and the second oxygen of pyrimidine bases. Finally, the active site makes extensive hydrogen bonds with the DNA ... DnaA DnaA dimers are needed to initiate replication, the ratio of DnaA to the number of DnaA boxes ... more details
Other people Richard Wood Richard D. Wood born June 3, 1955, Boulder, Colorado is an United States American molecular biologist specializing in research on DNA repair and mutation http www.sciencemag.org cgi content abstract 286 5446 1897 . He is known for pioneering studies on nucleotide excision repair NER , particularly for reconstituting the minimum set of proteins involved in this process, identifying proliferating cell nuclear antigen PCNA as part of the NER complex http www.sciencedirect.com science? ob ArticleURL& udi B6WSN 4C6BNK5 BC& user 10& rdoc 1& fmt & orig search& sort d& docanchor &view c& acct C000050221& version 1& urlVersion 0& userid 10&md5 e74b8e13e377bccfcd1948f4f423b8f8 and identifying mammalian repair polymerase s http www.jbc.org cgi content abstract 278 34 32014 http nar.oxfordjournals.org cgi content abstract 31 21 6117 . In humans, mutations affecting the NER DNA repair pathway cause the disease xeroderma pigmentosum or XP. Normal UV and sunlight exposure generates DNA mutations particularly pyrimidine dimers in epidermal cells that must be continually repaired through NER. XP patients are particularly sensitive to sun exposure and generally must stay indoors during the day, using heavy sunscreens to prevent skin damage and susceptibility to skin cancer. NER occurs through a programmed set of steps that includes recognition of the damaged site probably by sensing an unpaired bubble at the mutation site , nicking the DNA at upstream and downstream sites, excising the damaged DNA, then filling in the single stranded DNA gap using a polymerase , with the opposite strand serving as a template for the proper sequence for the repair patch. Since multiple proteins are involved in NER, different XP patients may have different gene mutations. Cells having different NER gene mutations can complement each other, when the cells are fused together, to reestablish DNA repair since one cell line has an intact enzyme that is defective or missing in the o ... more details
unreferenced date November 2010 protein name dihydropyrimidine dehydrogenase caption image width HGNCid 3012 Symbol DPYD AltSymbols EntrezGene 1806 OMIM 274270 RefSeq NM 000110 UniProt PDB ECnumber 1.3.1.2 Chromosome 1 Arm p Band 22 LocusSupplementaryData Dihydropyrimidine dehydrogenase DPD is an enzyme that is involved in pyrimidine degradation. It is the initial and rate limiting step in pyrimidine catabolism. It catalyzes the reduction of uracil and thymine . It is also involved in the degradation of the chemotherapeutic drugs 5 fluorouracil and Tegafur uracil . See also Dihydropyrimidine dehydrogenase deficiency External links enzyme stub Nucleotide metabolism de Dihydropyrimidin Dehydrogenase ... more details
regulated enzyme that catalyses the first committed step in pyrimidine biosynthesis, the condensation ... controls the rate of pyrimidine biosynthesis by altering its catalytic velocity in response to cellular levels of both pyrimidine s and purine s. The end product of the pyrimidine pathway, Cytidine ... that are in contact and held together by three regulatory dimers, so the native form of the enzyme ... more details
In molecular biology , activating transcription factor , ATF , is a class of AP 1 transcription factor AP 1 transcription factor dimers. ref name van Dam cite journal author van Dam H, Castellazzi M title Distinct roles of Jun Fos and Jun ATF dimers in oncogenesis journal Oncogene volume 20 issue 19 pages 2453 64 year 2001 pmid 11402340 doi 10.1038 sj.onc.1204239 ref Genes include ATF1 , Activating transcription factor 2 ATF2 , ATF3 , ATF4 , ATF5 , ATF6 , and ATF7 . References references External links MeshName Activating Transcription Factors protein stub Oncogenes Transcription factors g1 Category Transcription factors es Factor de transcripci n activador ... more details
acid inhibit the hydrolysis of barbituric acid. Dihydro L orotate is an intermediate in the pyrimidine ... acid inhibits multiple enzyme s that are involved in de novo pyrimidine synthesis. These last two points suggest a connection between pyrimidine anabolism and oxidative catabolism. Image with unknown ... of oxidative pyrimidine metabolism has not yet been discovered in mammals. References ... in oxidative pyrimidine metabolism analysis of the barbiturase reaction and discovery of a novel enzyme ... S title Barbiturase, a novel zinc containing amidohydrolase involved in oxidative pyrimidine metabolism ... more details
Circular molecules of DNA , such as plasmids and typical mitochondrial genome s, consist of Nucleic acid double helix two strands of DNA called the heavy strand or H strand and the light strand or L strand . The two strands have different masses due to different proportions of heavier nucleic acid s. While this difference is not known to have any functional significance, it can be used in the laboratory to segregate the strands of Denaturation biochemistry Nucleic acid denaturation denatured DNA, and hence to analyze the strands separately. Adenine and guanine purine s are heavier than cytosine and thymine pyrimidine s due to their extra ring. Because a purine always DNA Base pairing pairs with a pyrimidine, any excess of purines in one strand will occur with a corresponding excess of pyrimidines in the other strand and vice versa. Statistically, there is more likely to be such an imbalance than an exact 50 50 ratio. In addition, bias may arise due to differentials in the amount of protein coding sequence on each strand, as codon s do not all occur with equal frequency. Category DNA biology stub ... more details
Cleanup date June 2011 Photoaging or photoageing ref name Helfrich2008 cite pmid 18649702 ref also known as Dermatoheliosis ref name Bolognia cite book author Rapini, Ronald P. Bolognia, Jean L. Jorizzo, Joseph L. title Dermatology 2 Volume Set publisher Mosby location St. Louis year 2007 pages isbn 1 4160 2999 0 oclc doi accessdate ref is a term used for the characteristic changes induced by chronic UVA and UVB exposure. ref name Andrews cite book author James, William D. Berger, Timothy G. et al. title Andrews Diseases of the Skin clinical Dermatology publisher Saunders Elsevier location year 2006 pages isbn 0 7216 2921 0 oclc doi accessdate ref rp 29 Tretinoin is the best studied retinoid in the treatment of photoaging ref Cite doi 10.1111 j.1473 2165.2005.40215.x ref The deterioration of biological functions and ability to manage metabolic stress is one of the major consequences of the ageing aging process. Aging is a complex, progressive process which also leads to functional and esthetic changes in the skin. This process could result from both intrinsic, such that it is genetically determined, as well as extrinsic processes which include environmental factors. Photoaging is a process of aging of the skin attributed to continuous, long term exposure to ultraviolet ultraviolet UV radiation of approximately 245 290 nm, natural or synthetic, on an intrinsically aged skin. Photoaging is thus also known as aging of the skin of the face, ears, neck and hands, caused by UVA and UVB rays. Effects of UV light UV and molecular and genetic changes UVB ray is considered as a primary mutagen that can only penetrate through the epidermis skin epidermal or outermost layer of the skin, resulting in DNA mutations. These DNA mutations arise due to chemical changes, the formation of cyclobutane pyrimidine dimers and photoproducts formed between adjacent pyrimidine bases. These mutations may be clinically related to specific signs of photoaging such as wrinkling, increasing i ... more details
as a dimer of dimers with an overall diameter of approximately 90 . ref name Kim93 cite ... dimers has few interactions. There are a total of 4 active sites within the tetramer, each of which ... in place by hydrogen bonding with the pyrimidine portion and hydrophobic interactions with the dimethylbenzene ... more details
have been shown to stimulate TLR9 with variations in the number and location of CpG dimers, as well as the precise base sequences flanking the CpG dimers. This led to the creation of five unofficial classes ... the pattern, 5 Purine Pu Pu CG Pu Pyrimidine Py CG Py Py 3 , was found to be the most active when ... more details
S, Saccucci F, Magni G title Human erythrocyte pyrimidine 5 nucleotidase, PN I, is identical to p36 ... summary text Pyrimidine 5 prime nucleotidase P5N EC 3.1.3.5 , also called uridine 5 prime monophosphate hydrolase UMPH , catalyzes the dephosphorylation of the pyrimidine 5 prime monophosphates UMP and CMP to the corresponding nucleosides. There are 2 isozymes of pyrimidine 5 prime nucleotidase in red ... pyrimidine nucleotidase from human erythrocytes enzymic and molecular properties journal Biochem. J ... doi 10.1101 gr.6.9.807 cite journal author Amici A, Emanuelli M, Magni G, et al. title Pyrimidine nucleotidases from human erythrocyte possess phosphotransferase activities specific for pyrimidine nucleotides .... title Genetic basis of hemolytic anemia caused by pyrimidine 5 nucleotidase deficiency journal Blood ... author Amici A, Magni G title Human erythrocyte pyrimidine 5 nucleotidase, PN I journal Arch. Biochem ... enzyme intermediate in phosphotransferase activity of human red cell pyrimidine nucleotidases ... N, et al. title Molecular characterization of Turkish patients with pyrimidine 5 nucleotidase ... of six unrelated Italian patients affected by pyrimidine 5 nucleotidase deficiency journal Br ... of pyrimidine 5 nucleotidase deficiency journal Br. J. Haematol. volume 126 issue 2 pages 265 ... LR, Bianchi P, Fermo E, et al. title Functional analysis of pyrimidine 5 nucleotidase mutants ... more details
A salvage pathway is a Metabolic pathway pathway in which nucleotide s purine and pyrimidine are synthesized from intermediates in the degradative pathway for nucleotides. Salvage pathways are used to recover bases and nucleosides that are formed during biodegradation degradation of RNA and DNA . This is important in some organs because some tissues cannot undergo de novo synthesis . The salvaged bases and nucleosides can then be converted back into nucleotides. Substrates The salvage pathway requires distinct substrates Pyrimidines Uridine phosphorylase adds ribose 1 phosphate to the free base uracil, forming uridine monophosphate. Uridine kinase then phosphorylates this nucleoside into its diphosphate and triphosphate forms. Deoxythymidine phosphorylase adds deoxyribose 1 phosphate to thymine, forming deoxythymidine monophosphate. Thymidine kinase can then phosphorylate this compound to deoxythymidine diphosphate and triphosphate. Image Pyrimidine Ribonucleotide Salvage.png thumb none 400px The salvage of pyrimidine ribonucleotides. Purines Phosphoribosyltransferases add activated ribose 5 phosphate called phosphoribosyl pyrophosphate or PRPP to bases, creating nucleotide monophosphates. There are two types of phosphoribosyltransferases adenine phosphoribosyltransferase APRT and hypoxanthine guanine phosphoribosyltransferase HGPRT . Lesch Nyhan syndrome is associated with a deficiency of HGPRT. class wikitable Nucleoside Enzyme Nucleotide hypoxanthine hypoxanthine guanine phosphoribosyl transferase HGPRT Inosine monophosphate IMP guanine hypoxanthine guanine phosphoribosyl transferase HGPRT Guanosine monophosphate GMP adenine adenine phosphoribosyltransferase APRT Adenosine monophosphate AMP External links http www.chem.brandeis.edu pochapsky research.html Enzymes in the methionine salvage pathway structure and function at Brandeis University Category Genetics genetics stub Protein metabolism Nucleotide metabolism ca Salvament de nucle tids de Salvage Pathway ja ... more details
enzyme Name diaminohydroxyphosphoribosylaminopyrimidine deaminase EC number 3.5.4.26 CAS number 68994 19 4 IUBMB EC number 3 5 4 26 GO code 0008835 image width caption In enzymology , a diaminohydroxyphosphoribosylaminopyrimidine deaminase EC number 3.5.4.26 is an enzyme that catalysis catalyzes the chemical reaction 2,5 diamino 6 hydroxy 4 5 phosphoribosylamino pyrimidine H sub 2 sub O math rightleftharpoons math 5 amino 6 5 phosphoribosylamino uracil NH sub 3 sub Thus, the two substrate biochemistry substrates of this enzyme are 2,5 diamino 6 hydroxy 4 5 phosphoribosylamino pyrimidine and water H sub 2 sub O , whereas its two product chemistry products are 5 amino 6 5 phosphoribosylamino uracil and ammonia NH sub 3 sub . This enzyme belongs to the family of hydrolase s, those acting on carbon nitrogen bonds other than peptide bonds specifically in cyclic amidines . The systematic name of this enzyme class is 2,5 diamino 6 hydroxy 4 5 phosphoribosylamino pyrimidine 2 aminohydrolase . This enzyme participates in riboflavin metabolism . Structural studies As of late 2007, 6 tertiary structure structures have been solved for this class of enzymes, with Protein Data Bank PDB accession codes PDB link 2B3Z , PDB link 2D5N , PDB link 2G6V , PDB link 2HXV , PDB link 2O7P , and PDB link 2OBC . References reflist 1 cite journal author Burrows RB, Brown GM date 1978 title Presence of Escherichia coli of a deaminase and a reductase involved in biosynthesis of riboflavin journal J. Bacteriol. volume 136 pages 657&ndash 67 pmid 30756 issue 2 pmc 218591 hydrolase stub Category EC 3.5.4 Category Enzymes of known structure ... more details
Unreferenced date December 2009 Hamilton O. Smith H.O. Smith , K.W. Wilcox, and T.J. Kelley, working at Johns Hopkins University in 1968, isolated and characterized the first restriction nuclease whose functioning depended on a specific DNA nucleotide sequence. Citation needed date September 2011 Working with Haemophilus influenzae bacteria, this group isolated an enzyme , called HindII, that always cut DNA molecules at a particular point within a specific sequence of six base pairs. Citation needed date September 2011 This sequence is 5 G T pyrimidine T or C purine A or G A C 3 P3 C A purine A or G pyrimidine T or C T G 5 They found that the HindII enzyme always cuts directly in the center of this sequence. Citation needed date September 2011 Wherever this particular sequence of six base pairs occurs unmodified in a DNA molecule, HindII will cleave both DNA backbones between the 3rd and 4th base pairs of the sequence. Moreover, HindII will only cleave a DNA molecule at this particular site. For this reason, this specific base sequence is known as the recognition sequence for HindII. See also Nuclease HindIII DEFAULTSORT Hindii Category Molecular biology Category Biotechnology Category Restriction enzymes Category EC 3.1 es HindII ... more details
protein Name carbamoyl phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase caption image width HGNCid 1424 Symbol CAD AltSymbols EntrezGene 790 OMIM 114010 RefSeq NM 004341 UniProt P27708 PDB ECnumber Chromosome 2 Arm p Band 21 LocusSupplementaryData Carbamoyl phosphate synthetase II is an enzyme that catalyzes the reactions that produce carbamoyl phosphate in the cytosol as opposed to type I, which functions in the mitochondria . In pyrimidine biosynthesis, it catalyzes the following reaction Glutamine Gln CO sub 2 sub 2 ATP H sub 2 sub O carbamoyl phosphate Glutamate Glu 2 ADP P sub i sub It is activated by Adenosine triphosphate ATP and PRPP and it is inhibited by UMP Uridine monophosphate , the end product of the pyrimidine synthesis pathway . Both CPSI and CPSII do not require Biotin as a coenzyme, as seen with most carboxylation reactions. It is one of the three enzyme functions coded by the CAD gene. It is classified under EC number 6.3.5.5 . External links MeshName Carbamoyl Phosphate Synthase Glutamine Hydrolyzing enzyme stub Ligases Nucleotide metabolism Multienzyme complexes pl Syntetaza karbamoilofosforanowa II ... more details
Infobox rfam Name PyrR binding site image RF00515.jpg width caption Predicted secondary structure and sequence conservation of PyrR Symbol PyrR AltSymbols Rfam RF00515 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Bacteria GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The PyrR binding site is an cis regulatory element RNA element that is found upstream of a variety of genes involved in pyrimidine biosynthesis and transport. ref name Bon01 cite journal last Bonner first ER coauthors D Elia JN, Billips BK, Switzer RL year 2001 title Molecular recognition of pyr mRNA by the Bacillus subtilis attenuation regulatory protein PyrR journal Nucleic Acids Res volume 29 pages 4851&ndash 4865 pmid 11726695 doi 10.1093 nar 29.23.4851 issue 23 pmc 96680 ref The RNA secondary structure structure permits binding of PyrR protein which regulates pyrimidine biosynthesis in Bacillus subtilis . When the protein binds, a downstream Intrinsic termination terminator hairpin forms, repressing transcription genetics transcription of biosynthesis genes. ref name Bon01 References reflist 1 External links Rfam id RF00515 name PyrR binding site Category Cis regulatory RNA elements molecular cell biology stub ... more details
Context date October 2009 URA3 is gene on Chromosome V in Saccharomyces yeast . Its systematic name is YEL021W. URA3 is a gene that encodes orotidine 5 phosphate decarboxylase ODCase , which is an enzyme that catalyzes one reaction involved in the synthesis of pyrimidine ribonucleotides in yeast RNA. Loss of ODCase activity leads to a lack of cell growth unless uracil or uridine is added to the media. When the URA3 gene is added, auxotrophic bacteria can now grow positive selection . In contrast, if 5 FOA 5 Fluoroorotic acid is added to the media, the ODCase of prototrophic bacteria can convert 5 FOA into the toxic compound a suicide inhibitor 5 fluorouracil causing death negative selection . Since URA3 allows for both positive and negative selection, it has been developed as a genetic marker for DNA transformations and other genetic techniques in bacteria and many fungal species. It is one of the most important genetic markers in yeast genetic modification. References S. cerevisiae database 2005 URA3 gene. http db.yeastgenome.org cgi bin locus.pl?locus ura3 summaryParagraph accessed 16 10 07 . PAUL J. FLYNN AND RICHARD J. REECE. Activation of Transcription by Metabolic Intermediates of the Pyrimidine Biosynthetic Pathway. MOLECULAR AND CELLULAR BIOLOGY,Vol. 19, No. 1, 882 888 Category Molecular biology ... more details
chembox verifiedrevid 385317369 Name 4 Pyrimidone ImageFile Pyrimidone.png ImageSize 120px IUPACName Pyrimidone OtherNames Hydroxypyrimidine Pyrimidinone Section1 Chembox Identifiers CASNo 51953 17 4 PubChem 20695 SMILES O C1NC NC C1 Section2 Chembox Properties C 4 H 4 N 2 O 1 Appearance White to light yellow powder Density MeltingPt 163 168 C BoilingPt Solubility Section3 Chembox Hazards MainHazards Respiratory system, eye, skin irritation FlashPt Autoignition Pyrimidone is the name given to either of two heterocyclic compound s with the formula Carbon C sub 4 sub Hydrogen H sub 4 sub Nitrogen N sub 2 sub Oxygen O 2 pyrimidone and 4 pyrimidone . The compounds can also be called 2 hydroxypyrimidine or 4 hydroxypyrimidine respectively, based on a Substitution reaction substituted pyrimidine , or 1,3 diazine , ring. Derivatives Derivatives of pyrimidone are the basis of many other biological molecules, including Nucleobases , such as cytosine Barbiturates , such as metharbital gallery File Cytosine chemical structure.png Cytosine File Metharbital.png Metharbital gallery See also Pyrimidine Category Pyrimidones Heterocyclic stub fa zh ... more details
thymines, resulting in the formation of pyrimidinedimers . ref cite pmid 5328566 ref In human skin cells, thousands of dimers may be formed in a day due to normal exposure to sunlight. DNA polymerase ... more details
A ribonucleotide or ribotide is a nucleotide in which a purine or pyrimidine base is linked to a ribose molecule and exactly one phosphate group. ref cite book title The ACS style guide effective communication of scientific information year 2006 publisher American Chemical Society location Washington, D.C. isbn 9780841239999 edition 3rd editor Coghill, Anne M. Garson, Lorrin R. page 244 ref In living organisms the most common bases for ribonucleotides are adenine A , guanine G , cytosine C , or uracil U . See also Ribonucleosides or ribosides References reflist Nucleobases, nucleosides, and nucleotides Category RNA Category Ribosides Biochem stub bg de Ribonukleotide es Ribonucle tido fr Ribonucl otide it Ribonucleotide nl Ribonucleotide oc Ribonucleotid pl Rybonukleotydy ru sr Ribonukleotid ... more details
Image Transitions transversions.png thumb right 300px Definition of transitions and transversions. In molecular biology , transversion refers to the substitution of a purine for a pyrimidine or vice versa. ref http www.mun.ca biochem courses 3107 Topics Mutations.html Mutations & Mutagenesis ref It can only be reverted by a spontaneous reversion. Because this type of mutation changes the chemical structure dramatically, the consequences of this change tend to be more drastic than those of Transition genetics transitions . Transversions can be caused by ionizing radiation and alkylating agents. See also Transition genetics Transition References references External links http www.mun.ca biology scarr Transitions vs Transversions.html Diagram at mun.ca Mutation Category Mutation Molecular biology stub de Transversion pl Transwersja pt Transvers o ... more details
protein Name carbamoyl phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase caption image width HGNCid 1424 Symbol CAD AltSymbols EntrezGene 790 OMIM 114010 RefSeq NM 004341 UniProt P27708 PDB ECnumber 2.1.3.2 Chromosome 2 Arm p Band 21 LocusSupplementaryData CAD is a gene which encodes several enzymes involved in pyrimidine biosynthesis . De novo synthesis starts with cytosol ic carbamoylphosphate synthetase II which uses glutamine , carbon dioxide and 2 adenosine triphosphate ATP . This enzyme is inhibited by Uridine triphosphate UTP . External links MeshName CAD trifunctional enzyme biochemistry stub Multienzyme complexes ... more details
Encyclopedia
top
