Structure of PDB 1vrl Chain A Binding Site BS01

Receptor Information

>1vrl Chain A (length=346) Species: 1422 (Geobacillus stearothermophilus)

PAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIPYF
EQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRYGG
KVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVNGNVMRVLSRLFLVT
DDIAKPSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLLC
PVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRKRDS
TGLLANLWEFPSCETDDGKEKLEQMVGLQVELTEPIVSFEHAFSHLVWQL
TVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVSHQRVWREYKEWAS

Ligand information

>1vrl Chain B (length=11)

aagacgtggac

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1vrl Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): Q48 G85 L86 G87 Y88 Y89 G260 L261 L262 H305 A306 F307 S308 H309 P345 V346
• Binding residue (residue number reindexed from 1): Q40 G77 L78 G79 Y80 Y81 G252 L253 L254 H291 A292 F293 S294 H295 P331 V332

Enzymatic activity

• Catalytic site (original residue number in PDB): Y126 N144
• Catalytic site (residue number reindexed from 1): Y118 N136
• 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:1vrl, PDBe:1vrl, PDBj:1vrl
• PDBsum: 1vrl
• PubMed: 14961129
• UniProt: P83847|MUTY_GEOSE Adenine DNA glycosylase (Gene Name=mutY)