PDBsum entry 2w3u

Hydrolase

PDB id: 2w3u

Contents

Protein chain

165 a.a. *

Ligands

FMT

Metals

_NI

Waters ×96

* Residue conservation analysis

PDB id:

2w3u

Name:

Hydrolase

Title:

Formate complex of the ni-form of e.Coli deformylase

Structure:

Peptide deformylase. Chain: a. Fragment: residues 2-169. Synonym: pdf, polypeptide deformylase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Atcc: baa-1025. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.96Å R-factor: 0.250 R-free: 0.285

Authors:

Y.H.T.Ngo,G.J.Palm,W.Hinrichs

Key ref:

N.T.Yen et al. (2010). Structure of the Ni(II) complex of Escherichia coli peptide deformylase and suggestions on deformylase activities depending on different metal(II) centres. J Biol Inorg Chem, 15, 195-201. PubMed id: 20112455

Date:

14-Nov-08 Release date: 15-Dec-09

Protein chain

P0A6K3  (DEF_ECOLI) -  Peptide deformylase from Escherichia coli (strain K12)

Seq: 169 a.a.

Struc: 165 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.1.88 - peptide deformylase.
• Reaction: N-terminal N-formyl-L-methionyl-[peptide] + H2O = N-terminal L-methionyl- [peptide] + formate

N-terminal N-formyl-L-methionyl-[peptide] + H2O = N-terminal L-methionyl- [peptide] (Bound ligand (Het Group name = FMT) corresponds exactly) + formate

• Cofactor: Fe(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

J Biol Inorg Chem 15:195-201 (2010)

PubMed id: 20112455

Structure of the Ni(II) complex of Escherichia coli peptide deformylase and suggestions on deformylase activities depending on different metal(II) centres.

N.T.Yen, X.Bogdanović, G.J.Palm, O.Kühl, W.Hinrichs.

ABSTRACT

Crystal structures of polypeptide deformylase (PDF) of Escherichia coli with nickel(II) replacing the native iron(II) have been solved with chloride and formate as metal ligands. The chloro complex is a model for the correct protonation state of the hydrolytic hydroxo ligand and the protonated status of the Glu133 side chain as part of the hydrolytic mechanism. The ambiguity that recently some PDFs have been identified with Zn(2+) ion as the active-site centre whereas others are only active with Fe(2+) (or Co(2+), Ni(2+) is discussed with respect to Lewis acid criteria of the metal ion and substrate activation by the CD loop.