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Protein

DNA polymerase catalytic subunit

Gene

UL30

Organism
Human herpesvirus 1 (strain KOS) (HHV-1) (Human herpes simplex virus 1)
Status
Reviewed-Annotation score: Annotation score: 3 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 (By similarity).By similarity

Catalytic activityi

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

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

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

Keywords - Biological processi

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 KOS) (HHV-1) (Human herpes simplex virus 1)
Taxonomic identifieri10306 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageHerpesviralesHerpesviridaeAlphaherpesvirinaeSimplexvirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]

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

Complete GO annotation...

Keywords - Cellular componenti

Host nucleus

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL5944.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12351235DNA polymerase catalytic subunitPRO_0000046513Add
BLAST

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

Chemistry

BindingDBiP04292.

Structurei

Secondary structure

1
1235
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi72 – 798Combined sources
Helixi80 – 823Combined sources
Beta strandi92 – 10110Combined sources
Beta strandi104 – 1074Combined sources
Beta strandi110 – 1134Combined sources
Beta strandi128 – 1303Combined sources
Beta strandi145 – 15713Combined sources
Helixi160 – 1623Combined sources
Helixi169 – 1746Combined sources
Beta strandi179 – 1879Combined sources
Beta strandi193 – 1997Combined sources
Beta strandi203 – 2086Combined sources
Helixi209 – 2146Combined sources
Helixi221 – 23414Combined sources
Beta strandi235 – 2373Combined sources
Helixi245 – 2473Combined sources
Beta strandi249 – 25911Combined sources
Beta strandi266 – 2749Combined sources
Helixi276 – 28510Combined sources
Beta strandi288 – 2903Combined sources
Beta strandi292 – 2943Combined sources
Helixi299 – 3068Combined sources
Beta strandi312 – 3187Combined sources
Turni322 – 3243Combined sources
Helixi332 – 3343Combined sources
Beta strandi336 – 3383Combined sources
Beta strandi340 – 3467Combined sources
Helixi347 – 3493Combined sources
Beta strandi350 – 3523Combined sources
Beta strandi363 – 37210Combined sources
Beta strandi389 – 40012Combined sources
Turni401 – 4033Combined sources
Beta strandi406 – 41510Combined sources
Helixi421 – 4299Combined sources
Beta strandi436 – 4427Combined sources
Helixi443 – 45715Combined sources
Beta strandi460 – 4667Combined sources
Turni467 – 4704Combined sources
Helixi471 – 48111Combined sources
Turni488 – 4903Combined sources
Beta strandi491 – 4966Combined sources
Beta strandi499 – 5013Combined sources
Beta strandi515 – 5173Combined sources
Beta strandi520 – 5245Combined sources
Helixi525 – 5295Combined sources
Helixi540 – 5467Combined sources
Turni557 – 5593Combined sources
Helixi560 – 5667Combined sources
Helixi568 – 59225Combined sources
Helixi594 – 60512Combined sources
Helixi609 – 6113Combined sources
Helixi619 – 63214Combined sources
Beta strandi707 – 7093Combined sources
Beta strandi713 – 7197Combined sources
Helixi721 – 7288Combined sources
Turni733 – 7353Combined sources
Beta strandi736 – 7383Combined sources
Turni748 – 7514Combined sources
Beta strandi752 – 7565Combined sources
Beta strandi758 – 7658Combined sources
Turni767 – 7693Combined sources
Helixi773 – 79119Combined sources
Helixi792 – 7943Combined sources
Helixi797 – 81418Combined sources
Helixi817 – 8226Combined sources
Beta strandi826 – 8283Combined sources
Helixi831 – 85626Combined sources
Helixi859 – 8657Combined sources
Helixi867 – 8726Combined sources
Beta strandi879 – 8857Combined sources
Beta strandi887 – 8959Combined sources
Helixi902 – 91716Combined sources
Beta strandi923 – 93715Combined sources
Beta strandi940 – 9456Combined sources
Beta strandi950 – 9545Combined sources
Helixi964 – 97916Combined sources
Helixi981 – 9899Combined sources
Helixi990 – 9923Combined sources
Helixi995 – 10006Combined sources
Helixi1005 – 10073Combined sources
Helixi1008 – 102215Combined sources
Helixi1029 – 10313Combined sources
Helixi1041 – 10433Combined sources
Helixi1050 – 106011Combined sources
Turni1069 – 10713Combined sources
Beta strandi1074 – 10774Combined sources
Helixi1081 – 10855Combined sources
Helixi1087 – 10959Combined sources
Helixi1146 – 11516Combined sources
Helixi1158 – 117215Combined sources
Helixi1174 – 11774Combined sources
Helixi1181 – 11899Combined sources
Helixi1194 – 11963Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2GV9X-ray2.68A/B43-1235[»]
ProteinModelPortaliP04292.
SMRiP04292. Positions 59-639, 1200-1235.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04292.

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi4 – 74Poly-Gly
Compositional biasi659 – 68830Glu-richAdd
BLAST
Compositional biasi986 – 9916Poly-Ala

Sequence similaritiesi

Belongs to the DNA polymerase type-B family.Curated

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.

P04292-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFSGGGGPLS PGGKSAARAA SGFFAPAGPR GAGRGPPPCL 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 GRNNTLAQPR 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 PAYYATGPAQ RGVIGEYCIQ DSLLVGQLFF KFLPHLELSA
610 620 630 640 650
VARLAGINIT RTIYDGQQIR VFTCLLRLAD QKGFILPDTQ GRFRGAGGEA
660 670 680 690 700
PKRPAAARED EERPEEEGED EDEREEGGGE REPEGARETA GRHVGYQGAK
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
GLTAMGDKMA 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 TPSHADPPGG ASKPRKLLVS ELAEDPAYAI
1160 1170 1180 1190 1200
AHGVALNTDY YFSHLLGAAC VTFKALFGNN AKITESLLKR FIPEVWHPPD
1210 1220 1230
DVAARLRAAG FGAVGAGATA EETRRMLHRA FDTLA
Length:1,235
Mass (Da):136,520
Last modified:March 20, 1987 - v1
Checksum:i90415EF72ED2A607
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M10792 Genomic DNA. Translation: AAA66438.1.
PIRiA00714. DJBEK1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M10792 Genomic DNA. Translation: AAA66438.1.
PIRiA00714. DJBEK1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2GV9X-ray2.68A/B43-1235[»]
ProteinModelPortaliP04292.
SMRiP04292. Positions 59-639, 1200-1235.
ModBaseiSearch...
MobiDBiSearch...

Chemistry

BindingDBiP04292.
ChEMBLiCHEMBL5944.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP04292.

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_HHV1K
AccessioniPrimary (citable) accession number: P04292
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 1987
Last sequence update: March 20, 1987
Last modified: October 14, 2015
This is version 89 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, Multifunctional enzyme

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.