Structure of PDB 5yyd Chain F Binding Site BS02

Receptor Information

>5yyd Chain F (length=342) Species: 83333 (Escherichia coli K-12)

GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPAR
KFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEP
LSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLA
KIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRT
CGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTM
AEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTT
QEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP

Ligand information

>5yyd Chain H (length=13)

ggtcctaggaccc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5yyd Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
• Resolution: 2.05 Å
• Binding residue (original residue number in PDB): S101 E104 K150 G183 G185 V187 S188 R285 T298 T299 Q300 E301 V303 R323
• Binding residue (residue number reindexed from 1): S102 E105 K151 G184 G186 V188 S189 R286 T299 T300 Q301 E302 V304 R324

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003684 damaged DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0005515 protein binding
• GO:0008296 3'-5'-DNA exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0000731 DNA synthesis involved in DNA repair
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006281 DNA repair
• GO:0006974 DNA damage response
• GO:0009432 SOS response
• GO:0042276 error-prone translesion synthesis
• GO:0070987 error-free translesion synthesis

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5yyd, PDBe:5yyd, PDBj:5yyd
• PDBsum: 5yyd
• PubMed: 29850882
• UniProt: Q47155|DPO4_ECOLI DNA polymerase IV (Gene Name=dinB)