Structure of PDB 4jrp Chain A Binding Site BS02

Receptor Information

>4jrp Chain A (length=460) Species: 83333 (Escherichia coli K-12)

QQSTFLFHDYETFGTHPALDRPAQFAAIRTDSEFNVIGEPEVFYCKPADD
YLPQPGAVLITGITPQEARAKGENEAAFAARIHSLFTVPKTCILGYNNVR
FDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGINWPE
NDDGLPSFRLEHLTKANGIEHDAMADVYATIAMAKLVKTRQPRLFDYLFT
HRNKHKLMALIDVPQMKPLVHVSGMFGAWRGNTSWVAPLAWHPENRNAVI
MVDLAGDISPLLELDSDTLRERLYTAKTDLGDNAAVPVKLVHINKCPVLA
QANTLRPEDADRLGINRQHCLDNLKILRENPQVREKVVAIFAEASDNVDA
QLYNGFFSDADRAAMKIVLETEPRNLPALDITFVDKRIEKLLFNYRARNF
PGTLDYAEQQRWLEHRRQVFTPEFLQGYADELQMLVQQYADDKEKVALLK
ALWQYAEEIV

Ligand information

>4jrp Chain D (length=14)

tttttttttttttt

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4jrp Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): F209 T210 N213 H215 K216
• Binding residue (residue number reindexed from 1): F199 T200 N203 H205 K206

Enzymatic activity

• Enzyme Commision number: 3.1.11.1: exodeoxyribonuclease I.

Gene Ontology

Molecular Function

• GO:0000175 3'-5'-RNA exonuclease activity
• GO:0000287 magnesium ion binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003697 single-stranded DNA binding
• GO:0004527 exonuclease activity
• GO:0004529 DNA exonuclease activity
• GO:0005515 protein binding
• GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity
• GO:0046872 metal ion binding
• GO:0051575 5'-deoxyribose-5-phosphate lyase activity

Biological Process

• GO:0006259 DNA metabolic process
• GO:0006274 DNA replication termination
• GO:0006281 DNA repair
• GO:0006308 DNA catabolic process

External links

• PDB: RCSB:4jrp, PDBe:4jrp, PDBj:4jrp
• PDBsum: 4jrp
• PubMed: 23609540
• UniProt: P04995|EX1_ECOLI Exodeoxyribonuclease I (Gene Name=sbcB)