Structure of PDB 3g2d Chain A Binding Site BS02

Receptor Information

>3g2d Chain A (length=256) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H)

AVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLR
HVEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIAD
FDDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGN
FNTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPG
QYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPI
GLEIEL

Ligand information

>3g2d Chain K (length=8)

cctgugcg

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3g2d Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): G13 R15 A16 R19 K20 Q45 G67 Y208 R209
• Binding residue (residue number reindexed from 1): G12 R14 A15 R18 K19 Q44 G66 Y207 R208

Enzymatic activity

• Catalytic site (original residue number in PDB): N10 N12 E38 Y111 N151 N153 D222 D247 H248
• Catalytic site (residue number reindexed from 1): N9 N11 E37 Y110 N150 N152 D221 D246 H247
• Enzyme Commision number: 3.1.11.2: exodeoxyribonuclease III.
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003824 catalytic activity
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0004518 nuclease activity
• GO:0004519 endonuclease activity
• GO:0008081 phosphoric diester hydrolase activity
• GO:0008311 double-stranded DNA 3'-5' DNA exonuclease activity
• GO:0016787 hydrolase activity
• GO:0016829 lyase activity
• GO:0046872 metal ion binding
• GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

External links

• PDB: RCSB:3g2d, PDBe:3g2d, PDBj:3g2d
• PDBsum: 3g2d
• PubMed: 20434457
• UniProt: O26314|UREND_METTH DNA uridine endonuclease (Gene Name=MTH_212)