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Protein

DNA polymerase catalytic subunit

Gene

UL30

Organism
Human herpesvirus 1 (strain 17) (HHV-1) (Human herpes simplex virus 1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Replicates viral genomic DNA. The replication complex is composed of six viral proteins: the DNA polymerase, processivity factor, primase, primase-associated factor, helicase, and ssDNA-binding protein. Additionally, the polymerase contains an intrinsic ribonuclease H (RNase H) activity that specifically degrades RNA/DNA heteroduplexes or duplex DNA substrates in the 5' to 3' direction. Therefore, it can catalyze the excision of the RNA primers that initiate the synthesis of Okazaki fragments at a replication fork during viral DNA replication.1 Publication

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Endonucleolytic cleavage to 5'-phosphomonoester.

GO - Molecular functioni

  • 3'-5' exonuclease activity Source: InterPro
  • 5'-3' exonuclease activity Source: UniProtKB
  • DNA binding Source: UniProtKB-KW
  • DNA-directed DNA polymerase activity Source: UniProtKB-KW
  • DNA polymerase activity Source: AgBase
  • nucleotide binding Source: InterPro
  • RNA-DNA hybrid ribonuclease activity Source: UniProtKB

GO - Biological processi

  • bidirectional double-stranded viral DNA replication Source: UniProtKB
  • RNA phosphodiester bond hydrolysis, exonucleolytic Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

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

Keywords - Biological processi

DNA replication, Viral DNA replication

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase catalytic subunit (EC:2.7.7.7, EC:3.1.26.4)
Gene namesi
ORF Names:UL30
OrganismiHuman herpesvirus 1 (strain 17) (HHV-1) (Human herpes simplex virus 1)
Taxonomic identifieri10299 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageHerpesviralesHerpesviridaeAlphaherpesvirinaeSimplexvirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000009294 Componenti: Genome

Subcellular locationi

  • Host nucleus Curated

  • Note: The protein is present at discrete sites in nuclei, called replication compartments where viral DNA replication occurs.By similarity

GO - Cellular componenti

  • host cell nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Host nucleus

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL1872.
DrugBankiDB00787. Aciclovir.
DB00426. Famciclovir.
DB00529. Foscarnet.
DB01004. Ganciclovir.
DB00299. Penciclovir.
DB00577. Valaciclovir.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000465111 – 1235DNA polymerase catalytic subunitAdd BLAST1235

Proteomic databases

PRIDEiP04293.

Interactioni

Subunit structurei

Forms a complex with the ssDNA-binding protein UL29, the DNA polymerase processivity factor, and the alkaline exonuclease. Interacts with the putative helicase-primase complex subunit UL8; this interaction may coordinate leading and lagging strand DNA synthesis at the replication fork (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
UL42P102263EBI-8615017,EBI-1029310
UL8P101924EBI-8615017,EBI-7185538

Protein-protein interaction databases

BioGridi971473. 3 interactors.
IntActiP04293. 2 interactors.
MINTiMINT-6732532.

Chemistry databases

BindingDBiP04293.

Structurei

3D structure databases

ProteinModelPortaliP04293.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi4 – 7Poly-Gly4
Compositional biasi659 – 688Glu-richAdd BLAST30
Compositional biasi986 – 991Poly-Ala6
Compositional biasi1101 – 1128Pro-richAdd BLAST28

Sequence similaritiesi

Belongs to the DNA polymerase type-B family.Curated

Phylogenomic databases

KOiK18964.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.90.1600.10. 2 hits.
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.
IPR021639. DNAPolymera_Pol_C.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 1 hit.
PF11590. DNAPolymera_Pol. 1 hit.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 2 hits.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P04293-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFSGGGGPLS PGGKSAARAA SGFFAPAGPR GASRGPPPCL RQNFYNPYLA
60 70 80 90 100
PVGTQQKPTG PTQRHTYYSE CDEFRFIAPR VLDEDAPPEK RAGVHDGHLK
110 120 130 140 150
RAPKVYCGGD ERDVLRVGSG GFWPRRSRLW GGVDHAPAGF NPTVTVFHVY
160 170 180 190 200
DILENVEHAY GMRAAQFHAR FMDAITPTGT VITLLGLTPE GHRVAVHVYG
210 220 230 240 250
TRQYFYMNKE EVDRHLQCRA PRDLCERMAA ALRESPGASF RGISADHFEA
260 270 280 290 300
EVVERTDVYY YETRPALFYR VYVRSGRVLS YLCDNFCPAI KKYEGGVDAT
310 320 330 340 350
TRFILDNPGF VTFGWYRLKP GRNNTLAQPA APMAFGTSSD VEFNCTADNL
360 370 380 390 400
AIEGGMSDLP AYKLMCFDIE CKAGGEDELA FPVAGHPEDL VIQISCLLYD
410 420 430 440 450
LSTTALEHVL LFSLGSCDLP ESHLNELAAR GLPTPVVLEF DSEFEMLLAF
460 470 480 490 500
MTLVKQYGPE FVTGYNIINF DWPFLLAKLT DIYKVPLDGY GRMNGRGVFR
510 520 530 540 550
VWDIGQSHFQ KRSKIKVNGM VNIDMYGIIT DKIKLSSYKL NAVAEAVLKD
560 570 580 590 600
KKKDLSYRDI PAYYAAGPAQ RGVIGEYCIQ DSLLVGQLFF KFLPHLELSA
610 620 630 640 650
VARLAGINIT RTIYDGQQIR VFTCLLRLAD QKGFILPDTQ GRFRGAGGEA
660 670 680 690 700
PKRPAAARED EERPEEEGED EDEREEGGGE REPEGARETA GRHVGYQGAR
710 720 730 740 750
VLDPTSGFHV NPVVVFDFAS LYPSIIQAHN LCFSTLSLRA DAVAHLEAGK
760 770 780 790 800
DYLEIEVGGR RLFFVKAHVR ESLLSILLRD WLAMRKQIRS RIPQSSPEEA
810 820 830 840 850
VLLDKQQAAI KVVCNSVYGF TGVQHGLLPC LHVAATVTTI GREMLLATRE
860 870 880 890 900
YVHARWAAFE QLLADFPEAA DMRAPGPYSM RIIYGDTDSI FVLCRGLTAA
910 920 930 940 950
GLTAVGDKMA SHISRALFLP PIKLECEKTF TKLLLIAKKK YIGVIYGGKM
960 970 980 990 1000
LIKGVDLVRK NNCAFINRTS RALVDLLFYD DTVSGAAAAL AERPAEEWLA
1010 1020 1030 1040 1050
RPLPEGLQAF GAVLVDAHRR ITDPERDIQD FVLTAELSRH PRAYTNKRLA
1060 1070 1080 1090 1100
HLTVYYKLMA RRAQVPSIKD RIPYVIVAQT REVEETVARL AALRELDAAA
1110 1120 1130 1140 1150
PGDEPAPPAA LPSPAKRPRE TPSPADPPGG ASKPRKLLVS ELAEDPAYAI
1160 1170 1180 1190 1200
AHGVALNTDY YFSHLLGAAC VTFKALFGNN AKITESLLKR FIPEVWHPPD
1210 1220 1230
DVAARLRTAG FGAVGAGATA EETRRMLHRA FDTLA
Length:1,235
Mass (Da):136,421
Last modified:July 1, 1989 - v2
Checksum:iE8CD41D6EDED8343
GO

Sequence cautioni

The sequence CAA26941 differs from that shown. Reason: Frameshift at position 114.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti33S → G in strain: Nonneuroinvasive mutant HF10. 1
Natural varianti102A → T in strain: Nonneuroinvasive mutant HF10. 1
Natural varianti330A → R in strain: Nonneuroinvasive mutant HF10 and 17 syn+. 1
Natural varianti646A → T in strain: Nonneuroinvasive mutant HF10. 1
Natural varianti802L → F in strain: Nonneuroinvasive mutant HF10. 1
Natural varianti905V → M in strain: Nonneuroinvasive mutant HF10. 1
Natural varianti1203A → T in strain: Nonneuroinvasive mutant HF10. 1
Natural varianti1208 – 1209TA → AT in strain: Nonneuroinvasive mutant HF10. 2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X14112 Genomic DNA. Translation: CAA32323.1.
X03181 Genomic DNA. Translation: CAA26941.1. Frameshift.
DQ889502 Genomic DNA. Translation: ABI63492.1.
FJ593289 Genomic DNA. Translation: ACM62253.1.
PIRiA00715. DJBEV1.
C30085. DJBEH7.
RefSeqiYP_009137105.1. NC_001806.2.

Genome annotation databases

GeneIDi2703462.
KEGGivg:2703462.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X14112 Genomic DNA. Translation: CAA32323.1.
X03181 Genomic DNA. Translation: CAA26941.1. Frameshift.
DQ889502 Genomic DNA. Translation: ABI63492.1.
FJ593289 Genomic DNA. Translation: ACM62253.1.
PIRiA00715. DJBEV1.
C30085. DJBEH7.
RefSeqiYP_009137105.1. NC_001806.2.

3D structure databases

ProteinModelPortaliP04293.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi971473. 3 interactors.
IntActiP04293. 2 interactors.
MINTiMINT-6732532.

Chemistry databases

BindingDBiP04293.
ChEMBLiCHEMBL1872.
DrugBankiDB00787. Aciclovir.
DB00426. Famciclovir.
DB00529. Foscarnet.
DB01004. Ganciclovir.
DB00299. Penciclovir.
DB00577. Valaciclovir.

Proteomic databases

PRIDEiP04293.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi2703462.
KEGGivg:2703462.

Phylogenomic databases

KOiK18964.

Miscellaneous databases

PROiP04293.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.90.1600.10. 2 hits.
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.
IPR021639. DNAPolymera_Pol_C.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00136. DNA_pol_B. 1 hit.
PF03104. DNA_pol_B_exo1. 1 hit.
PF11590. DNAPolymera_Pol. 1 hit.
[Graphical view]
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 2 hits.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDPOL_HHV11
AccessioniPrimary (citable) accession number: P04293
Secondary accession number(s): B9VQF8, Q09IA3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 1987
Last sequence update: July 1, 1989
Last modified: November 2, 2016
This is version 111 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. 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.