Structure of PDB 8dw4 Chain A

Receptor sequence

>8dw4A (length=348) Species: 1422 (Geobacillus stearothermophilus)

RFPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIP
YFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRY
GGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVDGSVMRVLSRLFL
VTDDIAKPSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCL
LCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRKR
DSTGLLANLWEFPSCETDDGKEKLEQMVGEQVELTEPIVSFEHAFSHLVW
QLTVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVSHQRVWREYKEWAS

3D structure

• PDB: 8dw4 Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism.
• Chain: A
• Resolution: 2.49 Å

Enzymatic activity

• Enzyme Commision number: 3.2.2.31: adenine glycosylase.

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	Q48 G85 G87 Y88 Y89 G260 L261 L262 H305 A306 F307 S308 H309 P345 V346	Q42 G79 G81 Y82 Y83 G254 L255 L256 H293 A294 F295 S296 H297 P333 V334
BS02	dna	A	L46 Q47 Q48 R50 V51 G122 G124 Y126 T127 D144 G145 R149	L40 Q41 Q42 R44 V45 G116 G118 Y120 T121 D138 G139 R143
BS03	SF4	A	R153 C198 C205 C208 C214	R147 C192 C199 C202 C208

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:8dw4, PDBe:8dw4, PDBj:8dw4
• PDBsum: 8dw4
• PubMed: 36631987
• UniProt: P83847|MUTY_GEOSE Adenine DNA glycosylase (Gene Name=mutY)