DNA polymerase II - Escherichia coli (strain K12)

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P21189 (DPO2_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 115. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA polymerase II
Short name=Pol II
EC=2.7.7.7

Gene names

Name:	polB
Synonyms:	dinA
Ordered Locus Names:	b0060, JW0059

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	783 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Thought to be involved in DNA repair and/or mutagenesis.
Catalytic activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Enzyme regulation	DNA polymerase II activity is regulated by the lexA gene during the SOS response.
Sequence similarities	Belongs to the DNA polymerase type-B family.

Ontologies

Keywords
Biological process	DNA damage DNA repair SOS response
Ligand	DNA-binding
Molecular function	DNA-directed DNA polymerase Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: InterPro SOS response Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.1 Ref.6

Chain

2 – 783

782

DNA polymerase II

PRO_0000046473

Natural variations

Natural variant

401

G → D in allele POLB100.

Experimental info

Sequence conflict

172

G → A in AAA24406. Ref.2

Sequence conflict

172

G → A in AAA24407. Ref.2

Sequence conflict

257 – 258

EH → DD in AAA63764. Ref.6

Sequence conflict

257 – 258

EH → DD in AAA23684. Ref.6

Sequence conflict

272

R → G in AAA63764. Ref.6

Sequence conflict

272

R → G in AAA23684. Ref.6

Sequence conflict

735

N → T in AAA24406. Ref.2

Sequence conflict

735

N → T in AAA24407. Ref.2

Sequence conflict

740 – 783

LDYQR…QLGLF → PGLPTFTTGLRTLSDPPATT RGGGNTPFY Ref.2

Secondary structure

783

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P21189 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 1A12A21B2FDB0E22
Show »

FASTA

783

90,053

        10         20         30         40         50         60 
MAQAGFILTR HWRDTPQGTE VSFWLATDNG PLQVTLAPQE SVAFIPADQV PRAQHILQGE 

        70         80         90        100        110        120 
QGFRLTPLAL KDFHRQPVYG LYCRAHRQLM NYEKRLREGG VTVYEADVRP PERYLMERFI 

       130        140        150        160        170        180 
TSPVWVEGDM HNGTIVNARL KPHPDYRPPL KWVSIDIETT RHGELYCIGL EGCGQRIVYM 

       190        200        210        220        230        240 
LGPENGDASS LDFELEYVAS RPQLLEKLNA WFANYDPDVI IGWNVVQFDL RMLQKHAERY 

       250        260        270        280        290        300 
RLPLRLGRDN SELEWREHGF KNGVFFAQAK GRLIIDGIEA LKSAFWNFSS FSLETVAQEL 

       310        320        330        340        350        360 
LGEGKSIDNP WDRMDEIDRR FAEDKPALAT YNLKDCELVT QIFHKTEIMP FLLERATVNG 

       370        380        390        400        410        420 
LPVDRHGGSV AAFGHLYFPR MHRAGYVAPN LGEVPPHASP GGYVMDSRPG LYDSVLVLDY 

       430        440        450        460        470        480 
KSLYPSIIRT FLIDPVGLVE GMAQPDPEHS TEGFLDAWFS REKHCLPEIV TNIWHGRDEA 

       490        500        510        520        530        540 
KRQGNKPLSQ ALKIIMNAFY GVLGTTACRF FDPRLASSIT MRGHQIMRQT KALIEAQGYD 

       550        560        570        580        590        600 
VIYGDTDSTF VWLKGAHSEE EAAKIGRALV QHVNAWWAET LQKQRLTSAL ELEYETHFCR 

       610        620        630        640        650        660 
FLMPTIRGAD TGSKKRYAGL IQEGDKQRMV FKGLETVRTD WTPLAQQFQQ ELYLRIFRNE 

       670        680        690        700        710        720 
PYQEYVRETI DKLMAGELDA RLVYRKRLRR PLSEYQRNVP PHVRAARLAD EENQKRGRPL 

       730        740        750        760        770        780 
QYQNRGTIKY VWTTNGPEPL DYQRSPLDYE HYLTRQLQPV AEGILPFIED NFATLMTGQL 


GLF

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 2034216] [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: 2261080] [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: 1630901] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, 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. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] 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: 16738553] [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: 2217198] [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: 9079692] [Abstract] Cited for: VARIANT MUTANT ALLELE POLB100.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

JDEC22. S15943.

RefSeq

NP_414602.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P21189.

SMR

P21189. Positions 1-780.

ModBase

Search...

Protein-protein interaction databases

IntAct

P21189. 4 interactions.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000004906; EBESCP00000004906; EBESCG00000004006.
EBESCT00000016904; EBESCP00000016195; EBESCG00000015963.

GeneID

944779.

GenomeReviews

Gene locus JW0059 in contig AP009048_GR.
Gene locus b0060 in contig U00096_GR.

KEGG

ecj:JW0059.
eco:b0060.

PATRIC

32115221. VBIEscCol129921_0062.

Organism-specific databases

EchoBASE

EB0740.

EcoGene

EG10747. polB.

Phylogenomic databases

eggNOG

COG0417.

GeneTree

EBGT00050000010158.

HOGENOM

HBG298418.

OMA

VLDGIDW.

PhylomeDB

P21189.

ProtClustDB

PRK05762.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10747-MONOMER.
MetaCyc:EG10747-MONOMER.

Gene expression databases

Genevestigator

P21189.

Family and domain databases

InterPro

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]

Gene3D

G3DSA:3.90.1600.10. DNA_pol_palm_dom. 2 hits.

K02336.

Pfam

PF00136. DNA_pol_B. 2 hits.
PF03104. DNA_pol_B_exo1. 1 hit.
[Graphical view]

PRINTS

PR00106. DNAPOLB.

SMART

SM00486. POLBc. 1 hit.
[Graphical view]

SUPFAM

SSF53098. RNaseH_fold. 1 hit.

PROSITE

PS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DPO2_ECOLI

Accession

Primary (citable) accession number: P21189
Secondary accession number(s): Q8KMX7, Q8KMX8

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 115 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Natural variations

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents