Structure of PDB 1diz Chain A Binding Site BS02

Receptor Information

>1diz Chain A (length=282) Species: 562 (Escherichia coli)

MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTA
IPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGA
ARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFP
EYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPG
DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTP
AQIRRYAERWKPWRSYALLHIWYTEGWQPDEA

Ligand information

>1diz Chain F (length=13)

ggcaatcatgtca

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1diz DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): L125 M130 M174 P175
• Binding residue (residue number reindexed from 1): L125 M130 M174 P175

Enzymatic activity

• Catalytic site (original residue number in PDB): W218 Y222 D238
• Catalytic site (residue number reindexed from 1): W218 Y222 D238
• Enzyme Commision number: 3.2.2.21: DNA-3-methyladenine glycosylase II.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0003905 alkylbase DNA N-glycosylase activity
• GO:0005515 protein binding
• GO:0008725 DNA-3-methyladenine glycosylase activity
• GO:0016787 hydrolase activity
• GO:0032131 alkylated DNA binding
• GO:0043916 DNA-7-methylguanine glycosylase activity
• GO:0052821 DNA-7-methyladenine glycosylase activity
• GO:0052822 DNA-3-methylguanine glycosylase activity

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair
• GO:0006285 base-excision repair, AP site formation
• GO:0006307 DNA alkylation repair
• GO:0006950 response to stress
• GO:0006974 DNA damage response

Cellular Component

• GO:0005737 cytoplasm
• GO:0032993 protein-DNA complex

External links

• PDB: RCSB:1diz, PDBe:1diz, PDBj:1diz
• PDBsum: 1diz
• PubMed: 10675345
• UniProt: P04395|3MG2_ECOLI DNA-3-methyladenine glycosylase 2 (Gene Name=alkA)