2W3U

formate complex of the Ni-Form of E.coli deformylase

Summary for 2W3U

• Entry DOI: 10.2210/pdb2w3u/pdb
• Related: 1BS4 1BS5 1BS6 1BS7 1BS8 1BSJ 1BSK 1BSZ 1DEF 1DFF 1DTF 1G27 1G2A 1ICJ 1LRU 2AI8 2DEF 2DTF 2VHM 2W3T
• Descriptor: PEPTIDE DEFORMYLASE, NICKEL (II) ION, FORMIC ACID, ... (4 entities in total)
• Functional Keywords: hydrolase, nickel, formate complex
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 1
• Total formula weight: 21544.37

Authors

Ngo, Y.H.T.,Palm, G.J.,Hinrichs, W. (deposition date: 2008-11-14, release date: 2009-12-15, Last modification date: 2023-12-13)

Primary citation

Yen, N.T.H.,Bogdanovic, X.,Palm, G.J.,Kuhl, O.,Hinrichs, W.
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-, 2010

PubMed 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.

PubMed: 20112455
DOI: 10.1007/S00775-009-0583-8

Experimental method

X-RAY DIFFRACTION (1.96 Å)