Structural highlights
2w3u is a 1 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
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| Ligands: | , |
| Related: | 1def, 1lru, 1bs8, 1bsk, 2vhm, 1bs7, 2ai8, 2def, 1icj, 1bs4, 1bs5, 1bsz, 2w3t, 1dff, 1g2a, 1g27, 1bs6, 1dtf, 1bsj, 2dtf |
| Activity: | Formylmethionine deformylase, with EC number 3.5.1.31 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum |
Function
[DEF_ECOLI] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
Structure of the Ni(II) complex of Escherichia coli peptide deformylase and suggestions on deformylase activities depending on different metal(II) centres.,Yen NT, Bogdanovic X, Palm GJ, Kuhl O, Hinrichs W J Biol Inorg Chem. 2010 Feb;15(2):195-201. PMID:20112455[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yen NT, Bogdanovic X, Palm GJ, 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. 2010 Feb;15(2):195-201. PMID:20112455
