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P21189

- DPO2_ECOLI

UniProt

P21189 - DPO2_ECOLI

Protein

DNA polymerase II

Gene

polB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 133 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Thought to be involved in DNA repair and/or mutagenesis.

    Catalytic activityi

    Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

    Enzyme regulationi

    DNA polymerase II activity is regulated by the lexA gene during the SOS response.

    GO - Molecular functioni

    1. 3'-5'-exodeoxyribonuclease activity Source: EcoCyc
    2. 3'-5' exonuclease activity Source: RefGenome
    3. DNA binding Source: UniProtKB-KW
    4. DNA-directed DNA polymerase activity Source: EcoCyc
    5. nucleotide binding Source: InterPro

    GO - Biological processi

    1. DNA catabolic process, exonucleolytic Source: GOC
    2. DNA-dependent DNA replication Source: EcoCyc
    3. DNA replication proofreading Source: EcoCyc
    4. nucleic acid phosphodiester bond hydrolysis Source: GOC
    5. nucleotide-excision repair, DNA gap filling Source: RefGenome
    6. SOS response Source: EcoCyc
    7. translesion synthesis Source: RefGenome

    Keywords - Molecular functioni

    DNA-directed DNA polymerase, Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    DNA damage, DNA repair, SOS response

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10747-MONOMER.
    ECOL316407:JW0059-MONOMER.
    MetaCyc:EG10747-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA polymerase II (EC:2.7.7.7)
    Short name:
    Pol II
    Gene namesi
    Name:polB
    Synonyms:dinA
    Ordered Locus Names:b0060, JW0059
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10747. polB.

    Subcellular locationi

    GO - Cellular componenti

    1. chromosome Source: RefGenome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed2 Publications
    Chaini2 – 783782DNA polymerase IIPRO_0000046473Add
    BLAST

    Proteomic databases

    PRIDEiP21189.

    Expressioni

    Gene expression databases

    GenevestigatoriP21189.

    Interactioni

    Protein-protein interaction databases

    IntActiP21189. 5 interactions.
    STRINGi511145.b0060.

    Structurei

    Secondary structure

    1
    783
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 1514
    Beta strandi18 – 2710
    Beta strandi30 – 356
    Beta strandi41 – 466
    Helixi47 – 493
    Helixi50 – 567
    Turni57 – 593
    Beta strandi62 – 7110
    Beta strandi77 – 859
    Helixi86 – 9813
    Helixi110 – 1178
    Beta strandi121 – 13111
    Beta strandi134 – 1429
    Beta strandi152 – 1598
    Beta strandi165 – 1728
    Beta strandi175 – 1839
    Beta strandi192 – 2009
    Helixi201 – 21515
    Beta strandi218 – 2247
    Turni225 – 2284
    Helixi229 – 24012
    Turni248 – 2503
    Beta strandi254 – 2574
    Beta strandi259 – 2613
    Beta strandi265 – 2684
    Beta strandi273 – 2764
    Helixi277 – 2837
    Helixi293 – 3019
    Beta strandi305 – 3073
    Helixi310 – 32314
    Helixi325 – 34622
    Helixi348 – 35912
    Turni363 – 3664
    Helixi369 – 38315
    Beta strandi410 – 4134
    Beta strandi415 – 4206
    Helixi423 – 4319
    Helixi435 – 4439
    Turni447 – 4493
    Beta strandi450 – 4523
    Beta strandi454 – 4563
    Beta strandi458 – 4625
    Helixi466 – 48217
    Helixi486 – 50116
    Helixi502 – 5043
    Helixi513 – 53624
    Beta strandi540 – 5434
    Beta strandi545 – 5528
    Helixi559 – 58224
    Turni583 – 5853
    Beta strandi592 – 60312
    Beta strandi609 – 6124
    Beta strandi617 – 6237
    Beta strandi626 – 6349
    Helixi635 – 6373
    Helixi643 – 65715
    Helixi663 – 67412
    Turni675 – 6784
    Helixi679 – 6813
    Beta strandi684 – 6885
    Helixi692 – 6943
    Helixi701 – 71515
    Beta strandi725 – 7339
    Beta strandi736 – 7394
    Helixi740 – 7423
    Helixi749 – 7557
    Helixi757 – 7626
    Helixi765 – 7684
    Helixi772 – 7798

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Q8IX-ray2.00A1-783[»]
    3K57X-ray2.08A1-783[»]
    3K58X-ray2.05A1-783[»]
    3K59X-ray1.92A1-783[»]
    3K5LX-ray2.70A1-783[»]
    3K5MX-ray2.04A1-783[»]
    3K5NX-ray3.15A/B1-783[»]
    3K5OX-ray2.20A/B1-783[»]
    3MAQX-ray2.40A1-783[»]
    ProteinModelPortaliP21189.
    SMRiP21189. Positions 1-780.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP21189.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the DNA polymerase type-B family.Curated

    Phylogenomic databases

    eggNOGiCOG0417.
    HOGENOMiHOG000221829.
    KOiK02336.
    OMAiKAIDNPW.
    OrthoDBiEOG6KWXSX.
    PhylomeDBiP21189.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    3.90.1600.10. 2 hits.
    InterProiIPR006172. DNA-dir_DNA_pol_B.
    IPR017964. DNA-dir_DNA_pol_B_CS.
    IPR006133. DNA-dir_DNA_pol_B_exonuc.
    IPR006134. DNA-dir_DNA_pol_B_multi_dom.
    IPR023211. DNA_pol_palm_dom.
    IPR012337. RNaseH-like_dom.
    [Graphical view]
    PfamiPF00136. DNA_pol_B. 2 hits.
    PF03104. DNA_pol_B_exo1. 1 hit.
    [Graphical view]
    PRINTSiPR00106. DNAPOLB.
    SMARTiSM00486. POLBc. 1 hit.
    [Graphical view]
    SUPFAMiSSF53098. SSF53098. 1 hit.
    PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P21189-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAQAGFILTR HWRDTPQGTE VSFWLATDNG PLQVTLAPQE SVAFIPADQV    50
    PRAQHILQGE QGFRLTPLAL KDFHRQPVYG LYCRAHRQLM NYEKRLREGG 100
    VTVYEADVRP PERYLMERFI TSPVWVEGDM HNGTIVNARL KPHPDYRPPL 150
    KWVSIDIETT RHGELYCIGL EGCGQRIVYM LGPENGDASS LDFELEYVAS 200
    RPQLLEKLNA WFANYDPDVI IGWNVVQFDL RMLQKHAERY RLPLRLGRDN 250
    SELEWREHGF KNGVFFAQAK GRLIIDGIEA LKSAFWNFSS FSLETVAQEL 300
    LGEGKSIDNP WDRMDEIDRR FAEDKPALAT YNLKDCELVT QIFHKTEIMP 350
    FLLERATVNG LPVDRHGGSV AAFGHLYFPR MHRAGYVAPN LGEVPPHASP 400
    GGYVMDSRPG LYDSVLVLDY KSLYPSIIRT FLIDPVGLVE GMAQPDPEHS 450
    TEGFLDAWFS REKHCLPEIV TNIWHGRDEA KRQGNKPLSQ ALKIIMNAFY 500
    GVLGTTACRF FDPRLASSIT MRGHQIMRQT KALIEAQGYD VIYGDTDSTF 550
    VWLKGAHSEE EAAKIGRALV QHVNAWWAET LQKQRLTSAL ELEYETHFCR 600
    FLMPTIRGAD TGSKKRYAGL IQEGDKQRMV FKGLETVRTD WTPLAQQFQQ 650
    ELYLRIFRNE PYQEYVRETI DKLMAGELDA RLVYRKRLRR PLSEYQRNVP 700
    PHVRAARLAD EENQKRGRPL QYQNRGTIKY VWTTNGPEPL DYQRSPLDYE 750
    HYLTRQLQPV AEGILPFIED NFATLMTGQL GLF 783
    Length:783
    Mass (Da):90,053
    Last modified:January 23, 2007 - v2
    Checksum:i1A12A21B2FDB0E22
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti172 – 1721G → A in AAA24406. (PubMed:2261080)Curated
    Sequence conflicti172 – 1721G → A in AAA24407. (PubMed:2261080)Curated
    Sequence conflicti257 – 2582EH → DD in AAA63764. (PubMed:2217198)Curated
    Sequence conflicti257 – 2582EH → DD in AAA23684. (PubMed:2217198)Curated
    Sequence conflicti272 – 2721R → G in AAA63764. (PubMed:2217198)Curated
    Sequence conflicti272 – 2721R → G in AAA23684. (PubMed:2217198)Curated
    Sequence conflicti735 – 7351N → T in AAA24406. (PubMed:2261080)Curated
    Sequence conflicti735 – 7351N → T in AAA24407. (PubMed:2261080)Curated
    Sequence conflicti740 – 78344LDYQR…QLGLF → PGLPTFTTGLRTLSDPPATT RGGGNTPFY(PubMed:2261080)CuratedAdd
    BLAST

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti401 – 4011G → D in allele POLB100.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X54847 Genomic DNA. Translation: CAA38616.1.
    M62646 Genomic DNA. Translation: AAA24406.1.
    M35371 Genomic DNA. Translation: AAA24407.1.
    M38283 Genomic DNA. Translation: AAA63764.1.
    U00096 Genomic DNA. Translation: AAC73171.1.
    AP009048 Genomic DNA. Translation: BAB96628.2.
    M37727 Genomic DNA. Translation: AAA23684.1.
    PIRiS15943. JDEC22.
    RefSeqiNP_414602.1. NC_000913.3.
    YP_488366.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73171; AAC73171; b0060.
    BAB96628; BAB96628; BAB96628.
    GeneIDi12932627.
    944779.
    KEGGiecj:Y75_p0060.
    eco:b0060.
    PATRICi32115221. VBIEscCol129921_0062.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X54847 Genomic DNA. Translation: CAA38616.1 .
    M62646 Genomic DNA. Translation: AAA24406.1 .
    M35371 Genomic DNA. Translation: AAA24407.1 .
    M38283 Genomic DNA. Translation: AAA63764.1 .
    U00096 Genomic DNA. Translation: AAC73171.1 .
    AP009048 Genomic DNA. Translation: BAB96628.2 .
    M37727 Genomic DNA. Translation: AAA23684.1 .
    PIRi S15943. JDEC22.
    RefSeqi NP_414602.1. NC_000913.3.
    YP_488366.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1Q8I X-ray 2.00 A 1-783 [» ]
    3K57 X-ray 2.08 A 1-783 [» ]
    3K58 X-ray 2.05 A 1-783 [» ]
    3K59 X-ray 1.92 A 1-783 [» ]
    3K5L X-ray 2.70 A 1-783 [» ]
    3K5M X-ray 2.04 A 1-783 [» ]
    3K5N X-ray 3.15 A/B 1-783 [» ]
    3K5O X-ray 2.20 A/B 1-783 [» ]
    3MAQ X-ray 2.40 A 1-783 [» ]
    ProteinModelPortali P21189.
    SMRi P21189. Positions 1-780.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P21189. 5 interactions.
    STRINGi 511145.b0060.

    Proteomic databases

    PRIDEi P21189.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73171 ; AAC73171 ; b0060 .
    BAB96628 ; BAB96628 ; BAB96628 .
    GeneIDi 12932627.
    944779.
    KEGGi ecj:Y75_p0060.
    eco:b0060.
    PATRICi 32115221. VBIEscCol129921_0062.

    Organism-specific databases

    EchoBASEi EB0740.
    EcoGenei EG10747. polB.

    Phylogenomic databases

    eggNOGi COG0417.
    HOGENOMi HOG000221829.
    KOi K02336.
    OMAi KAIDNPW.
    OrthoDBi EOG6KWXSX.
    PhylomeDBi P21189.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG10747-MONOMER.
    ECOL316407:JW0059-MONOMER.
    MetaCyc:EG10747-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P21189.
    PROi P21189.

    Gene expression databases

    Genevestigatori P21189.

    Family and domain databases

    Gene3Di 3.30.420.10. 1 hit.
    3.90.1600.10. 2 hits.
    InterProi IPR006172. DNA-dir_DNA_pol_B.
    IPR017964. DNA-dir_DNA_pol_B_CS.
    IPR006133. DNA-dir_DNA_pol_B_exonuc.
    IPR006134. DNA-dir_DNA_pol_B_multi_dom.
    IPR023211. DNA_pol_palm_dom.
    IPR012337. RNaseH-like_dom.
    [Graphical view ]
    Pfami PF00136. DNA_pol_B. 2 hits.
    PF03104. DNA_pol_B_exo1. 1 hit.
    [Graphical view ]
    PRINTSi PR00106. DNAPOLB.
    SMARTi SM00486. POLBc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53098. SSF53098. 1 hit.
    PROSITEi PS00116. DNA_POLYMERASE_B. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Escherichia coli DNA polymerase II is homologous to alpha-like DNA polymerases."
      Iwasaki H., Ishino Y., Toh H., Nakata A., Shinagawa H.
      Mol. Gen. Genet. 226:24-33(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-9.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. "Nucleotide sequence and deletion analysis of the polB gene of Escherichia coli."
      Chen H., Sun Y., Stark T., Beattie W., Moses R.E.
      DNA Cell Biol. 9:631-635(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    3. "Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region."
      Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A.
      Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    6. "DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli."
      Bonner C.A., Hays S., McEntee K., Goodman M.F.
      Proc. Natl. Acad. Sci. U.S.A. 87:7663-7667(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-458, PROTEIN SEQUENCE OF 2-28.
      Strain: K12.
    7. "The Escherichia coli polB locus is identical to dinA, the structural gene for DNA polymerase II. Characterization of Pol II purified from a polB mutant."
      Qiu Z., Goodman M.F.
      J. Biol. Chem. 272:8611-8617(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT MUTANT ALLELE POLB100.

    Entry informationi

    Entry nameiDPO2_ECOLI
    AccessioniPrimary (citable) accession number: P21189
    Secondary accession number(s): Q8KMX7, Q8KMX8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1991
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 133 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3