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Protein

DNA-directed DNA polymerase

Gene

43

Organism
Enterobacteria phage T4 (Bacteriophage T4)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi112 – 1121Magnesium 1; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication
Metal bindingi114 – 1141Magnesium 1; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication
Metal bindingi219 – 2191Magnesium 2; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication
Metal bindingi324 – 3241Magnesium 1; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication
Metal bindingi324 – 3241Magnesium 2; catalytic; for 3'-5' exonuclease activityUniRule annotation1 Publication
Metal bindingi408 – 4081Magnesium 3; catalytic; for polymerase activityUniRule annotation
Metal bindingi408 – 4081Magnesium 4; catalytic; for polymerase activityUniRule annotation
Metal bindingi409 – 4091Magnesium 4; catalytic; via carbonyl oxygen; for polymerase activityUniRule annotation
Binding sitei479 – 4791SubstrateUniRule annotation
Binding sitei557 – 5571SubstrateUniRule annotation
Sitei618 – 6181Optimization of metal coordination by the polymerase active siteUniRule annotation
Metal bindingi620 – 6201Magnesium 3; catalytic; for polymerase activityUniRule annotation
Metal bindingi620 – 6201Magnesium 4; catalytic; for polymerase activityUniRule annotation
Sitei703 – 7031Optimization of metal coordination by the polymerase active siteUniRule annotation
Sitei711 – 7111Essential for viral replicationUniRule annotation

GO - Molecular functioni

  • 3'-5' exonuclease activity Source: UniProtKB
  • DNA binding Source: UniProtKB-KW
  • DNA-directed DNA polymerase activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • nucleotide binding Source: InterPro

GO - Biological processi

  • bidirectional double-stranded viral DNA replication Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

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

Keywords - Biological processi

DNA replication, Viral DNA replication

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

Enzyme and pathway databases

BRENDAi2.7.7.7. 9245.
SABIO-RKP04415.

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 stageCaudoviralesMyoviridaeTevenvirinaeT4likevirus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000009087 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi112 – 1121D → A: Almost complete loss of exonuclease activity. Decreased replication fidelity. 1 Publication
Mutagenesisi114 – 1141E → A: Almost complete loss of exonuclease activity. Decreased replication fidelity. 1 Publication
Mutagenesisi219 – 2191D → A: Almost complete loss of exonuclease activity. Decreased replication fidelity. 2 Publications
Mutagenesisi324 – 3241D → A: Almost complete loss of exonuclease activity. Decreased replication fidelity. 1 Publication

Chemistry

ChEMBLiCHEMBL5946.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 898898DNA-directed DNA polymerasePRO_0000046546Add
BLAST

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

BindingDBiP04415.

Structurei

Secondary structure

1
898
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 118Combined sources
Beta strandi14 – 207Combined sources
Beta strandi26 – 327Combined sources
Beta strandi36 – 383Combined sources
Helixi40 – 434Combined sources
Turni49 – 524Combined sources
Helixi63 – 7614Combined sources
Helixi82 – 9413Combined sources
Helixi103 – 1053Combined sources
Beta strandi108 – 1158Combined sources
Turni123 – 1253Combined sources
Beta strandi130 – 1378Combined sources
Turni138 – 1414Combined sources
Beta strandi142 – 1487Combined sources
Beta strandi150 – 1534Combined sources
Helixi161 – 1655Combined sources
Helixi168 – 1703Combined sources
Helixi177 – 1804Combined sources
Beta strandi183 – 1897Combined sources
Helixi191 – 20414Combined sources
Beta strandi208 – 2114Combined sources
Turni215 – 2184Combined sources
Helixi219 – 23618Combined sources
Helixi237 – 2393Combined sources
Beta strandi245 – 2495Combined sources
Helixi252 – 2543Combined sources
Beta strandi258 – 2625Combined sources
Beta strandi265 – 2673Combined sources
Helixi270 – 2778Combined sources
Helixi287 – 2959Combined sources
Helixi306 – 3083Combined sources
Helixi309 – 33527Combined sources
Helixi337 – 34812Combined sources
Helixi352 – 3565Combined sources
Helixi358 – 36912Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NOYX-ray2.20A/B1-388[»]
1NOZX-ray2.20A/B1-388[»]
ProteinModelPortaliP04415.
SMRiP04415. Positions 1-897.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04415.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni101 – 3372373'-5'exonucleaseUniRule annotation1 PublicationAdd
BLAST
Regioni245 – 26117Beta hairpinUniRule annotation1 PublicationAdd
BLAST
Regioni377 – 898522PolymeraseUniRule annotation1 PublicationAdd
BLAST
Regioni411 – 4133Substrate bindingUniRule annotation
Regioni702 – 7054Binding of DNA in B-conformationUniRule annotation
Regioni893 – 8986Interaction with the polymerase clampUniRule annotation1 Publication

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.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.90.1600.10. 3 hits.
HAMAPiMF_04100. DPOL_T4. 1 hit.
InterProiIPR006172. 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]
PfamiPF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 1 hit.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti89 – 891A → V in CAA25344 (PubMed:3054876).Curated

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.

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
EntryMethodResolution (Å)ChainPositionsPDBsum
1NOYX-ray2.20A/B1-388[»]
1NOZX-ray2.20A/B1-388[»]
ProteinModelPortaliP04415.
SMRiP04415. Positions 1-897.
ModBaseiSearch...
MobiDBiSearch...

Chemistry

BindingDBiP04415.
ChEMBLiCHEMBL5946.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1258685.
KEGGivg:1258685.

Phylogenomic databases

KOiK18942.

Enzyme and pathway databases

BRENDAi2.7.7.7. 9245.
SABIO-RKP04415.

Miscellaneous databases

EvolutionaryTraceiP04415.
PROiP04415.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.90.1600.10. 3 hits.
HAMAPiMF_04100. DPOL_T4. 1 hit.
InterProiIPR006172. 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]
PfamiPF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 1 hit.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDPOL_BPT4
AccessioniPrimary (citable) accession number: P04415
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 1, 1988
Last modified: September 7, 2016
This is version 129 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.