DNA polymerase I (P00582)

Identification
Name:DNA polymerase I
Synonyms:
  • POL I
Gene Name:polA
Enzyme Class:
Biological Properties
General Function:Involved in nucleic acid binding
Specific Function:In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity. It is able to utilize nicked circular duplex DNA as a template and can unwind the parental DNA strand from its template
Cellular Location:Cytoplasmic
SMPDB Pathways:
KEGG Pathways:
KEGG Reactions:
1.0Thumb+1.0DNA ↔ 1.0Thumb+1.0DNA
1.0dATP + 1.0DNA ↔ 1.0Pyrophosphate + 1.0DNA
ReactionCard
1.0Thumb+1.0DNA ↔ 1.0Thumb+1.0DNA
1.0dGTP + 1.0DNA ↔ 1.0Pyrophosphate + 1.0DNA
ReactionCard
1.0Thumb+1.0DNA ↔ 1.0Thumb+1.0DNA
1.0dCTP + 1.0DNA ↔ 1.0Pyrophosphate + 1.0DNA
ReactionCard
1.0Thumb+1.0DNA ↔ 1.0Thumb+1.0DNA
1.0Thymidine 5'-triphosphate + 1.0DNA ↔ 1.0Pyrophosphate + 1.0DNA
ReactionCard
1.0Deoxynucleoside triphosphate+1.0DNA ↔ 1.0Thumb
1.0Deoxynucleoside triphosphate + 1.0DNA ↔ 1.0Pyrophosphate
ReactionCard
EcoCyc Reactions:
1.0DNAn ? 1.0a nucleoside monophosphate
1.0DNAn ? 1.0a nucleoside monophosphate
ReactionCard
Complex Reactions:
1.0Deoxynucleoside triphosphate+1.0DNA(n) → 1.0Thumb+1.0DNA(n+1)
1.0Deoxynucleoside triphosphate + 1.0DNA(n) → 1.0Pyrophosphate + 1.0DNA(n+1)
ReactionCard
Metabolites:
ECMDB IDNameView
ECMDB01532dATPMetaboCard
ECMDB00998dCTPMetaboCard
ECMDB21527Deoxycytidine 5'-triphosphateMetaboCard
ECMDB01440dGTPMetaboCard
ECMDB04142PyrophosphateMetaboCard
ECMDB01342Thymidine 5'-triphosphateMetaboCard
GO Classification:
Component
cell part
intracellular
Function
3'-5' exonuclease activity
5'-3' exonuclease activity
binding
catalytic activity
DNA binding
DNA polymerase activity
DNA-directed DNA polymerase activity
exonuclease activity
hydrolase activity
hydrolase activity, acting on ester bonds
nuclease activity
nucleic acid binding
nucleotidyltransferase activity
transferase activity
transferase activity, transferring phosphorus-containing groups
Process
cellular macromolecule metabolic process
cellular nitrogen compound metabolic process
DNA metabolic process
DNA repair
DNA replication
macromolecule metabolic process
metabolic process
nitrogen compound metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
Gene Properties
Blattner:b3863
Gene OrientationClockwise
Centisome Percentage:87.18
Left Sequence End4044989
Right Sequence End4047775
Gene Sequence:
>2787 bp
ATGGTTCAGATCCCCCAAAATCCACTTATCCTTGTAGATGGTTCATCTTATCTTTATCGC
GCATATCACGCGTTTCCCCCGCTGACTAACAGCGCAGGCGAGCCGACCGGTGCGATGTAT
GGTGTCCTCAACATGCTGCGCAGTCTGATCATGCAATATAAACCGACGCATGCAGCGGTG
GTCTTTGACGCCAAGGGAAAAACCTTTCGTGATGAACTGTTTGAACATTACAAATCACAT
CGCCCGCCAATGCCGGACGATCTGCGTGCACAAATCGAACCCTTGCACGCGATGGTTAAA
GCGATGGGACTGCCGCTGCTGGCGGTTTCTGGCGTAGAAGCGGACGACGTTATCGGTACT
CTGGCGCGCGAAGCCGAAAAAGCCGGGCGTCCGGTGCTGATCAGCACTGGCGATAAAGAT
ATGGCGCAGCTGGTGACGCCAAATATTACGCTTATCAATACCATGACGAATACCATCCTC
GGACCGGAAGAGGTGGTGAATAAGTACGGCGTGCCGCCAGAACTGATCATCGATTTCCTG
GCGCTGATGGGTGACTCCTCTGATAACATTCCTGGCGTACCGGGCGTCGGTGAAAAAACC
GCGCAGGCATTGCTGCAAGGTCTTGGCGGACTGGATACGCTGTATGCCGAGCCAGAAAAA
ATTGCTGGGTTGAGCTTCCGTGGCGCGAAAACAATGGCAGCGAAGCTCGAGCAAAACAAA
GAAGTTGCTTATCTCTCATACCAGCTGGCGACGATTAAAACCGACGTTGAACTGGAGCTG
ACCTGTGAACAACTGGAAGTGCAGCAACCGGCAGCGGAAGAGTTGTTGGGGCTGTTCAAA
AAGTATGAGTTCAAACGCTGGACTGCTGATGTCGAAGCGGGCAAATGGTTACAGGCCAAA
GGGGCAAAACCAGCCGCGAAGCCACAGGAAACCAGTGTTGCAGACGAAGCACCAGAAGTG
ACGGCAACGGTGATTTCTTATGACAACTACGTCACCATCCTTGATGAAGAAACACTGAAA
GCGTGGATTGCGAAGCTGGAAAAAGCGCCGGTATTTGCATTTGATACCGAAACCGACAGC
CTTGATAACATCTCTGCTAACCTGGTCGGGCTTTCTTTTGCTATCGAGCCAGGCGTAGCG
GCATATATTCCGGTTGCTCATGATTATCTTGATGCGCCCGATCAAATCTCTCGCGAGCGT
GCACTCGAGTTGCTAAAACCGCTGCTGGAAGATGAAAAGGCGCTGAAGGTCGGGCAAAAC
CTGAAATACGATCGCGGTATTCTGGCGAACTACGGCATTGAACTGCGTGGGATTGCGTTT
GATACCATGCTGGAGTCCTACATTCTCAATAGCGTTGCCGGGCGTCACGATATGGACAGC
CTCGCGGAACGTTGGTTGAAGCACAAAACCATCACTTTTGAAGAGATTGCTGGTAAAGGC
AAAAATCAACTGACCTTTAACCAGATTGCCCTCGAAGAAGCCGGACGTTACGCCGCCGAA
GATGCAGATGTCACCTTGCAGTTGCATCTGAAAATGTGGCCGGATCTGCAAAAACACAAA
GGGCCGTTGAACGTCTTCGAGAATATCGAAATGCCGCTGGTGCCGGTGCTTTCACGCATT
GAACGTAACGGTGTGAAGATCGATCCGAAAGTGCTGCACAATCATTCTGAAGAGCTCACC
CTTCGTCTGGCTGAGCTGGAAAAGAAAGCGCATGAAATTGCAGGTGAGGAATTTAACCTT
TCTTCCACCAAGCAGTTACAAACCATTCTCTTTGAAAAACAGGGCATTAAACCGCTGAAG
AAAACGCCGGGTGGCGCGCCGTCAACGTCGGAAGAGGTACTGGAAGAACTGGCGCTGGAC
TATCCGTTGCCAAAAGTGATTCTGGAGTATCGTGGTCTGGCGAAGCTGAAATCGACCTAC
ACCGACAAGCTGCCGCTGATGATCAACCCGAAAACCGGGCGTGTGCATACCTCTTATCAC
CAGGCAGTAACTGCAACGGGACGTTTATCGTCAACCGATCCTAACCTGCAAAACATTCCG
GTGCGTAACGAAGAAGGTCGTCGTATCCGCCAGGCGTTTATTGCGCCAGAGGATTATGTG
ATTGTCTCAGCGGACTACTCGCAGATTGAACTGCGCATTATGGCGCATCTTTCGCGTGAC
AAAGGCTTGCTGACCGCATTCGCGGAAGGAAAAGATATCCACCGGGCAACGGCGGCAGAA
GTGTTTGGTTTGCCACTGGAAACCGTCACCAGCGAGCAACGCCGTAGCGCGAAAGCGATC
AACTTTGGTCTGATTTATGGCATGAGTGCTTTCGGTCTGGCGCGGCAATTGAACATTCCA
CGTAAAGAAGCGCAGAAGTACATGGACCTTTACTTCGAACGCTACCCTGGCGTGCTGGAG
TATATGGAACGCACCCGTGCTCAGGCGAAAGAGCAGGGCTACGTTGAAACGCTGGACGGA
CGCCGTCTGTATCTGCCGGATATCAAATCCAGCAATGGTGCTCGTCGTGCAGCGGCTGAA
CGTGCAGCCATTAACGCGCCAATGCAGGGAACCGCCGCCGACATTATCAAACGGGCGATG
ATTGCCGTTGATGCGTGGTTACAGGCTGAGCAACCGCGTGTACGTATGATCATGCAGGTA
CACGATGAACTGGTATTTGAAGTTCATAAAGATGATGTTGATGCCGTCGCGAAGCAGATT
CATCAACTGATGGAAAACTGTACCCGTCTGGATGTGCCGTTGCTGGTGGAAGTGGGGAGT
GGCGAAAACTGGGATCAGGCGCACTAA
Protein Properties
Pfam Domain Function:
Protein Residues:928
Protein Molecular Weight:103117
Protein Theoretical pI:5
PDB File:1KFD
Signaling Regions:
  • None
Transmembrane Regions:
  • None
Protein Sequence:
>DNA polymerase I
MVQIPQNPLILVDGSSYLYRAYHAFPPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAV
VFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEADDVIGT
LAREAEKAGRPVLISTGDKDMAQLVTPNITLINTMTNTILGPEEVVNKYGVPPELIIDFL
ALMGDSSDNIPGVPGVGEKTAQALLQGLGGLDTLYAEPEKIAGLSFRGAKTMAAKLEQNK
EVAYLSYQLATIKTDVELELTCEQLEVQQPAAEELLGLFKKYEFKRWTADVEAGKWLQAK
GAKPAAKPQETSVADEAPEVTATVISYDNYVTILDEETLKAWIAKLEKAPVFAFDTETDS
LDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQN
LKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKG
KNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRI
ERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLK
KTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYH
QAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRD
KGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQLNIP
RKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPDIKSSNGARRAAAE
RAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQI
HQLMENCTRLDVPLLVEVGSGENWDQAH
References
External Links:
ResourceLink
Uniprot ID:P00582
Uniprot Name:DPO1_ECOLI
GenBank Gene ID:AP009048
Genebank Protein ID:85676195
PDB ID:1KFD
Ecogene ID:EG10746
Ecocyc:EG10746
ColiBase:b3863
Kegg Gene:b3863
EchoBASE ID:EB0739
CCDB:DPO1_ECOLI
BacMap:16131704
General Reference:
  • Beese, L. S., Derbyshire, V., Steitz, T. A. (1993). "Structure of DNA polymerase I Klenow fragment bound to duplex DNA." Science 260:352-355. Pubmed: 8469987
  • Beese, L. S., Friedman, J. M., Steitz, T. A. (1993). "Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate." Biochemistry 32:14095-14101. Pubmed: 8260491
  • Beese, L. S., Steitz, T. A. (1991). "Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism." EMBO J 10:25-33. Pubmed: 1989886
  • Blattner, F. R., Plunkett, G. 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., Shao, Y. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277:1453-1462. Pubmed: 9278503
  • Brautigam, C. A., Steitz, T. A. (1998). "Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates." J Mol Biol 277:363-377. Pubmed: 9514742
  • Brautigam, C. A., Sun, S., Piccirilli, J. A., Steitz, T. A. (1999). "Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli." Biochemistry 38:696-704. Pubmed: 9888810
  • Brown, W. E., Stump, K. H., Kelley, W. S. (1982). "Escherichia coli DNA polymerase I. Sequence characterization and secondary structure prediction." J Biol Chem 257:1965-1972. Pubmed: 7035456
  • Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2:2006.0007. Pubmed: 16738553
  • Joyce, C. M., Grindley, N. D. (1982). "Identification of two genes immediately downstream from the polA gene of Escherichia coli." J Bacteriol 152:1211-1219. Pubmed: 6183253
  • Joyce, C. M., Kelley, W. S., Grindley, N. D. (1982). "Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I." J Biol Chem 257:1958-1964. Pubmed: 6276402
  • Kelley, W. S., Joyce, C. M. (1983). "Genetic characterization of early amber mutations in the Escherichia coli polA gene and purification of the amber peptides." J Mol Biol 164:529-560. Pubmed: 6302278
  • Mullen, G. P., Vaughn, J. B. Jr, Mildvan, A. S. (1993). "Sequential proton NMR resonance assignments, circular dichroism, and structural properties of a 50-residue substrate-binding peptide from DNA polymerase I." Arch Biochem Biophys 301:174-183. Pubmed: 8442659
  • Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G., Steitz, T. A. (1985). "Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP." Nature 313:762-766. Pubmed: 3883192
  • Plunkett, G. 3rd, Burland, V., Daniels, D. L., Blattner, F. R. (1993). "Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes." Nucleic Acids Res 21:3391-3398. Pubmed: 8346018
  • Teplova, M., Wallace, S. T., Tereshko, V., Minasov, G., Symons, A. M., Cook, P. D., Manoharan, M., Egli, M. (1999). "Structural origins of the exonuclease resistance of a zwitterionic RNA." Proc Natl Acad Sci U S A 96:14240-14245. Pubmed: 10588690