Structure of PDB 8oja Chain A

Receptor sequence

>8ojaA (length=1072) Species: 10306 (Human alphaherpesvirus 1 strain KOS)

TGPTQRHTYYSECDEFRFIAPRVLDEDAPPEKRAGVHDGHLKRAPKVYCG
GDERDVLRVGSGGFWPRRSRLWGGVDHAPAGFNPTVTVFHVYDILENVEH
AYGMRAAQFHARFMDAITPTGTVITLLGLTPEGHRVAVHVYGTRQYFYMN
KEEVDRHLQCRAPRDLCERMAAALRESPGASFRGISADHFEAEVVERTDV
YYYETRPALFYRVYVRSGRVLSYLCDNFCPAIKKYEGGVDATTRFILDNP
GFVTFGWYRLKPGRNNTLAQPRAPMAFGTSSDVEFNCTADNLAIEGGMSD
LPAYKLMCFDIECKAGGEDELAFPVAGHPEDLVIQISCLLYDLSTTALEH
VLLFSLGSCDLPESHLNELAARGLPTPVVLEFDSEFEMLLAFMTLVKQYG
PEFVTGYNIINFDWPFLLAKLTDIYKVPLDGYGRMNGRGVFRVWDIRSKI
KVNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLKDKKKDLSYRDIPAYYA
AGPAQRGVIGEYCIQDSLLVGQLFFKFLPHLELSAVARLAGINITRTIYD
GQQIRVFTCLLRLADQKGFILPDTRVLDPTSGFHVNPVVVFDFASLYPSI
IQAHNLCFSTLSLRADAVAHLEAGKDYLEIEVGGRRLFFVKAHVRESLLS
ILLRDWLAMRKQIRSRIPQSSPEEAVLLDKQQAAIKVVCNSVYGFTGVQH
GLLPCLHVAATVTTIGREMLLATREYVHARWAAFEQLLADFPEAADMRAP
GPYSMRIIYGDTDSIFVLCRGLTAAGLTAVGDKMASHISRALFLPPIKLE
CEKTFTKLLLIAKKKYIGVIYGGKMLIKGVDLVRKNNCAFINRTSRALVD
LLFYDDTVSGAAAALAERPAEEWLARPLPEGLQAFGAVLVDAHRRITDPE
RDIQDFVLTAELSRHPRAYTNKRLAHLTVYYKLMARRAQVPSIKDRIPYV
IVAQTREVEETVARLAALRKPRKLLVSELAEDPAYAIAHGVALNTDYYFS
HLLGAACVTFKALFGNNAKITESLLKRFIPEVWHPPDDVAARLRTAGFGA
VGAGATAEETRRMLHRAFDTLA

3D structure

• PDB: 8oja Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM
• Chain: A
• Resolution: 1.87 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	E370 C371 F381 N466 F470 S537 Y538 K539 L540 Y557 E1036 S1038 R1039 Y1044 T1045 N1046 L1049 H1051 R1071	E312 C313 F323 N408 F412 S472 Y473 K474 L475 Y492 E911 S913 R914 Y919 T920 N921 L924 H926 R946
BS02	dna	A	R959 N961 R1048 L1138 S1140 H1164	R834 N836 R923 L975 S977 H1001
BS03	CA	A	D368 Y465 D471	D310 Y407 D413
BS04	CA	A	D368 I369 E370	D310 I311 E312

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