Hmdb loader

Showing Protein DNA polymerase beta (HMDBP00950)

IdentificationBiological propertiesGene propertiesProtein propertiesExternal linksReferencesXMLShow 8 metabolites
Identification
HMDB Protein ID HMDBP00950
Secondary Accession Numbers
  • 6238
Name DNA polymerase beta
Synonyms Not Available
Gene Name POLB
Protein Type Unknown
Biological Properties
General Function Involved in DNA binding
Specific Function Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.
Pathways
  • Base excision repair
  • Human T-cell leukemia virus 1 infection
  • Viral carcinogenesis
Reactions
Deoxynucleoside triphosphate + DNA(n) → Pyrophosphate + DNA(n+1) details
GO Classification
Biological Process
response to ethanol
DNA-dependent DNA replication
pyrimidine dimer repair
base-excision repair
cell death
Cellular Component
cytoplasm
nucleoplasm
spindle microtubule
Function
binding
catalytic activity
transferase activity
transferase activity, transferring phosphorus-containing groups
nucleotidyltransferase activity
dna polymerase activity
dna-directed dna polymerase activity
nucleic acid binding
dna binding
Molecular Function
metal ion binding
DNA-directed DNA polymerase activity
damaged DNA binding
microtubule binding
lyase activity
Process
metabolic process
macromolecule metabolic process
cellular macromolecule metabolic process
dna metabolic process
dna replication
dna repair
Cellular Location
  1. Nucleus
Gene Properties
Chromosome Location 8
Locus 8p11.2
SNPs POLB
Gene Sequence 
>1008 bp
ATGAGCAAACGGAAGGCGCCGCAGGAGACTCTCAACGGGGGAATCACCGACATGCTCACA
GAACTCGCAAACTTTGAGAAGAACGTGAGCCAAGCTATCCACAAGTACAATGCTTACAGA
AAAGCAGCATCTGTTATAGCAAAATACCCACACAAAATAAAGAGTGGAGCTGAAGCTAAG
AAATTGCCTGGAGTAGGAACAAAAATTGCTGAAAAGATTGATGAGTTTTTAGCAACTGGA
AAATTACGTAAACTGGAAAAGATTCGGCAGGATGATACGAGTTCATCCATCAATTTCCTG
ACTCGAGTTAGTGGCATTGGTCCATCTGCTGCAAGGAAGTTTGTAGATGAAGGAATTAAA
ACACTAGAAGATCTCAGAAAAAATGAAGATAAATTGAACCATCATCAGCGAATTGGGCTG
AAATATTTTGGGGACTTTGAAAAAAGAATTCCTCGTGAAGAGATGTTACAAATGCAAGAT
ATTGTACTAAATGAAGTTAAAAAAGTGGATTCTGAATACATTGCTACAGTCTGTGGCAGT
TTCAGAAGAGGTGCAGAGTCCAGTGGTGACATGGATGTTCTCCTGACCCATCCCAGCTTC
ACTTCAGAATCAACCAAACAGCCAAAACTGTTACATCAGGTTGTGGAGCAGTTACAAAAG
GTTCATTTTATCACAGATACCCTGTCAAAGGGTGAGACAAAGTTCATGGGTGTTTGCCAG
CTTCCCAGTAAAAATGATGAAAAAGAATATCCACACAGAAGAATTGATATCAGGTTGATA
CCCAAAGATCAGTATTACTGTGGTGTTCTCTATTTCACTGGGAGTGATATTTTCAATAAG
AATATGAGGGCTCATGCCCTAGAAAAGGGTTTCACAATCAATGAGTACACCATCCGTCCC
TTGGGAGTCACTGGAGTTGCAGGAGAACCCCTGCCAGTGGATAGTGAAAAAGACATCTTT
GATTACATCCAGTGGAAATACCGGGAACCCAAGGACCGGAGCGAATGA
Protein Properties
Number of Residues 335
Molecular Weight 38177.34
Theoretical pI 8.947
Pfam Domain Function
Signals Not Available
Transmembrane Regions Not Available
Protein Sequence 
>DNA polymerase beta
MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAK
KLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIK
TLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGS
FRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQ
LPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRP
LGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
GenBank ID Protein 292397
UniProtKB/Swiss-Prot ID P06746
UniProtKB/Swiss-Prot Entry Name DPOLB_HUMAN
PDB IDs
GenBank Gene ID L11607
GeneCard ID POLB
GenAtlas ID POLB
HGNC ID HGNC:9174
References
General References
  1. Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y, Nakamura Y, Nagahari K, Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M, Takahashi M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki M, Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Chiba Y, Ishida S, Ono Y, Takiguchi S, Watanabe S, Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii A, Hara H, Tanase TO, Nomura Y, Togiya S, Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, Matsunawa H, Ichihara T, Shiohata N, Sano S, Moriya S, Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Nakagawa S, Senoh A, Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Takemoto M, Kawakami B, Yamazaki M, Watanabe K, Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, Fujii Y, Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Kawakami T, Noguchi S, Itoh T, Shigeta K, Senba T, Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki M, Togashi T, Oyama M, Hata H, Watanabe M, Komatsu T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y, Yamashita R, Nakai K, Yada T, Nakamura Y, Ohara O, Isogai T, Sugano S: Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet. 2004 Jan;36(1):40-5. Epub 2003 Dec 21. [PubMed:14702039 ]
  2. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. [PubMed:15489334 ]
  3. Patterson TA, Little W, Cheng X, Widen SG, Kumar A, Beard WA, Wilson SH: Molecular cloning and high-level expression of human polymerase beta cDNA and comparison of the purified recombinant human and rat enzymes. Protein Expr Purif. 2000 Feb;18(1):100-10. [PubMed:10648175 ]
  4. Dobashi Y, Kubota Y, Shuin T, Torigoe S, Yao M, Hosaka M: Polymorphisms in the human DNA polymerase beta gene. Hum Genet. 1995 Apr;95(4):389-90. [PubMed:7705833 ]
  5. Chyan YJ, Ackerman S, Shepherd NS, McBride OW, Widen SG, Wilson SH, Wood TG: The human DNA polymerase beta gene structure. Evidence of alternative splicing in gene expression. Nucleic Acids Res. 1994 Jul 25;22(14):2719-25. [PubMed:7914364 ]
  6. Widen SG, Kedar P, Wilson SH: Human beta-polymerase gene. Structure of the 5'-flanking region and active promoter. J Biol Chem. 1988 Nov 15;263(32):16992-8. [PubMed:3182828 ]
  7. Abbotts J, SenGupta DN, Zmudzka B, Widen SG, Notario V, Wilson SH: Expression of human DNA polymerase beta in Escherichia coli and characterization of the recombinant enzyme. Biochemistry. 1988 Feb 9;27(3):901-9. [PubMed:3284575 ]
  8. SenGupta DN, Zmudzka BZ, Kumar P, Cobianchi F, Skowronski J, Wilson SH: Sequence of human DNA polymerase beta mRNA obtained through cDNA cloning. Biochem Biophys Res Commun. 1986 Apr 14;136(1):341-7. [PubMed:2423078 ]
  9. Matsumoto Y, Kim K, Katz DS, Feng JA: Catalytic center of DNA polymerase beta for excision of deoxyribose phosphate groups. Biochemistry. 1998 May 5;37(18):6456-64. [PubMed:9572863 ]
  10. DeMott MS, Beyret E, Wong D, Bales BC, Hwang JT, Greenberg MM, Demple B: Covalent trapping of human DNA polymerase beta by the oxidative DNA lesion 2-deoxyribonolactone. J Biol Chem. 2002 Mar 8;277(10):7637-40. Epub 2002 Jan 22. [PubMed:11805079 ]
  11. El-Andaloussi N, Valovka T, Toueille M, Steinacher R, Focke F, Gehrig P, Covic M, Hassa PO, Schar P, Hubscher U, Hottiger MO: Arginine methylation regulates DNA polymerase beta. Mol Cell. 2006 Apr 7;22(1):51-62. [PubMed:16600869 ]
  12. Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J: A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. Biochemistry. 1996 Oct 1;35(39):12762-77. [PubMed:8841119 ]
  13. Pelletier H, Sawaya MR: Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Biochemistry. 1996 Oct 1;35(39):12778-87. [PubMed:8841120 ]
  14. Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H: Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism. Biochemistry. 1997 Sep 16;36(37):11205-15. [PubMed:9287163 ]
  15. Krahn JM, Beard WA, Miller H, Grollman AP, Wilson SH: Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure. 2003 Jan;11(1):121-7. [PubMed:12517346 ]