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Protein

DNA-directed DNA polymerase

Gene

5

Organism
Enterobacteria phage T7 (Bacteriophage T7)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Replicates viral genomic DNA. This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction. Non-processive DNA polymerase that achieves processivity by binding to host thioredoxin (TrxA). This interaction increases the rate of dNTP incorporation to yield a processivity of approximately 800 nucleotides (nt) per binding event. Interacts with DNA helicase gp4 to coordinate nucleotide polymerization with unwinding of the DNA. The leading strand is synthesized continuously while synthesis of the lagging strand requires the synthesis of oligoribonucleotides by the primase domain of gp4.4 Publications

Catalytic activityi

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

GO - Molecular functioni

  • 3'-5' exonuclease activity Source: UniProtKB
  • DNA binding Source: UniProtKB-KW
  • DNA-directed DNA polymerase activity Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication, Host-virus interaction, Viral DNA replication

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed DNA polymerase (EC:2.7.7.71 Publication, EC:3.1.11.-2 Publications)
Alternative name(s):
DNA polymerase gp5
Gene product 5
Short name:
Gp5
T7 DNA polymerase
Gene namesi
Ordered Locus Names:5
OrganismiEnterobacteria phage T7 (Bacteriophage T7)
Taxonomic identifieri10760 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesPodoviridaeAutographivirinaeT7likevirus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000000840 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi123 – 1231H → S: 83% loss of exonuclease activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 704704DNA-directed DNA polymerasePRO_0000101269Add
BLAST

Interactioni

Subunit structurei

Composed of two subunits. One is encoded by the phage and the other is encoded by the host thioredoxin. Interacts with helicase/primase gp4; this interaction is essential for the coordination of DNA unwinding and nucleotide polymerization on duplex DNA. Interacts with the ssDNA-binding protein gp2.5.2 Publications

Protein-protein interaction databases

DIPiDIP-41665N.
IntActiP00581. 3 interactions.
MINTiMINT-1513442.

Structurei

Secondary structure

1
704
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 109Combined sources
Helixi12 – 143Combined sources
Beta strandi18 – 258Combined sources
Turni26 – 283Combined sources
Beta strandi31 – 344Combined sources
Helixi36 – 383Combined sources
Helixi39 – 5113Combined sources
Beta strandi56 – 605Combined sources
Turni61 – 644Combined sources
Helixi65 – 7713Combined sources
Helixi85 – 873Combined sources
Beta strandi88 – 903Combined sources
Helixi91 – 988Combined sources
Turni99 – 1013Combined sources
Turni106 – 1094Combined sources
Helixi112 – 1143Combined sources
Helixi117 – 1193Combined sources
Helixi127 – 14923Combined sources
Helixi158 – 1603Combined sources
Helixi165 – 18622Combined sources
Turni189 – 1913Combined sources
Helixi198 – 2003Combined sources
Helixi203 – 2097Combined sources
Helixi212 – 23019Combined sources
Beta strandi232 – 2343Combined sources
Helixi236 – 26025Combined sources
Beta strandi264 – 2674Combined sources
Turni277 – 2793Combined sources
Beta strandi284 – 2863Combined sources
Turni306 – 3083Combined sources
Beta strandi318 – 3203Combined sources
Beta strandi326 – 3327Combined sources
Helixi339 – 34810Combined sources
Turni358 – 3603Combined sources
Helixi366 – 3716Combined sources
Helixi377 – 39923Combined sources
Helixi406 – 4094Combined sources
Beta strandi414 – 4163Combined sources
Beta strandi419 – 4213Combined sources
Beta strandi431 – 4355Combined sources
Helixi437 – 4393Combined sources
Helixi448 – 4536Combined sources
Helixi457 – 4593Combined sources
Turni463 – 4653Combined sources
Beta strandi470 – 4767Combined sources
Helixi479 – 49214Combined sources
Helixi495 – 5028Combined sources
Helixi505 – 5128Combined sources
Helixi518 – 52912Combined sources
Helixi534 – 5385Combined sources
Turni539 – 5424Combined sources
Helixi545 – 55713Combined sources
Helixi560 – 57112Combined sources
Beta strandi574 – 5763Combined sources
Beta strandi581 – 5833Combined sources
Beta strandi587 – 5893Combined sources
Beta strandi591 – 5944Combined sources
Beta strandi600 – 6023Combined sources
Helixi606 – 6083Combined sources
Helixi609 – 63527Combined sources
Beta strandi644 – 6529Combined sources
Beta strandi655 – 6628Combined sources
Helixi663 – 68321Combined sources
Beta strandi692 – 6998Combined sources
Turni700 – 7034Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SKRX-ray2.40A1-704[»]
1SKSX-ray2.30A1-704[»]
1SKWX-ray2.30A1-704[»]
1SL0X-ray3.20A/C1-704[»]
1SL1X-ray2.20A1-704[»]
1SL2X-ray2.30A1-704[»]
1T7PX-ray2.20A1-704[»]
1T8EX-ray2.54A1-704[»]
1TK0X-ray2.30A1-704[»]
1TK5X-ray2.20A1-704[»]
1TK8X-ray2.50A1-704[»]
1TKDX-ray2.49A1-704[»]
1X9MX-ray2.10A1-704[»]
1X9SX-ray2.70A1-704[»]
1X9WX-ray2.30A1-704[»]
1ZYQX-ray2.70A1-698[»]
2AJQX-ray2.60A/F1-704[»]
ProteinModelPortaliP00581.
SMRiP00581. Positions 1-704.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00581.

Family & Domainsi

Sequence similaritiesi

Belongs to the DNA polymerase type-A family.Curated

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR019760. DNA-dir_DNA_pol_A_CS.
IPR001098. DNA-dir_DNA_pol_A_palm_dom.
IPR002298. DNA_polymerase_A.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00476. DNA_pol_A. 1 hit.
[Graphical view]
PRINTSiPR00868. DNAPOLI.
SMARTiSM00482. POLAc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00447. DNA_POLYMERASE_A. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P00581-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIVSDIEANA LLESVTKFHC GVIYDYSTAE YVSYRPSDFG AYLDALEAEV
60 70 80 90 100
ARGGLIVFHN GHKYDVPALT KLAKLQLNRE FHLPRENCID TLVLSRLIHS
110 120 130 140 150
NLKDTDMGLL RSGKLPGKRF GSHALEAWGY RLGEMKGEYK DDFKRMLEEQ
160 170 180 190 200
GEEYVDGMEW WNFNEEMMDY NVQDVVVTKA LLEKLLSDKH YFPPEIDFTD
210 220 230 240 250
VGYTTFWSES LEAVDIEHRA AWLLAKQERN GFPFDTKAIE ELYVELAARR
260 270 280 290 300
SELLRKLTET FGSWYQPKGG TEMFCHPRTG KPLPKYPRIK TPKVGGIFKK
310 320 330 340 350
PKNKAQREGR EPCELDTREY VAGAPYTPVE HVVFNPSSRD HIQKKLQEAG
360 370 380 390 400
WVPTKYTDKG APVVDDEVLE GVRVDDPEKQ AAIDLIKEYL MIQKRIGQSA
410 420 430 440 450
EGDKAWLRYV AEDGKIHGSV NPNGAVTGRA THAFPNLAQI PGVRSPYGEQ
460 470 480 490 500
CRAAFGAEHH LDGITGKPWV QAGIDASGLE LRCLAHFMAR FDNGEYAHEI
510 520 530 540 550
LNGDIHTKNQ IAAELPTRDN AKTFIYGFLY GAGDEKIGQI VGAGKERGKE
560 570 580 590 600
LKKKFLENTP AIAALRESIQ QTLVESSQWV AGEQQVKWKR RWIKGLDGRK
610 620 630 640 650
VHVRSPHAAL NTLLQSAGAL ICKLWIIKTE EMLVEKGLKH GWDGDFAYMA
660 670 680 690 700
WVHDEIQVGC RTEEIAQVVI ETAQEAMRWV GDHWNFRCLL DTEGKMGPNW

AICH
Length:704
Mass (Da):79,692
Last modified:July 21, 1986 - v1
Checksum:i17089CE2AD9FB596
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01146 Genomic DNA. Translation: CAA24412.1.
PIRiA00716. DJBPT7.
RefSeqiNP_041982.1. NC_001604.1.

Genome annotation databases

GeneIDi1261044.
KEGGivg:1261044.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01146 Genomic DNA. Translation: CAA24412.1.
PIRiA00716. DJBPT7.
RefSeqiNP_041982.1. NC_001604.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SKRX-ray2.40A1-704[»]
1SKSX-ray2.30A1-704[»]
1SKWX-ray2.30A1-704[»]
1SL0X-ray3.20A/C1-704[»]
1SL1X-ray2.20A1-704[»]
1SL2X-ray2.30A1-704[»]
1T7PX-ray2.20A1-704[»]
1T8EX-ray2.54A1-704[»]
1TK0X-ray2.30A1-704[»]
1TK5X-ray2.20A1-704[»]
1TK8X-ray2.50A1-704[»]
1TKDX-ray2.49A1-704[»]
1X9MX-ray2.10A1-704[»]
1X9SX-ray2.70A1-704[»]
1X9WX-ray2.30A1-704[»]
1ZYQX-ray2.70A1-698[»]
2AJQX-ray2.60A/F1-704[»]
ProteinModelPortaliP00581.
SMRiP00581. Positions 1-704.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-41665N.
IntActiP00581. 3 interactions.
MINTiMINT-1513442.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1261044.
KEGGivg:1261044.

Miscellaneous databases

EvolutionaryTraceiP00581.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR019760. DNA-dir_DNA_pol_A_CS.
IPR001098. DNA-dir_DNA_pol_A_palm_dom.
IPR002298. DNA_polymerase_A.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00476. DNA_pol_A. 1 hit.
[Graphical view]
PRINTSiPR00868. DNAPOLI.
SMARTiSM00482. POLAc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00447. DNA_POLYMERASE_A. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements."
    Dunn J.J., Studier F.W.
    J. Mol. Biol. 166:477-535(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  2. "Nucleotide sequence of the gene for bacteriophage T7 RNA polymerase."
    Moffatt B.A., Dunn J.J., Studier F.W.
    J. Mol. Biol. 173:265-269(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Selective inactivation of the exonuclease activity of bacteriophage T7 DNA polymerase by in vitro mutagenesis."
    Tabor S., Richardson C.C.
    J. Biol. Chem. 264:6447-6458(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF HIS-123, CATALYTIC ACTIVITY.
  4. "The acidic carboxyl terminus of the bacteriophage T7 gene 4 helicase/primase interacts with T7 DNA polymerase."
    Notarnicola S.M., Mulcahy H.L., Lee J., Richardson C.C.
    J. Biol. Chem. 272:18425-18433(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH PROTEIN GP4.
  5. "A unique region in bacteriophage t7 DNA polymerase important for exonucleolytic hydrolysis of DNA."
    Kumar J.K., Chiu E.T., Tabor S., Richardson C.C.
    J. Biol. Chem. 279:42018-42025(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  6. "A unique loop in T7 DNA polymerase mediates the binding of helicase-primase, DNA binding protein, and processivity factor."
    Hamdan S.M., Marintcheva B., Cook T., Lee S.J., Tabor S., Richardson C.C.
    Proc. Natl. Acad. Sci. U.S.A. 102:5096-5101(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH GP2.5; GP4 AND HOST TRXA.
  7. "Choreography of bacteriophage T7 DNA replication."
    Lee S.J., Richardson C.C.
    Curr. Opin. Chem. Biol. 15:580-586(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW ON FUNCTION.
  8. "Helicase-DNA polymerase interaction is critical to initiate leading-strand DNA synthesis."
    Zhang H., Lee S.J., Zhu B., Tran N.Q., Tabor S., Richardson C.C.
    Proc. Natl. Acad. Sci. U.S.A. 108:9372-9377(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery."
    Geertsema H.J., Kulczyk A.W., Richardson C.C., van Oijen A.M.
    Proc. Natl. Acad. Sci. U.S.A. 111:4073-4078(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY.
  10. "Crystal structure of a bacteriophage T7 DNA replication complex at 2.2-A resolution."
    Doublie S., Tabor S., Long A.M., Richardson C.C., Ellenberger T.
    Nature 391:251-258(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).

Entry informationi

Entry nameiDPOL_BPT7
AccessioniPrimary (citable) accession number: P00581
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: July 6, 2016
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.