Structure of PDB 5yv2 Chain A Binding Site BS02

Receptor Information

>5yv2 Chain A (length=342) Species: 83333 (Escherichia coli K-12)

GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPAR
KFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEP
LSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLA
KIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRT
CGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTM
AEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTT
QEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP

Ligand information

>5yv2 Chain B (length=18)

tctagggtcctaggaccc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5yv2 Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): R35 R38 V40 P58 M61 K217 R238 R240 K241 V243 G244 V245 E246 R247 T248 R273 F295 R330
• Binding residue (residue number reindexed from 1): R36 R39 V41 P59 M62 K218 R239 R241 K242 V244 G245 V246 E247 R248 T249 R274 F296 R331

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:5yv2, PDBe:5yv2, PDBj:5yv2
• PDBsum: 5yv2
• PubMed: 29850882
• UniProt: Q47155|DPO4_ECOLI DNA polymerase IV (Gene Name=dinB)