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P21189

- DPO2_ECOLI

UniProt

P21189 - DPO2_ECOLI

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Protein

DNA polymerase II

Gene

polB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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
Complete GO annotation...

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
Complete GO annotation...

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.
InParanoidiP21189.
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

        10         20         30         40         50
MAQAGFILTR HWRDTPQGTE VSFWLATDNG PLQVTLAPQE SVAFIPADQV
60 70 80 90 100
PRAQHILQGE QGFRLTPLAL KDFHRQPVYG LYCRAHRQLM NYEKRLREGG
110 120 130 140 150
VTVYEADVRP PERYLMERFI TSPVWVEGDM HNGTIVNARL KPHPDYRPPL
160 170 180 190 200
KWVSIDIETT RHGELYCIGL EGCGQRIVYM LGPENGDASS LDFELEYVAS
210 220 230 240 250
RPQLLEKLNA WFANYDPDVI IGWNVVQFDL RMLQKHAERY RLPLRLGRDN
260 270 280 290 300
SELEWREHGF KNGVFFAQAK GRLIIDGIEA LKSAFWNFSS FSLETVAQEL
310 320 330 340 350
LGEGKSIDNP WDRMDEIDRR FAEDKPALAT YNLKDCELVT QIFHKTEIMP
360 370 380 390 400
FLLERATVNG LPVDRHGGSV AAFGHLYFPR MHRAGYVAPN LGEVPPHASP
410 420 430 440 450
GGYVMDSRPG LYDSVLVLDY KSLYPSIIRT FLIDPVGLVE GMAQPDPEHS
460 470 480 490 500
TEGFLDAWFS REKHCLPEIV TNIWHGRDEA KRQGNKPLSQ ALKIIMNAFY
510 520 530 540 550
GVLGTTACRF FDPRLASSIT MRGHQIMRQT KALIEAQGYD VIYGDTDSTF
560 570 580 590 600
VWLKGAHSEE EAAKIGRALV QHVNAWWAET LQKQRLTSAL ELEYETHFCR
610 620 630 640 650
FLMPTIRGAD TGSKKRYAGL IQEGDKQRMV FKGLETVRTD WTPLAQQFQQ
660 670 680 690 700
ELYLRIFRNE PYQEYVRETI DKLMAGELDA RLVYRKRLRR PLSEYQRNVP
710 720 730 740 750
PHVRAARLAD EENQKRGRPL QYQNRGTIKY VWTTNGPEPL DYQRSPLDYE
760 770 780
HYLTRQLQPV AEGILPFIED NFATLMTGQL GLF
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.
InParanoidi P21189.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 134 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