Structure of PDB 8oj6 Chain A

Receptor sequence

>8oj6A (length=1085) Species: 10306 (Human alphaherpesvirus 1 strain KOS)

TGPTQRHTYYSECDEFRFIAPRVLDEDAPPEKRAGVHDGHLKRAPKVYCG
GDERDVLRVGSGGFWPRRSRLWGGVDHAPAGFNPTVTVFHVYDILENVEH
AYGMRAAQFHARFMDAITPTGTVITLLGLTPEGHRVAVHVYGTRQYFYMN
KEEVDRHLQCRAPRDLCERMAAALRESPGASFRGISADHFEAEVVERTDV
YYYETRPALFYRVYVRSGRVLSYLCDNFCPAIKKYEGGVDATTRFILDNP
GFVTFGWYRLKPGRNNTLAQPRAPMAFGTSSDVEFNCTADNLAIEGGMSD
LPAYKLMCFDIECKAGGEDELAFPVAGHPEDLVIQISCLLYDLSTTALEH
VLLFSLGSCDLPESHLNELAARGLPTPVVLEFDSEFEMLLAFMTLVKQYG
PEFVTGYNIINFDWPFLLAKLTDIYKVPLDGYGRMNGRGVFRVWDIGQSH
FQKRSKIKVNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLKDKKKDLSYR
DIPAYYAAGPAQRGVIGEYCIQDSLLVGQLFFKFLPHLELSAVARLAGIN
ITRTIYDGQQIRVFTCLLRLADQKGFILPDTQGRRHVGYQGARVLDPTSG
FHVNPVVVFDFASLYPSIIQAHNLCFSTLSLRADAVAHLEAGKDYLEIEV
GGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSSPEEAVLLDKQQ
AAIKVVCNSVYGFTGVQHGLLPCLHVAATVTTIGREMLLATREYVHARWA
AFEQLLADFPEAADMRAPGPYSMRIIYGDTDSIFVLCRGLTAAGLTAVGD
KMASHISRALFLPPIKLECEKTFTKLLLIAKKKYIGVIYGGKMLIKGVDL
VRKNNCAFINRTSRALVDLLFYDDTVSGAAAALAERPAEEWLARPLPEGL
QAFGAVLVDAHRRITDPERDIQDFVLTAELSRHPRAYTNKRLAHLTVYYK
LMARRAQVPSIKDRIPYVIVAQTREVEETVARLARKLLVSELAEDPAYAI
AHGVALNTDYYFSHLLGAACVTFKALFGNNAKITESLLKRFIPEVWHPPD
DVAARLRTAGFGAVGAGATAEETRRMLHRAFDTLA

3D structure

• PDB: 8oj6 Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM
• Chain: A
• Resolution: 2.41 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	K534 L721 Y722 Y818 T887 D888 K939 K953 G954 R959 K960 E1036 S1038 R1039 Y1044 T1045 N1046 H1051 R1071	K476 L614 Y615 Y711 T780 D781 K832 K846 G847 R852 K853 E929 S931 R932 Y937 T938 N939 H944 R964
BS02	dna	A	R241 R277 F509 Q510 K511 K514 G616 Q617 Q618 V694 Y696 G698 G822 V823 G826 L827 K938 K939 R1048 L1138 S1140 Y1160 V1171	R183 R219 F451 Q452 K453 K456 G558 Q559 Q560 V587 Y589 G591 G715 V716 G719 L720 K831 K832 R941 L988 S990 Y1010 V1021
BS03	MG	A	D717 F718 D888	D610 F611 D781

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:8oj6, PDBe:8oj6, PDBj:8oj6
• PDBsum: 8oj6
• PubMed: 38806233
• UniProt: P04293|DPOL_HHV11 DNA polymerase catalytic subunit (Gene Name=UL30)