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Protein

DNA-directed DNA polymerase

Gene

5

Organism
Enterobacteria phage T7 (Bacteriophage T7)
Status
Reviewed-Annotation score: Annotation score: 4 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 (By similarity). 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.UniRule annotation4 Publications

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).UniRule annotation1 Publication

Cofactori

Mg2+UniRule annotation1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi5Magnesium 1; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication1
Metal bindingi5Magnesium 2; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication1
Metal bindingi7Magnesium 2; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication1
Metal bindingi174Magnesium 2; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication1
Metal bindingi475Magnesium 3; catalytic; for polymerase activityUniRule annotation1 Publication1 Publication1
Metal bindingi475Magnesium 4; catalytic; for polymerase activityUniRule annotation1 Publication1 Publication1
Metal bindingi476Magnesium 4; catalytic; via carbonyl oxygen; for polymerase activityUniRule annotation1 Publication1 Publication1
Binding sitei506SubstrateUniRule annotation1 Publication1
Binding sitei518SubstrateUniRule annotation1 Publication1
Binding sitei522SubstrateUniRule annotation1 Publication1
Binding sitei526SubstrateUniRule annotation1 Publication1
Metal bindingi654Magnesium 3; catalytic; for polymerase activityUniRule annotation1 Publication1 Publication1
Metal bindingi654Magnesium 4; catalytic; for polymerase activityUniRule annotation1 Publication1 Publication1

GO - Molecular functioni

  • 3'-5' exonuclease activity Source: UniProtKB
  • DNA binding Source: UniProtKB-KW
  • DNA-directed DNA polymerase activity Source: UniProtKB-KW
  • metal ion binding 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, Magnesium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed DNA polymeraseUniRule annotation (EC:2.7.7.7UniRule annotation1 Publication, EC:3.1.11.-UniRule annotation2 Publications)
Alternative name(s):
Gene product 5
Short name:
Gp5
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)DescriptionActionsGraphical viewLength
Mutagenesisi123H → S: 83% loss of exonuclease activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001012691 – 704DNA-directed DNA polymeraseAdd BLAST704

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 interactors.
MINTiMINT-1513442.

Structurei

Secondary structure

1704
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 10Combined sources9
Helixi12 – 14Combined sources3
Beta strandi18 – 25Combined sources8
Turni26 – 28Combined sources3
Beta strandi31 – 34Combined sources4
Helixi36 – 38Combined sources3
Helixi39 – 51Combined sources13
Beta strandi56 – 60Combined sources5
Turni61 – 64Combined sources4
Helixi65 – 77Combined sources13
Helixi85 – 87Combined sources3
Beta strandi88 – 90Combined sources3
Helixi91 – 98Combined sources8
Turni99 – 101Combined sources3
Turni106 – 109Combined sources4
Helixi112 – 114Combined sources3
Helixi117 – 119Combined sources3
Helixi127 – 149Combined sources23
Helixi158 – 160Combined sources3
Helixi165 – 186Combined sources22
Turni189 – 191Combined sources3
Helixi198 – 200Combined sources3
Helixi203 – 209Combined sources7
Helixi212 – 230Combined sources19
Beta strandi232 – 234Combined sources3
Helixi236 – 260Combined sources25
Beta strandi264 – 267Combined sources4
Turni277 – 279Combined sources3
Beta strandi284 – 286Combined sources3
Turni306 – 308Combined sources3
Beta strandi318 – 320Combined sources3
Beta strandi326 – 332Combined sources7
Helixi339 – 348Combined sources10
Turni358 – 360Combined sources3
Helixi366 – 371Combined sources6
Helixi377 – 399Combined sources23
Helixi406 – 409Combined sources4
Beta strandi414 – 416Combined sources3
Beta strandi419 – 421Combined sources3
Beta strandi431 – 435Combined sources5
Helixi437 – 439Combined sources3
Helixi448 – 453Combined sources6
Helixi457 – 459Combined sources3
Turni463 – 465Combined sources3
Beta strandi470 – 476Combined sources7
Helixi479 – 492Combined sources14
Helixi495 – 502Combined sources8
Helixi505 – 512Combined sources8
Helixi518 – 529Combined sources12
Helixi534 – 538Combined sources5
Turni539 – 542Combined sources4
Helixi545 – 557Combined sources13
Helixi560 – 571Combined sources12
Beta strandi574 – 576Combined sources3
Beta strandi581 – 583Combined sources3
Beta strandi587 – 589Combined sources3
Beta strandi591 – 594Combined sources4
Beta strandi600 – 602Combined sources3
Helixi606 – 608Combined sources3
Helixi609 – 635Combined sources27
Beta strandi644 – 652Combined sources9
Beta strandi655 – 662Combined sources8
Helixi663 – 683Combined sources21
Beta strandi692 – 699Combined sources8
Turni700 – 703Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00581.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 1873'-5'exonucleaseUniRule annotation1 PublicationAdd BLAST187
Regioni202 – 704PolymeraseUniRule annotation1 PublicationAdd BLAST503
Regioni262 – 338Binding to host TrxA1 Publication1 PublicationAdd BLAST77

Sequence similaritiesi

Belongs to the DNA polymerase type-A family.UniRule annotation

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
HAMAPiMF_04101. DPOL_T7. 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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-41665N.
IntActiP00581. 3 interactors.
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.
HAMAPiMF_04101. DPOL_T7. 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...

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: November 2, 2016
This is version 115 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, Multifunctional enzyme, 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.