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Protein

DNA-directed DNA polymerase

Gene

43

Organism
Enterobacteria phage T4 (Bacteriophage T4)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Replicates the 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 for proofreading purpose.UniRule annotation2 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 bindingi112Magnesium 1; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication1
Metal bindingi114Magnesium 1; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication1
Metal bindingi219Magnesium 2; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication1
Metal bindingi324Magnesium 1; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication1
Metal bindingi324Magnesium 2; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication1
Metal bindingi408Magnesium 3; catalytic; for polymerase activityUniRule annotation1
Metal bindingi408Magnesium 4; catalytic; for polymerase activityUniRule annotation1
Metal bindingi409Magnesium 4; catalytic; via carbonyl oxygen; for polymerase activityUniRule annotation1
Binding sitei479SubstrateUniRule annotation1
Binding sitei557SubstrateUniRule annotation1
Sitei618Optimization of metal coordination by the polymerase active siteUniRule annotation1
Metal bindingi620Magnesium 3; catalytic; for polymerase activityUniRule annotation1
Metal bindingi620Magnesium 4; catalytic; for polymerase activityUniRule annotation1
Sitei703Optimization of metal coordination by the polymerase active siteUniRule annotation1
Sitei711Essential for viral replicationUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, DNA-directed DNA polymerase, Exonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Transferase
Biological processDNA replication, Viral DNA replication
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BRENDAi2.7.7.7 9245
SABIO-RKiP04415

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed DNA polymeraseUniRule annotation (EC:2.7.7.7UniRule annotation1 Publication, EC:3.1.11.-UniRule annotation4 Publications)
Alternative name(s):
Gene product 43
Short name:
Gp43
Gene namesi
Name:43
OrganismiEnterobacteria phage T4 (Bacteriophage T4)
Taxonomic identifieri10665 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeTevenvirinaeT4virus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000009087 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi112D → A: Almost complete loss of exonuclease activity. Decreased replication fidelity. 1 Publication1
Mutagenesisi114E → A: Almost complete loss of exonuclease activity. Decreased replication fidelity. 1 Publication1
Mutagenesisi219D → A: Almost complete loss of exonuclease activity. Decreased replication fidelity. 2 Publications1
Mutagenesisi324D → A: Almost complete loss of exonuclease activity. Decreased replication fidelity. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL5946

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000465461 – 898DNA-directed DNA polymeraseAdd BLAST898

Interactioni

Subunit structurei

Part of the replicase complex that includes the DNA polymerase, the polymerase clamp, the clamp loader complex, the single-stranded DNA binding protein, the primase, the helicase and the helicase assembly factor (PubMed:16800624). Interacts with the polymerase clamp; this interaction constitutes the polymerase holoenzyme (PubMed:8475061, PubMed:8917503).3 Publications

Chemistry databases

BindingDBiP04415

Structurei

Secondary structure

1898
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP04415
SMRiP04415
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04415

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni101 – 3373'-5'exonucleaseUniRule annotation1 PublicationAdd BLAST237
Regioni245 – 261Beta hairpinUniRule annotation1 PublicationAdd BLAST17
Regioni377 – 898PolymeraseUniRule annotation1 PublicationAdd BLAST522
Regioni411 – 413Substrate bindingUniRule annotation3
Regioni702 – 705Binding of DNA in B-conformationUniRule annotation4
Regioni893 – 898Interaction with the polymerase clampUniRule annotation1 Publication6

Domaini

The N-terminus contains the 3'-5' exonuclease activity (PubMed:7592876). The C-terminus contains the polymerase activity and is involved in binding to the polymerase clamp protein (PubMed:7592876). A beta hairpin structure is necessary for the proofreading function of the polymerase (PubMed:25753811).UniRule annotation2 Publications

Sequence similaritiesi

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

Phylogenomic databases

KOiK18942
OrthoDBiVOG0900001M

Family and domain databases

Gene3Di3.30.420.10, 1 hit
HAMAPiMF_04100 DPOL_T4, 1 hit
InterProiView protein in 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
IPR034749 DPOL_T4
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF00136 DNA_pol_B, 1 hit
PF03104 DNA_pol_B_exo1, 1 hit
PRINTSiPR00106 DNAPOLB
SMARTiView protein in SMART
SM00486 POLBc, 1 hit
SUPFAMiSSF53098 SSF53098, 1 hit
PROSITEiView protein in PROSITE
PS00116 DNA_POLYMERASE_B, 1 hit

Sequencei

Sequence statusi: Complete.

P04415-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKEFYISIET VGNNIVERYI DENGKERTRE VEYLPTMFRH CKEESKYKDI
60 70 80 90 100
YGKNCAPQKF PSMKDARDWM KRMEDIGLEA LGMNDFKLAY ISDTYGSEIV
110 120 130 140 150
YDRKFVRVAN CDIEVTGDKF PDPMKAEYEI DAITHYDSID DRFYVFDLLN
160 170 180 190 200
SMYGSVSKWD AKLAAKLDCE GGDEVPQEIL DRVIYMPFDN ERDMLMEYIN
210 220 230 240 250
LWEQKRPAIF TGWNIEGFDV PYIMNRVKMI LGERSMKRFS PIGRVKSKLI
260 270 280 290 300
QNMYGSKEIY SIDGVSILDY LDLYKKFAFT NLPSFSLESV AQHETKKGKL
310 320 330 340 350
PYDGPINKLR ETNHQRYISY NIIDVESVQA IDKIRGFIDL VLSMSYYAKM
360 370 380 390 400
PFSGVMSPIK TWDAIIFNSL KGEHKVIPQQ GSHVKQSFPG AFVFEPKPIA
410 420 430 440 450
RRYIMSFDLT SLYPSIIRQV NISPETIRGQ FKVHPIHEYI AGTAPKPSDE
460 470 480 490 500
YSCSPNGWMY DKHQEGIIPK EIAKVFFQRK DWKKKMFAEE MNAEAIKKII
510 520 530 540 550
MKGAGSCSTK PEVERYVKFS DDFLNELSNY TESVLNSLIE ECEKAATLAN
560 570 580 590 600
TNQLNRKILI NSLYGALGNI HFRYYDLRNA TAITIFGQVG IQWIARKINE
610 620 630 640 650
YLNKVCGTND EDFIAAGDTD SVYVCVDKVI EKVGLDRFKE QNDLVEFMNQ
660 670 680 690 700
FGKKKMEPMI DVAYRELCDY MNNREHLMHM DREAISCPPL GSKGVGGFWK
710 720 730 740 750
AKKRYALNVY DMEDKRFAEP HLKIMGMETQ QSSTPKAVQE ALEESIRRIL
760 770 780 790 800
QEGEESVQEY YKNFEKEYRQ LDYKVIAEVK TANDIAKYDD KGWPGFKCPF
810 820 830 840 850
HIRGVLTYRR AVSGLGVAPI LDGNKVMVLP LREGNPFGDK CIAWPSGTEL
860 870 880 890
PKEIRSDVLS WIDHSTLFQK SFVKPLAGMC ESAGMDYEEK ASLDFLFG
Length:898
Mass (Da):103,610
Last modified:January 1, 1988 - v1
Checksum:i925300C4CA5C7A24
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti89A → V in CAA25344 (PubMed:3054876).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M10160 Genomic DNA Translation: AAC05397.1
X00769 Genomic DNA Translation: CAA25344.1
AF158101 Genomic DNA Translation: AAD42468.1
M37159 Genomic DNA Translation: AAA21706.1
PIRiJS0791 DJBPT4
RefSeqiNP_049662.1, NC_000866.4

Genome annotation databases

GeneIDi1258685
KEGGivg:1258685

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M10160 Genomic DNA Translation: AAC05397.1
X00769 Genomic DNA Translation: CAA25344.1
AF158101 Genomic DNA Translation: AAD42468.1
M37159 Genomic DNA Translation: AAA21706.1
PIRiJS0791 DJBPT4
RefSeqiNP_049662.1, NC_000866.4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NOYX-ray2.20A/B1-388[»]
1NOZX-ray2.20A/B1-388[»]
ProteinModelPortaliP04415
SMRiP04415
ModBaseiSearch...
MobiDBiSearch...

Chemistry databases

BindingDBiP04415
ChEMBLiCHEMBL5946

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1258685
KEGGivg:1258685

Phylogenomic databases

KOiK18942
OrthoDBiVOG0900001M

Enzyme and pathway databases

BRENDAi2.7.7.7 9245
SABIO-RKiP04415

Miscellaneous databases

EvolutionaryTraceiP04415
PROiPR:P04415

Family and domain databases

Gene3Di3.30.420.10, 1 hit
HAMAPiMF_04100 DPOL_T4, 1 hit
InterProiView protein in 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
IPR034749 DPOL_T4
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF00136 DNA_pol_B, 1 hit
PF03104 DNA_pol_B_exo1, 1 hit
PRINTSiPR00106 DNAPOLB
SMARTiView protein in SMART
SM00486 POLBc, 1 hit
SUPFAMiSSF53098 SSF53098, 1 hit
PROSITEiView protein in PROSITE
PS00116 DNA_POLYMERASE_B, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDPOL_BPT4
AccessioniPrimary (citable) accession number: P04415
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 1, 1988
Last modified: October 10, 2018
This is version 139 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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