic diseases such as osteopoikilosis , melorheostosis and Buschke Ollendorff syndrome . See also Inner nuclear membrane proteins References reflist External links MeshName LEMD3 protein, human biochemistry stub ... more details
Infobox protein family Symbol Cementoin Name Cementoin image PDB 2rel EBI.jpg width caption solution structure of r elafin, a specific inhibitor of elastase, nmr, 11 structures Pfam PF10511 Pfam clan InterPro IPR019541 SMART PROSITE MEROPS SCOP TCDB OPM family OPM protein CAZy CDD In molecular biology, the trappin protein transglutaminase binding domain or cementoin is a proteindomain found at the N terminus of Whey Acidic Protein WAP domain containing protease inhibitors such as trappin 2. This N terminal domain enables it to become cross linked to extracellular matrix protein s by transglutaminase . ref name pmid10359639 cite journal author Schalkwijk J, Wiedow O, Hirose S title The trappin gene family proteins defined by an N terminal transglutaminase substrate domain and a C terminal four disulphide core journal Biochem. J. volume 340 issue 3 pages 569 77 year 1999 month June pmid 10359639 pmc 1220286 doi url ref This domain contains several repeated protein motif motif s with the consensus sequence Gly Gln Asp Pro Val Lys, and these together can anchor the whole molecule to extracellular matrix proteins, such as laminin , fibronectin , beta crystallin , collagen IV, fibrinogen , and elastin , by transglutaminase catalysed cross links. The whole domain is rich in glutamine and lysine , thus allowing transglutaminase s to catalyse the formation of an intermolecular epsilon gamma glutamyl lysine isopeptide bond . ref name pmid17964057 cite journal author Moreau T, Baranger K, Dade S, Dallet Choisy S, Guyot N, Zani ML title Multifaceted roles of human elafin and secretory leukocyte proteinase inhibitor SLPI , two serine protease inhibitors of the chelonianin family journal Biochimie volume 90 issue 2 pages 284 95 year 2008 month February pmid 17964057 doi 10.1016 j.biochi.2007.09.007 url ref References reflist InterPro content IPR019541 Category Protein families ... more details
Infobox protein family Symbol LIM bind Name LIM domain binding protein image width caption Pfam PF01803 Pfam clan InterPro IPR002691 SMART PROSITE MEROPS SCOP 1j2o TCDB OPM family OPM protein CAZy CDD In molecular biology, the LIM domain binding protein family is a protein family family of proteins which Molecular binding bind s to the LIM domain of LIM homeodomain homeodomain proteins which are Transcription genetics transcriptional regulators of development. Examples Nuclear LIM interactor NLI LIM domain binding protein 1 LDB1 is located in the nucleus biology nuclei of neuron neuronal cells during development, it is co expressed with ISL1 in early motor neuron differentiation cellular differentiation and has a suggested role in the ISL1 dependent development of motor neurons . ref name pmid8876198 cite journal author Jurata LW, Kenny DA, Gill GN title Nuclear LIM interactor, a rhombotin and LIM homeodomain interacting protein, is expressed early in neuronal development journal Proc. Natl. Acad. Sci. U.S.A. volume 93 issue 21 pages 11693 8 year 1996 month October pmid 8876198 pmc 38120 doi 10.1073 pnas.93.21.11693 url ref It is suggested that these protein proteins act Synergy synergistically to enhance transcriptional efficiency by acting as co factors for LIM homeodomain and Otx ... domain associated cofactors confer transcriptional synergism between LIM and Otx homeodomain proteins ... ref The Drosophila melanogaster protein Chip is required for segmentation and activity of a remote ... D title Chip, a widely expressed chromosomal protein required for segmentation and activity of a remote ... expressed chromosomal protein required for segmentation and activity of a remote wing margin ... 9334334 pmc 316608 doi url ref It is suggested that Chip cooperates with different LIM domain proteins ... chromosomal protein required for segmentation and activity of a remote wing margin enhancer in Drosophila ... 316608 doi url ref References reflist InterPro content IPR002691 Category Protein families ... more details
orphan date October 2011 Infobox protein family Symbol EcoEI R C Name EcoEI R C image width caption Pfam PF08463 Pfam clan InterPro IPR013670 SMART PROSITE MEROPS SCOP TCDB OPM family OPM protein CAZy CDD In molecular biology, the EcoEI R protein C terminal domain is a proteindomain found at the C terminus of both the R subunit of type I restriction enzymes and the Res subunit of type III restriction enzymes. The type I enzymes include EcoEI, which recognises 5 GAGN 7 ATGC 3 the R protein HsdR is required for both nuclease and ATPase activity. ref name pmid8412658 cite journal author Murray NE, Daniel AS, Cowan GM, Sharp PM title Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes journal Mol. Microbiol. volume 9 issue 1 pages 133 43 year 1993 month July pmid 8412658 doi 10.1111 j.1365 2958.1993.tb01675.x url ref ref name pmid10449767 cite journal author Makovets S, Doronina VA, Murray NE title Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes journal Proc. Natl. Acad. Sci. U.S.A. volume 96 issue 17 pages 9757 62 year 1999 month August pmid 10449767 pmc 22283 doi 10.1073 pnas.96.17.9757 url ref References reflist InterPro content IPR013670 Category Protein families Category Protein domains ... more details
orphan date May 2010 PBB geneid 84229 Coiled coil domain containing protein 135 , also known as CCDC135 , is a protein that in humans is encoded by the CCDC135 gene . ref name pmid11230166 cite journal ... protein 84000035?report genpept NP 001033120.1 86 93 872 coiled coil domain containing protein 135 Canis familiaris Dog http www.ncbi.nlm.nih.gov protein 73950345?report genpept XP 544386.2 85 ... protein 194208644 XP 001915581 81 87 831 Predicted similar to Coiled coil domain containing ... protein 149640764 XP 001508368.1 71 85 860 Predicted similar to Coiled coil domain containing ... domain containing 135 Danio rerio Zebrafish http www.ncbi.nlm.nih.gov protein 292628136 XP 683491 46 66 721 Predicted similar to Coiled coil domain containing protein 135 Tetraodon nigroviridis Tetraodon ... protein 198431234 XP 002123665 49 69 837 Predicted similar to coiled coil domain containing 135 ... genes and proteins sequencing and analysis of 500 novel complete protein coding human cDNAs journal ... gr.GR1547R url issn ref ref name entrez cite web title Entrez Gene coiled coil domain containing ...&hgtgroup encodeChrom close 1&hgtgroup encodeCompAndVar close 1 ref GPR97 , G protein coupled receptor 97. GPR56 , encodes a member of the G protein coupled receptor family G protein coupled receptor 56 . The gene is implicated in the regulation of brain cortical patterning. The protein binds specifically ... protein that helps targets the enzyme to the centrosome. KIFC3 , kinesin family member C3 isoform ... hydrolysis to translocate cargoes along microtubules. Protein Structure This protein is characterized ... The protein has 17 predicted alpha helices sites, a characteristic of coiled ... align center style background f0f0f0 Gene common name Homo sapiens Human http www.ncbi.nlm.nih.gov protein 223941912?report genpept NP 115645.4 100 100 874 Homo sapiens coiled coil domain containing 135 CCDC135 Macaca mulatta Rhesus Monkey http www.ncbi.nlm.nih.gov protein 109128753 XP 001100628.1 96 ... more details
PBB geneid 8932 Methyl CpG binding domainprotein 2 is a protein that in humans is encoded by the MBD2 ... Entrez Gene MBD2 methyl CpG binding domainprotein 2 url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch 8932 accessdate ref Interactions Methyl CpG binding domainprotein 2 has been shown to Proteinprotein interaction interact with HDAC1 , ref name pmid12183469 cite ... pmc 139742 cite journal author Bakker J, Lin X, Nelson WG title Methyl CpG binding domainprotein 2 ... Summary template is automatically maintained by Protein Box Bot. See Template PBB Controls to Stop ... CpG binding domain MBD . Each of these proteins, with the exception of MBD3, is capable of binding ... gene promoters. The protein encoded by this gene may function as a mediator of the biological consequences of the methylation signal. It is also reported that this protein functions as a demethylase ... Ammerpohl O, Kegel S, Moehren U, Renkawitz R year 2000 month Nov. title The minimal repression domain of MBD2b overlaps with the methyl CpG binding domain and binds directly to Sin3A journal J. Biol ... protein, MIZF, in transcriptional repression by interacting with a methyl CpG binding protein, MBD2 ... MBD3L1 is a transcriptional repressor that interacts with methyl CpG binding protein 2 MBD2 and components ... protein with specific demethylase activity for mCpG DNA journal Nature volume 397 issue 6720 pages ... Boeke J, Ammerpohl O, Kegel S, et al. title The minimal repression domain of MBD2b overlaps with the methyl CpG binding domain and binds directly to Sin3A journal J. Biol. Chem. volume 275 issue ... of SANT domain proteins CoREST kiaa0071 and Mta L1 journal J. Biol. Chem. volume 276 issue 9 pages ... Y title Involvement of a novel zinc finger protein, MIZF, in transcriptional repression by interacting with a methyl CpG binding protein, MBD2 journal J. Biol. Chem. volume 276 issue 46 pages ... K, Diederichs S, et al. title Loss of expression of HDAC recruiting methyl CpG binding domain proteins ... more details
Orphan date May 2011 PBB geneid 55246 The Coiled Coil Domain Containing Protein 25 CCDC25 is a human protein whose function is not presently understood. Gene The gene encoding the CCDC25 protein is located at 8p21.1, on the short arm of human chromosome eight, ref name NCBI cite web title Gene CCDC25 url http www.ncbi.nlm.nih.gov gene?term ccdc25 20AND 20homo 20sapiens accessdate ref and is transcribed into an mRNA product approximately 3,583 nucleotides in length. Protein General The protein is highly conserved among mammals as well as eukaryotes as diverse as Arabidopsis thaliana . CCDC25 is made up of a single polypeptide chain 208 amino acids in length and is expressed at a high level, nearly 4.2 times that of a normal human protein . ref name AceView cite web title AceView CCDC25 url http www.ncbi.nlm.nih.gov IEB Research Acembly av.cgi?db human&term ccdc25&submit Go accessdate ref Its expression is nearly ubiquitous in human tissues with little indication that its expression level changes drastically in diseased tissues. ref name NCBI cite web title EST Profile CCDC25 url http www.ncbi.nlm.nih.gov UniGene ESTProfileViewer.cgi?uglist Hs.445512 ref Despite currently lacking a well understood function, CCDC25 is predicted to localize to the nucleus ref name AceView and was shown by a microarray experiment to be upregulated in Metaphase II oocytes . ref name GEO Profiles cite web title GEO Profiles GDS3256 CCDC25 url http www.ncbi.nlm.nih.gov geo gds profileGraph.cgi?&dataset 3ziAAA&dataset xyy03Z &gmin 41.665400&gmax 2021.900000&absc &uid 52842405&gds 3256&idref 222525 s at&annot CCDC25 accessdate ref Interactions CCDC25 was shown by a yeast two hybrid assay to interact with Smad2 , a latent transcription factor that is part of the TGF signaling pathway. ref name MINT cite web title MINT CCDC25 url http mint.bio.uniroma2.it mint search search.do accessdate ref The protein ... dependent protein kinase , and the Insulin Receptor all of which have well defined roles in cell signaling ... more details
PBB geneid 8295 Transformation transcription domain associated protein , also known as TRRAP , is a protein that in humans is encoded by the TRRAP gene . ref name pmid9708738 cite journal author McMahon SB, Van Buskirk HA, Dugan KA, Copeland TD, Cole MD title The novel ATM related protein TRRAP is an essential cofactor for the c Myc and E2F oncoproteins journal Cell volume 94 issue 3 pages 363 74 date August 1998 pmid 9708738 doi 10.1016 S0092 8674 00 81479 8 url ref ref name pmid9885574 cite journal ... name mgp reference Interactions Transformation transcription domain associated protein has been shown to Proteinprotein interaction interact with ACTL6A , ref name pmid11839798 cite journal last ... url ref TRRAP belongs to the phosphatidylinositol 3 kinase related kinase protein family. Function TRRAP is an adapter protein , which is found in various multiprotein chromatin complexes with histone ... Sharon Y R, Martinez Ernest date May 2003 title c Myc transformation domain recruits the human ... K A, Copeland T D, Cole M D date August 1998 title The novel ATM related protein TRRAP is an essential ... accessdate laysummary laysource laydate quote pmc 99856 ref Transcription initiation protein SPT3 ... journal author McMahon SB title The novel ATM related protein TRRAP is an essential cofactor for the c ... Brand M, Yamamoto K, Staub A, Tora L title Identification of TATA binding protein free TAFII containing ... Yoshihiro cite journal author Brand M title UV damaged DNA binding protein in the TFTC complex ... Park J, Kunjibettu S, McMahon SB, Cole MD title The ATM related domain of TRRAP is required for histone ... protein free TAFII containing transcription complex identified by matrix assisted laser desorption ... author Liu X title c Myc transformation domain recruits the human STAGA complex and requires TRRAP ... J refend The PBB Controls template provides controls for Protein Box Bot, please see Template PBB Controls for details. PBB Controls update page yes require manual inspection no update protein box ... more details
PBB geneid 9372 Zinc finger FYVE domain containing protein 9 or SARA u S u MAD u a u nchor for u r u eceptor u a u ctivation is a protein that in humans is encoded by the ZFYVE9 gene . ref name pmid9865696 cite journal author Tsukazaki T, Chiang TA, Davison AF, Attisano L, Wrana JL title SARA, a FYVE domainprotein that recruits Smad2 to the TGFbeta receptor journal Cell volume 95 issue 6 pages 779 791 year 1998 month December pmid 9865696 doi 10.1016 S0092 8674 00 81701 8 url issn ref SARA contains a double zinc finger FYVE domain . SARA is an anchoring protein involved in TGF beta signaling pathway SMAD phosphorylation TGF beta signaling . It binds to the MH2 domain of the R SMAD s SMAD2 and SMAD3 as well as the type I TGF beta receptors. ref name pmid15356634 cite journal author Lin HK, Bergmann S, Pandolfi PP title Cytoplasmic PML function in TGF beta signalling journal Nature volume 431 issue 7005 pages 205 211 year 2004 month September pmid 15356634 doi 10.1038 nature02783 url issn ref It facilitates the phosphorylation of the R SMAD, which subsequently dissociates form SARA and the receptor and binds a coSMAD where they enter the nucleus as transcription factor s. References reflist TGF beta signaling gene 1 stub Category Developmental genes and proteins Category FYVE domain ... more details
PBB geneid 7704 Zinc finger and BTB domain containing protein 16 is a protein that in humans is encoded by the ZBTB16 gene . Function This gene is a member of the Krueppel C2H2 type zinc finger protein ... and BTB domain containing protein 16 has been shown to Proteinprotein interaction interact with ZBTB32 ... proteinprotein interaction motif POZ domain is responsible for activities of the promyelocytic ... Domain Containing Protein 16 Category Transcription factors es ZBTB16 ... at the carboxyl terminus. This protein is located in the nucleus, is involved in cell cycle progression ... domain containing 16 url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch ... A novel BTB POZ transcriptional repressor protein interacts with the Fanconi anemia group C protein ... first3 S title Roles of charged amino acid residues in the cytoplasmic domain of proHB EGF ... protein PLZF volume 23 issue 54 pages 8777 84 journal Oncogene ref ref name pmid11929873 cite journal ... Sch fer first5 BW title The LIM only protein DRAL FHL2 interacts with and is a corepressor for the promyelocytic leukemia zinc finger protein volume 277 issue 40 pages 37045 53 journal The Journal of Biological ... repression by the acute promyelocytic leukemia associated PLZF protein volume 16 issue 19 pages ... domain oncoproteins PLZF, PLZF RARalpha, and BCL 6 volume 273 issue 42 pages 27695 702 journal ... protein, promyelocytic leukemia zinc finger, regulates 1,25 dihydroxyvitamin D 3 induced monocytic ... last9 Licht first9 JD title The ETO Protein Disrupted in t 8 21 Associated Acute Myeloid Leukemia Is a Corepressor for the Promyelocytic Leukemia Zinc Finger Protein volume 20 issue 6 pages 2075 86 ... 1 ETO fusion protein is a dominant negative inhibitor of transcriptional repression by the promyelocytic leukemia zinc finger protein volume 96 issue 12 pages 3939 47 journal Blood ref HDAC4 , ref name ... receptor expression and interacts with GATA1 protein volume 21 issue 43 pages 6669 79 journal Oncogene ... more details
NOTOC Wiktionary domainDomain may refer to Domain can be used for a name and science General Territory ... government Public domain , a body of works and knowledge without proprietary interest Eminent domain , the power of government to confiscate private property for public use Steve Alten Domain trilogy Domain trilogy is a trilogy of books regarding the Mayanism December 21.2C 2012 Mayan 2012 myths , written by Steve Alten Domain board game Domain , a game published by Parker Brothers in 1983 Sciences Domain biology , a subdivision even larger than a kingdom Domain knowledge , a specific expert knowledge valid for a pre selected area of activity, such as surgery Domain specificity , a theoretical ... Domain wall , a term used in physics which can have one of two distinct but similar meanings in either magnetism or string theory Magnetic domain , a region within a magnetic material which has uniform magnetization Proteindomain , a part of a protein that can exist independently of the rest of the protein chain Information technology Administrative domain , a service provider holding a security repository permitting to easily authenticate and authorize clients with credentials Application domain , the kinds of purposes for which users use a software system Broadcast domain , in computer networking, a group of special purpose addresses to receive network announcements Clock domain crossing , when a signal crosses from one clock domain into another CLR application domain , a mechanism for separating executed applications similar to a process Collision domain , a physical network segment that is a shared medium where data packets can collide with one another Data domain , in database theory, a set of all permitted values Domain software engineering , a field of study that defines a set ... a problem in that field Domain analysis , the process of analyzing related software systems in a domain to find their common and variable parts Domain driven design , an approach to the design of software ... more details
Pfam box Symbol SpA Name Protein A image Protein A 1DEE 1L6X.png width caption Structure of a domain of protein A as a three helix bundle binding to the heavy variable chain of a VH3 human Fab ref name ... JB, Silverman GJ. title Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab ... month May pmid 10805799 doi pmc 25840 ref left. Minimized protein A bound to Fc fragment of Rituximab ... April pmid 10754313 doi ref Pfam InterPro SMART PROSITE SCOP 1DEE TCDB OPM family OPM protein PDB PDB2 1dee , PDB2 1l6x Protein A is a 56 Atomic mass unit kDa MSCRAMM surface protein originally found ... helix bundle. Each domain is able to bind proteins from many of mammalian species, most notably IgG ... and phagocytosis . Protein A antibody binding Protein A binds with high affinity to human IgG1 and IgG2 as well as mouse IgG2a and IgG2b. Protein A binds with moderate affinity to human IgM ... or IgD , nor will it react to mouse IgM, IgA or IgE. The capacity of protein A to bind antibodies with such high .... The protein A used for production of antibodies in bio pharmaceuticals is most commonly bound to a stationary phase chromatography resin. Other antibody binding proteins In addition to Protein A, other immunoglobulin binding bacterial proteins such as Protein G , Protein A G and Protein L are all ... Staphylococcus aureus utilizes Protein A, along with a host of other proteins and surface factors to aid its survival and, thus, virulence. Protein A helps inhibit phagocytic engulfment and acts as an immunological disguise. Mutants of S. aureus lacking protein A are more efficiently phagocytosed ... toxin. J. Exp. Med. 2003 197 1125 1139. ref Research Recombinant Staphylococcal Protein ... form of Protein A is called MabSelect. ref http www.gelifesciences.com aptrix upp00919.nsf Content 17D93C2E6A580E57C1257628001CE677 file 18114994AE.pdf ref Protein A is often coupled to other molecules .... Protein A is often immobilized onto a solid support and used as reliable method for purifying ... more details
18695379 doi 10.1097 MOH.0b013e328309ec97 url ref Protein S can bind to negatively charged phospholipids via the carboxylated Gla domain GLA domain . This property allows Protein S to function in the removal ... acid in the first epidermal growth factor like domain of protein C. Its role in Ca2 binding and biological ...PBB geneid 5627 Protein S is a vitamin K dependent plasma glycoprotein synthesized in the endothelium. In the circulation, Protein S exists in two forms a free form and a complex form bound to complement system complement protein C4b binding protein C4BP . In humans, protein S is encoded by the PROS1 ... B, Stenflo J, Wydro R title Isolation and sequence of the cDNA for human protein S, a regulator ... url ref In 1979, researchers in Seattle , Washington first discovered protein S and arbitrarily ... X Stuart factor , and protein S journal Biochemistry volume 16 issue 4 pages 698 706 year 1977 ... RG, Davie EW title Characterization of protein S, a gamma carboxyglutamic acid containing protein ... March pmid 420821 doi 10.1021 bi00572a026 ref Function The best characterized function of Protein S is its role in the anti coagulation pathway, where it functions as a cofactor to Protein C in the inactivation .... ref name pmid18695379 cite journal author Castoldi E, Hackeng TM title Regulation of coagulation by protein ... such as macrophages . Protein S can bind to the negatively charged phospholipids and function as a bridging molecule between the apoptotic cell and the phagocyte. The bridging property of Protein ... lead to Protein S deficiency which is a rare blood disorder which can lead to an increased risk of thrombosis ... R, Daly ME title The prevalence of, and molecular defects underlying, inherited protein S deficiency ... author Garc a de Frutos P, Fuentes Prior P, Hurtado B, Sala N title Molecular basis of protein S deficiency ... doi url ref Interactions Protein S has been shown to Proteinprotein interaction interact with Factor ... 621 635 of protein S are essential for binding to factor Va journal J. Biol. Chem. volume 274 issue ... more details
name Zhou2008 and computational protein structure prediction of small protein structural domain domains ...About a class of molecules protein as a nutrient Protein nutrient other uses pp semi indef File Myoglobin.png thumb right A representation of the 3D structure of the protein myoglobin showing colored alpha helix alpha helices . This protein was the first to have its structure solved by X ray crystallography ... folded into a globular protein globular or fibrous protein fibrous form, facilitating a biological ... . The peptide sequence sequence of amino acids in a protein is defined by the DNA sequence sequence ... archaea pyrrolysine . Shortly after or even during synthesis, the residues in a protein are often ... to form stable protein complex es. Like other biological macromolecules such as polysaccharide ... acid s from food. Through the process of digestion , animals break down ingested protein into free amino acids that are then used in metabolism. Proteins may be protein purification purified from ... made possible a number of methods to facilitate purification. Methods commonly used to study protein ... chains in a protein that ultimately determines its three dimensional structure and its chemical reactivity ... linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone. ref Murray ... structures of the peptide bond that links individual amino acids to form a protein polymer The peptide ... angle s in the peptide bond determine the local shape assumed by the protein backbone. ref Murray et al ., p. 31. ref The end of the protein with a free carboxyl group is known as the C terminus .... The words protein , polypeptide, and peptide are a little ambiguous and can overlap in meaning. Protein is generally used to refer to the complete biological molecule in a stable tertiary structure ... structure conformation . Synthesis Main Protein biosynthesis Image Ribosome mRNA translation en.svg ... more details
Unreferenced date October 2010 A binding domain is a proteindomain which binding molecular binds to a specific atom or molecule, such as calcium or DNA . Upon binding, proteins may undergo a conformational change . Binding domains are essential for the function of many proteins. Examples of binding domains include Zinc finger , which binds to DNA, and EF hand , which binds to calcium. See also DNA binding domainprotein stub Protein topics Category Protein structure Category Protein domains ... more details
Infobox protein family Symbol HECT Name HECT domain ubiquitin transferase image PDB 1d5f EBI.jpg width caption structure of an e6ap ubch7 complex insights into the ubiquitination pathway Pfam PF00632 Pfam clan InterPro IPR000569 SMART PROSITE MEROPS SCOP 1d5f TCDB OPM family OPM protein CAZy CDD In molecular biology, the HECT domain is a proteindomain found in ubiquitin protein ligases . The name HECT comes from H omologous to the E 6 AP C arboxyl T erminus . ref name pmid7708685 cite journal author Huibregtse JM, Scheffner M, Beaudenon S, Howley PM title A family of proteins structurally and functionally related to the E6 AP ubiquitin protein ligase journal Proc. Natl. Acad. Sci. U.S.A. volume 92 issue 7 pages 2563 7 year 1995 month March pmid 7708685 pmc 42258 doi url ref Protein s containing this domain at the C terminus include ubiquitin protein ligase , which regulates ubiquitination of disambiguation needed CDC25 date October 2011 . Ubiquitin protein ligase accepts ubiquitin from an ubiquitin conjugating enzyme E2 ubiquitin conjugating enzyme in the form of a thioester , and then directly transfers the ubiquitin to targeted substrate biochemistry substrates . A cysteine residue is required for ubiquitin thiolester formation. Human thyroid receptor interacting protein 12 TRIP12 , which also contains this domain, is a component of an Adenosine triphosphate ATP dependent multisubunit protein that Proteinprotein interaction interact s with the ligand binding domain of the thyroid hormone receptor . It could be an E3 ubiquitin protein ligase. Human UBE3A ubiquitin protein ligase E3A Proteinprotein interaction interact s with the E6 protein of the cancer associated Human papillomavirus type 16 and Human papillomavirus type 18. The E6 E6 AP Protein complex complex Molecular binding bind s to and targets the P53 Tumour suppressor gene tumour suppressor protein for ubiquitin mediated proteolysis . References reflist InterPro content IPR000569 Category Protein domains ... more details
Infobox protein family Symbol Cohesin Name Cohesin image PDB 1aoh EBI.jpg width caption single cohesin domain from the scaffolding protein cipa of the clostridium thermocellum cellulosome Pfam PF00963 Pfam clan CL0203 InterPro IPR002102 SMART PROSITE MEROPS SCOP 1anu TCDB OPM family OPM protein CAZy CDD In molecular biology, the cohesin domain is a proteindomain . It Proteinprotein interaction interacts with a wikt complementary complementary domain, termed the dockerin dockerin domain . The cohesin dockerin interaction is the crucial interaction for Protein complex complex formation in the cellulosome . ref name pmid9083107 cite journal author Shimon LJ, Bayer EA, Morag E, Lamed R, Yaron S, Shoham Y, Frolow F title A cohesin domain from Clostridium thermocellum the crystal structure provides new insights into cellulosome assembly journal Structure volume 5 issue 3 pages 381 90 year 1997 month March pmid 9083107 doi url ref The scaffoldin component of the cellulolytic bacterium Clostridium thermocellum is a non hydrolytic protein which organises the hydrolytic enzymes into a large complex, called the cellulosome. Scaffoldin comprises a series of functional domains, amongst which is a single cellulose binding domain and nine cohesin domains which are responsible for integrating the individual enzyme enzymatic protein subunit subunits into the complex. References reflist InterPro content IPR002102 Category Protein domains ... more details
Infobox protein family Symbol HEPN Name HEPN domain image PDB 1ufb EBI.jpg width caption crystal structure of tt1696 from thermus thermophilus hb8 Pfam PF05168 Pfam clan CL0291 InterPro IPR007842 SMART PROSITE MEROPS SCOP 1o3u TCDB OPM family OPM protein CAZy CDD In molecular biology, the HEPN domain higher eukaryotes and prokaryotes nucleotide binding proteindomaindomain is a region of approximately 110 amino acids found in the C terminus of sacsin , a chaperonin implicated in an early onset neurodegenerative disease in human, and in many bacterial and archaea archaea protein s. There are three classes of proteins with HEPN domains Single domain HEPN protein proteins found in many bacteria. Two domain proteins with N terminal nucleotidyltransferase NT and C terminal HEPN proteindomain domains . This N terminal NT domain belongs to a large family of NTs, which includes several classes of enzyme s that are responsible for some types of bacteria bacterial resistance to aminoglycosides . These enzymes deactivate various antibiotic s by transferring a nucleotidyl group to the drug. A multidomain sacsin protein in genomes of fish and mammal s. The HEPN domain is located at the C terminus of the protein, directly after the DnaJ domain. The crystal structure of the HEPN domain from the TM0613 protein of Thermotoga maritima indicates that it is structurally similar to the C terminal all alpha helical domain of kanamycin nucleotidyltransferase kanamycin nucleotidyltransferases KNTases . It is composed of five alpha helices, three of which form an up and down helical bundle, with a pair of short Alpha helix helices on the side. The distant structural similarity suggests that the HEPN domain might be involved in nucleotide binding. ref name pmid12765831 cite journal author Grynberg M, Erlandsen H, Godzik A title HEPN a common domain in bacterial drug resistance and human neurodegenerative ... pmid 12765831 doi url ref References reflist InterPro content IPR007842 Category Protein families ... more details
A binding protein is any protein that acts as an agent to Molecular binding bind two or more molecules together. Examples include DNA binding protein Single strand binding protein Telomere binding protein RNA binding protein Poly A binding protein Nuclear cap binding protein complex CREB binding protein Calcium binding protein Calcium binding protein 1 S100 calcium binding protein A1 TATA binding protein Actin binding protein Penicillin binding proteins Retinol binding protein Retinol binding protein 4 EP300 Binding immunoglobulin protein Odorant binding protein Lipopolysaccharide binding protein C4b binding protein Rap GTP binding protein Calmodulin binding proteins Iron binding proteins Thyroxine binding proteins Folate binding protein Sterol regulatory element binding protein GTP binding protein Retinaldehyde binding protein 1 Ccaat enhancer binding proteins Androgen binding protein Maltose binding protein Phosphatidylethanolamine binding protein 1 Syntaxin binding protein 3 Insulin like growth factor binding protein Methyl CpG binding domainprotein 2 Growth hormone binding protein Vitamin D binding protein Syntaxin binding protein 2 Oxysterol binding protein E3 binding protein Iron responsive element binding protein Polypyrimidine tract binding protein Fatty acid binding protein Myosin binding protein C, cardiac CPE binding protein Category Proteins biochem stub ... more details
Infobox protein family Symbol BLUF Name BLUF image PDB 1x0p EBI.jpg width caption structure of a cyanobacterial bluf protein, tll0078 Pfam PF04940 Pfam clan InterPro IPR007024 SMART PROSITE MEROPS SCOP TCDB OPM family OPM protein CAZy CDD In molecular biology, the BLUF domain sensors of b lue l ight u sing F AD is a FAD binding proteindomain . They are present in various proteins, primarily from bacteria , for example a BLUF domain is found at the N terminus of the AppA protein from Rhodobacter sphaeroides . The BLUF domain is involved in sensing blue light and possibly redox using FAD and is similar to the flavin binding PAS domain PAS domains and cryptochromes . The predicted secondary structure reveals that the BLUF domain has a novel FAD binding protein folding fold . ref name pmid12368079 cite journal author Gomelsky M, Klug G title BLUF a novel FAD binding domain involved in sensory transduction in microorganisms journal Trends Biochem. Sci. volume 27 issue 10 pages 497 500 year 2002 month October pmid 12368079 doi url ref References reflist InterPro content IPR007024 Category Protein domains ... more details
orphan date October 2011 Infobox protein family Symbol EMI Name EMI domain image width caption Pfam PF07546 Pfam clan InterPro IPR011489 SMART PROSITE MEROPS SCOP TCDB OPM family OPM protein CAZy CDD In molecular biology, the EMI domain , first named after its presence in proteins of the EMILIN family, is a small cysteine rich proteindomain of around 75 amino acid s. The EMI domain is most often found at the N terminus of metazoan extracellular protein s that are forming or are compatible with multimer formation. ref name pmid11068053 cite journal author Doliana R, Bot S, Bonaldo P, Colombatti A title EMI, a novel cysteine rich domain of EMILINs and other extracellular proteins, interacts with the gC1q domains and participates in multimerization journal FEBS Lett. volume 484 issue 2 pages ... III domain FN3 , Whey Acidic Protein WAP , Zona pellucida like domain ZP or FAS1. ref name pmid12507493 ... S0006 291X 02 02904 2 url ref It has been suggested that the EMI domain could be a proteinprotein interaction module, as the EMI domain of EMILIN1 EMILIN 1 was found to Proteinprotein interaction interact with the C1q domain of EMILIN2 EMILIN 2 . ref name pmid11068053 The EMI domain possesses ... and reveal the probable orthologs of the Caenorhabditis elegans CED 1 protein journal Biochem. Biophys ... domain are the C C x G WYFH pattern, a hydrophobic position just preceding the first cysteine Cys1 of the domain and a cluster of hydrophobic residues between Cys3 and Cys4. The EMI domain could be made of two sub domains, the protein folding fold of the second one sharing similarities with the C terminal sub module characteristic of EGF like domain s. ref name pmid12507493 Proteins known to contain a EMI domain include Vertebrate Emilins, extracellular matrix glycoproteins . Vertebrate Multimerins, extracellular matrix glycoproteins. Vetebrate Emu proteins, which could Proteinprotein ... cell corpse engulfment. References reflist InterPro content IPR011489 Category Protein domains ... more details
Infobox protein family Symbol BAH Name BAH image PDB 1m4z EBI.jpg width caption crystal structure of the n terminal bah domain of orc1p Pfam PF01426 Pfam clan InterPro IPR001025 SMART PROSITE MEROPS C89 SCOP 1m4z TCDB OPM family OPM protein CAZy CDD In molecular biology, the BAH domain bromo adjacent homology domain is found in protein s such as eukaryotic DNA cytosine 5 methyltransferase s, the origin recognition complex 1 Orc1 proteins, as well as several protein proteins involved in Transcription genetics transcriptional regulation . The BAH domain appears to act as a proteinprotein interaction module specialised in gene silencing, as suggested for example by its interaction within Saccharomyces cerevisiae yeast Orc1p with the silent information regulator Sir1p. The BAH domain might therefore play an important role by linking DNA methylation , replication and transcriptional regulation . ref name pmid10100640 cite journal author Callebaut I, Courvalin JC, Mornon JP title The BAH bromo adjacent homology domain a link between DNA methylation, replication and transcriptional regulation journal FEBS Lett. volume 446 issue 1 pages 189 93 year 1999 month March pmid 10100640 doi 10.1016 S0014 5793 99 00132 5 url ref References reflist InterPro content IPR001025 Category Protein domains ... more details
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