3MKJ

Methionine gamma-lyase from Citrobacter freundii with pyridoximine-5'-phosphate

Summary for 3MKJ

• Entry DOI: 10.2210/pdb3mkj/pdb
• Related: 1Y4I 2RFV 3JW9 3JWA 3JWB
• Descriptor: Methionine gamma-lyase, [5-hydroxy-4-(iminomethyl)-6-methyl-pyridin-3-yl]methyl dihydrogen phosphate (3 entities in total)
• Functional Keywords: pyridoxal-5'-phosphate, plp-dependent enzyme, lyase, x-ray damage
• Biological source: Citrobacter freundii
• Total number of polymer chains: 1
• Total formula weight: 43246.96

Authors

Revtovich, S.V.,Nikulin, A.D.,Morozova, E.A.,Demidkina, T.V. (deposition date: 2010-04-15, release date: 2010-08-11, Last modification date: 2024-10-16)

Primary citation

Ronda, L.,Bazhulina, N.P.,Morozova, E.A.,Revtovich, S.V.,Chekhov, V.O.,Nikulin, A.D.,Demidkina, T.V.,Mozzarelli, A.
Exploring methionine gamma-lyase structure-function relationship via microspectrophotometry and X-ray crystallography
Biochim.Biophys.Acta, 1814:834-842, 2011

PubMed Abstract: Pyridoxal 5'-phosphate (PLP) dependent methionine γ-lyase catalyzes the breakdown of L-methionine to α-ketobutyric acid, methanethiol and ammonia. This enzyme, present in anaerobic microorganisms, has biomedical interest both for its activity as antitumor agent, depleting methionine supply in methionine-dependent cancers, and as target in the treatment of human pathogen infections, activating the pro-drug trifluoromethionine. To validate the structure of the enzyme from Citrobacter freundii, crystallized from monomethyl ether polyethylene glycol 2000, for the development of lead compounds, the reactivity of the crystalline enzyme towards L-methionine, substrate analogs and inhibitors was determined by polarized absorption microspectrophotometry. Spectral data were also collected for enzyme crystals, grown in monomethyl ether polyethylene glycol 2000 in the presence of ammonium sulfate. The three-dimensional structure of these enzyme crystals, solved at 1.65Å resolution with R(free) 23.2%, revealed the surprising absence of the aldimine bond between the active site Lys210 and PLP. Different hypothesis are proposed and discussed in the light of spectral and structural data, pointing out to the relevance of the complementarity between X-ray crystallography and single crystal spectroscopy for the understanding of biological mechanisms at molecular level. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

PubMed: 20601224
DOI: 10.1016/j.bbapap.2010.06.017

Experimental method

X-RAY DIFFRACTION (1.65 Å)