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› 6izi

Electron Microscopy
11.8Å resolution

Crystal structure of E. coli peptide deformylase and methionine aminopeptidase fitted into the cryo-EM density map of the complex

Released:
DOI: 10.2210/pdb6izi/pdb
PDB entry 6izi coloured by chain, front view.
PDB entry 6izi coloured by chain, side view.
PDB entry 6izi coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit.
Bhakta S, Akbar S, Sengupta J
J Mol Biol 431 1426-1439 (2019)
PMID: 30753870
Related structures: EMD-9753

Function and Biology Details

Reactions catalysed: 
N-terminal N-formyl-L-methionyl-[peptide] + H2O = N-terminal L-methionyl-[peptide] + formate.
Release of N-terminal amino acids, preferentially methionine, frompeptides and arylamides.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141368 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Peptide deformylase Chain: P
Molecule details ›
Chain: P
Length: 169 amino acids
Theoretical weight: 19.36 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6K3 (Residues: 1-169; Coverage: 100%)
Gene names: JW3248, b3287, def, fms
Sequence domains: Polypeptide deformylase
Methionine aminopeptidase Chain: Q
Molecule details ›
Chain: Q
Length: 264 amino acids
Theoretical weight: 29.34 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AE18 (Residues: 1-264; Coverage: 100%)
Gene names: JW0163, b0168, map
Sequence domains: Metallopeptidase family M24

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 11.8Å
Relevant EMDB volumes: EMD-9753
Expression system: Escherichia coli

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Citations

3 review citations

Mechanisms of Cotranslational Protein Maturation in Bacteria.
Koubek et al. (2021)
2 more