Human Metabolome Database: Showing Protein DNA polymerase delta catalytic subunit (HMDBP00958)

Identification Biological properties Gene properties Protein properties External links References XML Show 6 metabolites

Identification

HMDB Protein ID

HMDBP00958

Secondary Accession Numbers

6246

Name

DNA polymerase delta catalytic subunit

Synonyms

DNA polymerase subunit delta p125

Gene Name

POLD1

Protein Type

Enzyme

Biological Properties

General Function

Involved in nucleotide binding

Specific Function

Possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction. Required with its accessory proteins (proliferating cell nuclear antigen (PCNA) and replication factor C (RFC) or activator 1) for leading strand synthesis. Also involved in completing Okazaki fragments initiated by the DNA polymerase alpha/primase complex.

Pathways

Base excision repair
DNA replication
Homologous recombination
Human T-cell leukemia virus 1 infection
Mismatch repair
Nucleotide excision repair
Purine metabolism
Pyrimidine metabolism

Reactions

Deoxynucleoside triphosphate + DNA(n) → Pyrophosphate + DNA(n+1)	details
Deoxyadenosine triphosphate + DNA → Pyrophosphate + DNA	details
dGTP + DNA → Pyrophosphate + DNA	details
dCTP + DNA → Pyrophosphate + DNA	details
Thymidine 5'-triphosphate + DNA → Pyrophosphate + DNA	details

GO Classification

Biological Process
DNA replication, removal of RNA primer
telomere maintenance via recombination
telomere maintenance via semi-conservative replication
nucleotide-excision repair, DNA gap filling
transcription-coupled nucleotide-excision repair
S phase of mitotic cell cycle
base-excision repair, gap-filling
DNA replication proofreading
DNA synthesis involved in DNA repair
regulation of mitotic cell cycle
response to UV
Cellular Component
nucleoplasm
delta DNA polymerase complex
nucleotide-excision repair complex
Function
binding
nucleotide 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
4 iron, 4 sulfur cluster binding
3'-5' exonuclease activity
DNA-directed DNA polymerase activity
chromatin binding
DNA binding
nucleotide binding
Process
metabolic process
nitrogen compound metabolic process
cellular nitrogen compound metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
macromolecule metabolic process
cellular macromolecule metabolic process
dna metabolic process
dna replication

Cellular Location

Nucleus

Gene Properties

Chromosome Location

Locus

19q13.3

SNPs

POLD1

Gene Sequence

>3324 bp
ATGGATGGCAAGCGGCGGCCAGGCCCAGGGCCCGGGGTGCCCCCAAAGCGGGCCCGTGGG
GGCCTCTGGGATGATGATGATGCACCTCGGCCATCCCAATTCGAGGAGGACCTGGCACTG
ATGGAGGAGATGGAGGCAGAACACAGGCTGCAGGAGCAGGAGGAGGAGGAGCTGCAGTCA
GTCCTGGAGGGGGTTGCAGACGGGCAGGTCCCACCATCAGCCATAGATCCTCGCTGGCTT
CGGCCCACACCACCAGCGCTGGACCCCCAGACAGAGCCCCTCATCTTCCAACAGTTGGAG
ATTGACCATTATGTGGGCCCAGCGCAGCCTGTGCCTGGGGGGCCCCCACCATCCCGCGGC
TCCGTGCCTGTGCTCCGCGCCTTCGGGGTCACCGATGAGGGGTTCTCTGTCTGCTGCCAC
ATCCACGGCTTCGCTCCCTACTTCTACACCCCAGCGCCCCCTGGTTTCGGGCCCGAGCAC
ATGGGTGACCTGCAACGGGAGCTGAACTTGGCCATCAGCCGGGACAGTCGCGGGGGGAGG
GAGCTGACTGGGCCGGCCGTGCTGGCTGTGGAACTGTGCTCCCGAGAGAGCATGTTTGGG
TACCACGGGCACGGCCCCTCCCCGTTCCTGCGCATCACCGTGGCGCTGCCGCGCCTCGTG
GCCCCGGCCCGCCGTCTCCTGGAACAGGGCATCCGTGTGGCAGGCCTGGGCACGCCCAGC
TTCGCGCCCTACGAGGCCAACGTCGACTTTGAGATCCGGTTCATGGTGGACACGGACATC
GTCGGCTGCAACTGGCTGGAGCTCCCAGCTGGGAAATACGCCCTGAGGCTGAAGGAGAAG
GCTACGCAGTGCCAGCTGGAGGCGGACGTGCTGTGGTCTGACGTGGTCAGTCACCCACCG
GAAGGGCCATGGCAGCGCATTGCGCCCTTGCGCGTGCTCAGCTTCGATATCGAGTGCGCC
GGCCGCAAAGGCATCTTCCCTGAGCCTGAGCGGGACCCTGTCATCCAGATCTGCTCGCTG
GGCCTGCGCTGGGGGGAGCCGGAGCCCTTCCTACGCCTGGCGCTCACCCTGCGGCCCTGT
GCCCCCATCCTGGGTGCCAAGGTGCAGAGCTACGAGAAGGAGGAGGACCTGCTGCAGGCC
TGGTCCACCTTCATCCGTATCATGGACCCCGACGTGATCACCGGTTACAACATCCAGAAC
TTCGACCTTCCGTACCTCATCTCTCGGGCCCAGACCCTCAAGGTACAAACATTCCCTTTC
CTGGGCCGTGTGGCCGGCCTTTGCTCCAACATCCGGGACTCTTCATTCCAGTCCAAGCAG
ACGGGCCGGCGGGACACCAAGGTTGTCAGCATGGTGGGCCGCGTGCAGATGGACATGCTG
CAGGTGCTGCTGCGGGAGTACAAGCTCCGCTCCTACACGCTCAATGCCGTGAGCTTCCAC
TTCCTGGGCGAGCAGAAGGAGGACGTGCAGCACAGCATCATCACCGACCTGCAGAATGGG
AACGACCAGACCCGCCGCCGCCTGGCTGTGTACTGCCTGAAGGATGCCTACCTGCCACTG
CGGCTGCTGGAGCGGCTCATGGTGCTGGTGAACGCCGTGGAGATGGCGAGGGTCACTGGC
GTGCCCCTCAGCTACCTGCTCAGTCGTGGCCAGCAGGTCAAGGTCGTATCCCAGCTGTTG
CGGCAGGCCATGCACGAGGGGCTGCTGATGCCCGTGGTGAAGTCAGAGGGCGGCGAGGAC
TACACGGGAGCCACTGTCATCGAGCCCCTCAAAGGGTACTACGACGTCCCCATCGCCACC
CTGGACTTCTCCTCGCTGTACCCGTCCATCATGATGGCCCACAACCTGTGTTACACCACG
CTCCTTCGGCCCGGGACTGCACAGAAACTGGGCCTGACTGAGGATCAGTTCATCAGGACC
CCCACCGGGGACGAGTTTGTGAAGACCTCAGTGCGGAAGGGGCTGCTGCCCCAGATCCTG
GAGAACCTGCTCAGTGCCCGGAAGAGGGCCAAGGCCGAGCTGGCCAAGGAGACAGACCCC
CTCCGGCGCCAGGTCCTGGATGGACGGCAGCTGGCGCTGAAGGTGAGCGCCAACTCCGTA
TACGGCTTCACTGGCGCCCAGGTGGGCAAGTTGCCGTGCCTGGAGATCTCACAGAGCGTC
ACGGGGTTCGGACGTCAGATGATCGAGAAAACCAAGCAGCTGGTGGAGTCTAAGTACACA
GTGGAGAATGGCTACAGCACCAGTGCCAAGGTGGTGTATGGTGACACTGACTCCGTCATG
TGCCGATTCGGCGTGTCCTCGGTGGCTGAGGCGATGGCCCTGGGGCGGGAGGCCGCGGAC
TGGGTGTCAGGTCACTTCCCGTCGCCCATCCGGCTGGAGTTTGAGAAGGTCTACTTCCCA
TACCTGCTTATCAGCAAGAAGCGCTACGCGGGCCTGCTCTTCTCCTCCCGGCCCGACGCC
CACGACCGCATGGACTGCAAGGGCCTGGAGGCCGTGCGCAGGGACAACTGCCCCCTCGTG
GCCAACCTGGTCACTGCCTCACTGCGCCGCCTGCTCATCGACCGAGACCCTGAGGGCGCG
GTGGCTCACGCACAGGACGTCATCTCGGACCTGCTGTGCAACCGCATCGATATCTCCCAG
CTGGTCATCACCAAGGAGCTGACCCGCGCGGCCTCCGACTATGCCGGCAAGCAGGCCCAC
GTGGAGCTGGCCGAGAGGATGAGGAAGCGGGACCCCGGGAGTGCGCCCAGCCTGGGCGAC
CGCGTCCCCTACGTGATCATCAGTGCCGCCAAGGGTGTGGCCGCCTACATGAAGTCGGAG
GACCCGCTGTTCGTGCTGGAGCACAGCCTGCCCATTGACACGCAGTACTACCTGGAGCAG
CAGCTGGCCAAGCCCCTCCTGCGCATCTTCGAGCCCATCCTGGGCGAGGGCCGTGCCGAG
GCTGTGCTACTGCGGGGGGACCACACGCGCTGCAAGACGGTGCTCACGGGCAAGGTGGGC
GGCCTCCTGGCCTTCGCCAAACGCCGCAACTGCTGCATTGGCTGCCGCACAGTGCTCAGC
CACCAGGGAGCCGTGTGTGAGTTCTGCCAGCCCCGGGAGTCTGAGCTGTATCAGAAGGAG
GTATCCCATCTGAATGCCCTGGAGGAGCGCTTCTCGCGCCTCTGGACGCAGTGCCAGCGC
TGCCAGGGCAGCCTGCACGAGGACGTCATCTGCACCAGCCGGGACTGCCCCATCTTCTAC
ATGCGCAAGAAGGTGCGGAAGGACCTGGAAGACCAGGAGCAGCTCCTGCGGCGCTTCGGA
CCCCCTGGACCTGAGGCCTGGTGA

Protein Properties

Number of Residues

1107

Molecular Weight

123629.95

Theoretical pI

7.036

Pfam Domain Function

DNA_pol_B (PF00136 )
DNA_pol_B_exo (PF03104 )
zf-C4pol (PF14260 )

Signals

Not Available

Transmembrane Regions

Not Available

Protein Sequence

>DNA polymerase delta catalytic subunit
MDGKRRPGPGPGVPPKRARGGLWDDDDAPRPSQFEEDLALMEEMEAEHRLQEQEEEELQS
VLEGVADGQVPPSAIDPRWLRPTPPALDPQTEPLIFQQLEIDHYVGPAQPVPGGPPPSRG
SVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPPGFGPEHMGDLQRELNLAISRDSRGGR
ELTGPAVLAVELCSRESMFGYHGHGPSPFLRITVALPRLVAPARRLLEQGIRVAGLGTPS
FAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRLKEKATQCQLEADVLWSDVVSHPP
EGPWQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPC
APILGAKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPF
LGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVSFH
FLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTG
VPLSYLLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGGEDYTGATVIEPLKGYYDVPIAT
LDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRTPTGDEFVKTSVRKGLLPQIL
ENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSV
TGFGRQMIEKTKQLVESKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAAD
WVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLV
ANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYAGKQAH
VELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQ
QLAKPLLRIFEPILGEGRAEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLS
HQGAVCEFCQPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFY
MRKKVRKDLEDQEQLLRRFGPPGPEAW

External Links

GenBank ID Protein

21885469

UniProtKB/Swiss-Prot ID

P28340

UniProtKB/Swiss-Prot Entry Name

DPOD1_HUMAN

PDB IDs

Not Available

GenBank Gene ID

GeneCard ID

GenAtlas ID

HGNC ID

References

General References

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 ]
Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M: Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science. 2009 Aug 14;325(5942):834-40. doi: 10.1126/science.1175371. Epub 2009 Jul 16. [PubMed:19608861 ]
Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP: A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi: 10.1073/pnas.0805139105. Epub 2008 Jul 31. [PubMed:18669648 ]
Li H, Xie B, Zhou Y, Rahmeh A, Trusa S, Zhang S, Gao Y, Lee EY, Lee MY: Functional roles of p12, the fourth subunit of human DNA polymerase delta. J Biol Chem. 2006 May 26;281(21):14748-55. Epub 2006 Feb 28. [PubMed:16510448 ]
Chung DW, Zhang JA, Tan CK, Davie EW, So AG, Downey KM: Primary structure of the catalytic subunit of human DNA polymerase delta and chromosomal location of the gene. Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11197-201. [PubMed:1722322 ]
Yang CL, Chang LS, Zhang P, Hao H, Zhu L, Toomey NL, Lee MY: Molecular cloning of the cDNA for the catalytic subunit of human DNA polymerase delta. Nucleic Acids Res. 1992 Feb 25;20(4):735-45. [PubMed:1542570 ]
Tsurimoto T, Shinozaki A, Yano M, Seki M, Enomoto T: Human Werner helicase interacting protein 1 (WRNIP1) functions as a novel modulator for DNA polymerase delta. Genes Cells. 2005 Jan;10(1):13-22. [PubMed:15670210 ]