Structure of PDB 8dvp Chain A Binding Site BS01

Receptor Information

>8dvp Chain A (length=350) Species: 1422 (Geobacillus stearothermophilus)

RFPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIP
YFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRY
GGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVDGSVMRVLSRLFL
VTDDIAKPSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCL
LCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRKR
DSTGLLANLWEFPSCETDGADGKEKLEQMVGEQVELTEPIVSFEHAFSHL
VWQLTVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVSHQRVWREYKEWAS

Ligand information

>8dvp Chain B (length=11)

aagacgtggac

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dvp Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism.
• Resolution: 1.54 Å
• Binding residue (original residue number in PDB): Q48 R50 G85 G87 Y88 Y89 G260 L261 L262 H305 F307 S308 H309 V346
• Binding residue (residue number reindexed from 1): Q42 R44 G79 G81 Y82 Y83 G254 L255 L256 H295 F297 S298 H299 V336

Enzymatic activity

• Enzyme Commision number: 3.2.2.31: adenine glycosylase.

Gene Ontology

Molecular Function

• GO:0000701 purine-specific mismatch base pair DNA N-glycosylase activity
• GO:0003677 DNA binding
• GO:0003824 catalytic activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0019104 DNA N-glycosylase activity
• GO:0032357 oxidized purine DNA binding
• GO:0034039 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
• GO:0035485 adenine/guanine mispair binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair
• GO:0006298 mismatch repair
• GO:0006950 response to stress

External links

• PDB: RCSB:8dvp, PDBe:8dvp, PDBj:8dvp
• PDBsum: 8dvp
• PubMed: 36631987
• UniProt: P83847|MUTY_GEOSE Adenine DNA glycosylase (Gene Name=mutY)