Structure of PDB 4ypr Chain B Binding Site BS01

Receptor Information

>4ypr Chain B (length=350) Species: 1422 (Geobacillus stearothermophilus)

ERFPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVI
PYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTR
YGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVNGNVMRVLSRLF
LVTDDIAKCSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSC
LLCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRK
RDSTGLLANLWEFPSCETDGADGKEKLEQMVGQVELTEPIVSFEHAFSHL
VWQLTVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVSHQRVWREYKEWAS

Ligand information

>4ypr Chain E (length=10)

gtccacgtct

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ypr Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase.
• Resolution: 2.59 Å
• Binding residue (original residue number in PDB): E43 L46 Q47 Q48 R50 V51 G122 G124 Y126 T127 N144 N146 I191 K228 K230 K231
• Binding residue (residue number reindexed from 1): E38 L41 Q42 Q43 R45 V46 G117 G119 Y121 T122 N139 N141 I186 K223 K225 K226

Enzymatic activity

• Catalytic site (original residue number in PDB): E43 Y126 N144
• Catalytic site (residue number reindexed from 1): E38 Y121 N139
• 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:4ypr, PDBe:4ypr, PDBj:4ypr
• PDBsum: 4ypr
• PubMed: 25995449
• UniProt: P83847|MUTY_GEOSE Adenine DNA glycosylase (Gene Name=mutY)