Structure of PDB 8oj7 Chain A

Receptor sequence

>8oj7A (length=1089) Species: 10306 (Human alphaherpesvirus 1 strain KOS)

TGPTQRHTYYSECDEFRFIAPRVLDEDAPPEKRAGVHDGHLKRAPKVYCG
GDERDVLRVGSGGFWPRRSRLWGGVDHAPAGFNPTVTVFHVYDILENVEH
AYGMRAAQFHARFMDAITPTGTVITLLGLTPEGHRVAVHVYGTRQYFYMN
KEEVDRHLQCRAPRDLCERMAAALRESPGASFRGISADHFEAEVVERTDV
YYYETRPALFYRVYVRSGRVLSYLCDNFCPAIKKYEGGVDATTRFILDNP
GFVTFGWYRLKPGRNNTLAQPRAPMAFGTSSDVEFNCTADNLAIEGGMSD
LPAYKLMCFDIECKAGGEDELAFPVAGHPEDLVIQISCLLYDLSTTALEH
VLLFSLGSCDLPESHLNELAARGLPTPVVLEFDSEFEMLLAFMTLVKQYG
PEFVTGYNIINFDWPFLLAKLTDIYKVPLDGYGRMNGRGVFRVWDIGQSH
FQKRSKIKVNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLKDKKKDLSYR
DIPAYYAAGPAQRGVIGEYCIQDSLLVGQLFFKFLPHLELSAVARLAGIN
ITRTIYDGQQIRVFTCLLRLADQKGFILPDTQGRFGRHVGYQGARVLDPT
SGFHVNPVVVFDFASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKDYLEI
EVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLLDK
QQAAIKVVCNSVYGFTGVQHGLLPCLHVAATVTTIGREMLLATREYVHAR
WAAFEQLLADFPEAADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAV
GDKMASHISRALFLPPIKLECEKTFTKLLLIAKKKYIGVIYGGKMLIKGV
DLVRKNNCAFINRTSRALVDLLFYDDTVSGAAAALAERPAEEWLARPLPE
GLQAFGAVLVDAHRRITDPERDIQDFVLTAELSRHPRAYTNKRLAHLTVY
YKLMARRAQVPSIKDRIPYVIVAQTREVEETVARLAAPRKLLVSELAEDP
AYAIAHGVALNTDYYFSHLLGAACVTFKALFGNNAKITESLLKRFIPEVW
HPPDDVAARLRTAGFGAVGAGATAEETRRMLHRAFDTLA

3D structure

• PDB: 8oj7 Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM
• Chain: A
• Resolution: 2.46 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.26.4: ribonuclease H.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	D886 K939 K953 G954 R959 K960 N961 E1036 S1038 R1039 Y1044 T1045 N1046 H1051 R1071	D781 K834 K848 G849 R854 K855 N856 E931 S933 R934 Y939 T940 N941 H946 R966
BS02	dna	A	Y160 R241 S280 F509 K511 K514 Q617 Q618 F643 V694 Y696 G698 S816 G819 G822 K938 K940 R1048 S1140	Y102 R183 S222 F451 K453 K456 Q559 Q560 F585 V589 Y591 G593 S711 G714 G717 K833 K835 R943 S994
BS03	MG	A	D717 F718 D888	D612 F613 D783
BS04	DTP	A	D717 F718 S720 Y722 R785 K811 N815 D888	D612 F613 S615 Y617 R680 K706 N710 D783

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0004519 endonuclease activity
• GO:0004523 RNA-DNA hybrid ribonuclease activity
• GO:0005515 protein binding
• GO:0008409 5'-3' exonuclease activity
• GO:0034061 DNA polymerase activity

Biological Process

• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0039686 bidirectional double-stranded viral DNA replication
• GO:0039693 viral DNA genome replication

Cellular Component

• GO:0042025 host cell nucleus
• GO:0042575 DNA polymerase complex

External links

• PDB: RCSB:8oj7, PDBe:8oj7, PDBj:8oj7
• PDBsum: 8oj7
• PubMed: 38806233
• UniProt: P04293|DPOL_HHV11 DNA polymerase catalytic subunit (Gene Name=UL30)