DNA polymerase - Enterobacteria phage RB69

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Q38087 (DPOL_BPR69) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 91. History...

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

Documents (2) |

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
EC=2.7.7.7

Alternative name(s):
Gp43

Gene names

Name:

Organism

Enterobacteria phage RB69 (Bacteriophage RB69)

Taxonomic identifier

12353 [NCBI]

Taxonomic lineage

Viruses › dsDNA viruses, no RNA stage › Caudovirales › Myoviridae › T4-like viruses

Virus host

Escherichia coli [TaxID: 562]

Protein attributes

Sequence length	903 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
Catalytic activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Sequence similarities	Belongs to the DNA polymerase type-B family.

Ontologies

Keywords
Biological process	DNA replication
Ligand	DNA-binding
Molecular function	DNA-directed DNA polymerase Exonuclease Hydrolase Nuclease Nucleotidyltransferase Transferase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	DNA replication 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 exonuclease 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

Chain

1 – 903

903

DNA polymerase

PRO_0000046547

Secondary structure

903

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q38087 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: A3983FC16D4C0509
Show »

FASTA

903

104,613

        10         20         30         40         50         60 
MKEFYLTVEQ IGDSIFERYI DSNGRERTRE VEYKPSLFAH CPESQATKYF DIYGKPCTRK 

        70         80         90        100        110        120 
LFANMRDASQ WIKRMEDIGL EALGMDDFKL AYLSDTYNYE IKYDHTKIRV ANFDIEVTSP 

       130        140        150        160        170        180 
DGFPEPSQAK HPIDAITHYD SIDDRFYVFD LLNSPYGNVE EWSIEIAAKL QEQGGDEVPS 

       190        200        210        220        230        240 
EIIDKIIYMP FDNEKELLME YLNFWQQKTP VILTGWNVES FDIPYVYNRI KNIFGESTAK 

       250        260        270        280        290        300 
RLSPHRKTRV KVIENMYGSR EIITLFGISV LDYIDLYKKF SFTNQPSYSL DYISEFELNV 

       310        320        330        340        350        360 
GKLKYDGPIS KLRESNHQRY ISYNIIDVYR VLQIDAKRQF INLSLDMGYY AKIQIQSVFS 

       370        380        390        400        410        420 
PIKTWDAIIF NSLKEQNKVI PQGRSHPVQP YPGAFVKEPI PNRYKYVMSF DLTSLYPSII 

       430        440        450        460        470        480 
RQVNISPETI AGTFKVAPLH DYINAVAERP SDVYSCSPNG MMYYKDRDGV VPTEITKVFN 

       490        500        510        520        530        540 
QRKEHKGYML AAQRNGEIIK EALHNPNLSV DEPLDVDYRF DFSDEIKEKI KKLSAKSLNE 

       550        560        570        580        590        600 
MLFRAQRTEV AGMTAQINRK LLINSLYGAL GNVWFRYYDL RNATAITTFG QMALQWIERK 

       610        620        630        640        650        660 
VNEYLNEVCG TEGEAFVLYG DTDSIYVSAD KIIDKVGESK FRDTNHWVDF LDKFARERME 

       670        680        690        700        710        720 
PAIDRGFREM CEYMNNKQHL MFMDREAIAG PPLGSKGIGG FWTGKKRYAL NVWDMEGTRY 

       730        740        750        760        770        780 
AEPKLKIMGL ETQKSSTPKA VQKALKECIR RMLQEGEESL QEYFKEFEKE FRQLNYISIA 

       790        800        810        820        830        840 
SVSSANNIAK YDVGGFPGPK CPFHIRGILT YNRAIKGNID APQVVEGEKV YVLPLREGNP 

       850        860        870        880        890        900 
FGDKCIAWPS GTEITDLIKD DVLHWMDYTV LLEKTFIKPL EGFTSAAKLD YEKKASLFDM 


FDF

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Modular organization of T4 DNA polymerase. Evidence from phylogenetics." Wang C.C., Yeh L.-S., Karam J.D. J. Biol. Chem. 270:26558-26564(1995) [PubMed: 7592876] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Enterobacteria phage RB69 complete genome." Petrov V., Nolan J., Chin D., Letarov A., Krisch H.M., Karam J.D. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69." Wang J., Sattar A.K., Wang C.C., Karam J.D., Konigsberg W.H., Steitz T.A. Cell 89:1087-1099(1997) [PubMed: 9215631] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
[4]	"Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex." Shamoo Y., Steitz T.A. Cell 99:155-166(1999) [PubMed: 10535734] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF COMPLEX WITH GP45.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U34036 Genomic DNA. Translation: AAA93077.1.
AY303349 Genomic DNA. Translation: AAP75958.1.

RefSeq

NP_861746.1. NC_004928.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1B1F	model	-	R	387-892	[»]
1B8H	X-ray	3.00	D	893-903	[»]
1CLQ	X-ray	2.70	A	1-903	[»]
1IG9	X-ray	2.60	A	1-903	[»]
1IH7	X-ray	2.21	A	1-903	[»]
1Q9X	X-ray	2.69	A/B/C/D	1-903	[»]
1Q9Y	X-ray	2.80	A	1-903	[»]
1QE4	model	-	F	1-903	[»]
1WAF	X-ray	3.20	A/B	1-903	[»]
1WAG	model	-	R	1-903	[»]
1WAH	model	-	R	1-903	[»]
1WAI	model	-	R	1-903	[»]
1WAJ	X-ray	2.80	A	1-903	[»]
2ATQ	X-ray	3.20	A	1-903	[»]
2DTU	X-ray	2.37	A/B/C/D	1-902	[»]
2DY4	X-ray	2.65	A/B/C/D	1-903	[»]
2OYQ	X-ray	2.86	A/B/C/D	1-903	[»]
2OZM	X-ray	2.86	A	1-903	[»]
2OZS	X-ray	2.75	A	1-903	[»]
2P5G	X-ray	2.80	A/B/C/D	1-903	[»]
2P5O	X-ray	2.80	A/B/C/D	2-903	[»]
3CFO	X-ray	2.60	A	1-903	[»]
3CFP	X-ray	2.50	A	1-903	[»]
3CFR	X-ray	2.40	A	1-903	[»]
3CQ8	X-ray	2.50	A	1-903	[»]
3KD1	X-ray	2.66	E	1-903	[»]
3KD5	X-ray	2.69	E	1-903	[»]
3L8B	X-ray	2.15	A/B	1-903	[»]
3LDS	X-ray	3.00	A	1-903	[»]
3LZI	X-ray	2.30	A	1-903	[»]
3LZJ	X-ray	2.05	A	1-903	[»]
3NAE	X-ray	2.00	A	1-903	[»]
3NCI	X-ray	1.79	A	1-903	[»]
3NDK	X-ray	2.00	A	1-903	[»]
3NE6	X-ray	2.00	A	1-903	[»]
3NGI	X-ray	1.89	A	1-903	[»]
3NHG	X-ray	2.50	A	1-903	[»]
3QEP	X-ray	1.80	A	1-903	[»]
3RMA	X-ray	2.84	A/B/C/D	1-903	[»]
3RMB	X-ray	2.65	A/B/C/D	1-903	[»]
3RMC	X-ray	3.00	A/B/C/D	1-903	[»]
3RMD	X-ray	2.98	A/B/C/D	1-903	[»]
3RWU	X-ray	2.33	A	1-901	[»]
3S9H	X-ray	1.95	A	1-903	[»]
3SCX	X-ray	2.35	A	1-901	[»]
3SI6	X-ray	1.85	A	1-901	[»]
3SJJ	X-ray	2.38	A	1-901	[»]
3SNN	X-ray	2.00	A	1-901	[»]
3SPY	X-ray	2.14	A	1-901	[»]
3SPZ	X-ray	2.43	A	1-903	[»]
3SQ0	X-ray	2.00	A	1-903	[»]
3SQ1	X-ray	1.82	A	1-901	[»]
3SQ2	X-ray	2.10	A	1-902	[»]
3SQ4	X-ray	2.23	A	1-902	[»]
3SUN	X-ray	2.42	A	1-895	[»]
3SUO	X-ray	2.23	A	1-900	[»]
3SUP	X-ray	2.32	A	1-903	[»]
3SUQ	X-ray	3.15	A	1-897	[»]
3TAB	X-ray	2.80	A/B/C/D	1-903	[»]
3TAE	X-ray	2.71	A/B/C/D	1-903	[»]
3TAF	X-ray	3.00	A/B/C/D	1-903	[»]
3TAG	X-ray	2.95	A/B/C/D	1-903	[»]

ProteinModelPortal

Q38087.

SMR

Q38087. Positions 1-903.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1494172.

GenomeReviews

Gene locus RB69p057 in contig AY303349_GR.

Phylogenomic databases

ProtClustDB

PHA2528.

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.

Pfam

PF00136. DNA_pol_B. 1 hit.
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

DPOL_BPR69

Accession

Primary (citable) accession number: Q38087
Secondary accession number(s): Q76XX8

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	November 1, 1996
Last modified:	January 25, 2012
This is version 91 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program

Relevant documents

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

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents