4HF8
Crystal structure of L-methionine gamma-lyase from Citrobacter freundii with glycine
Summary for 4HF8
| Entry DOI | 10.2210/pdb4hf8/pdb |
| Related | 1Y4I 2RFV 3JW9 3JWA 3JWB |
| Descriptor | Methionine gamma-lyase, N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE], GLYCINE, ... (5 entities in total) |
| Functional Keywords | complex, pyridoxal-5'-phosphate, plp-dependent enzyme, lyase, l-methionine |
| Biological source | Citrobacter freundii |
| Total number of polymer chains | 1 |
| Total formula weight | 43722.55 |
| Authors | Revtovich, S.V.,Morozova, E.A.,Anufrieva, N.V.,Nikulin, A.D.,Demidkina, T.V. (deposition date: 2012-10-05, release date: 2013-11-06, Last modification date: 2024-11-13) |
| Primary citation | Revtovich, S.V.,Faleev, N.G.,Morozova, E.A.,Anufrieva, N.V.,Nikulin, A.D.,Demidkina, T.V. Crystal structure of the external aldimine of Citrobacter freundii methionine gamma-lyase with glycine provides insight in mechanisms of two stages of physiological reaction and isotope exchange of alpha- and beta-protons of competitive inhibitors. Biochimie, 101:161-167, 2014 Cited by PubMed Abstract: The three-dimensional structure of the external aldimine of Citrobacter freundii methionine γ-lyase with competitive inhibitor glycine has been determined at 2.45 Å resolution. It revealed subtle conformational changes providing effective binding of the inhibitor and facilitating labilization of Cα-protons of the external aldimine. The structure shows that 1, 3-prototropic shift of Cα-proton to C4'-atom of the cofactor may proceed with participation of active site Lys210 residue whose location is favorable for performing this transformation by a concerted mechanism. The observed stereoselectivity of isotopic exchange of enantiotopic Cα-protons of glycine may be explained on the basis of external aldimine structure. The exchange of Cα-pro-(R)-proton of the external aldimine might proceed in the course of the concerted transfer of the proton from Cα-atom of glycine to C4'-atom of the cofactor. The exchange of Cα-pro-(S)-proton may be performed with participation of Tyr113 residue which should be present in its basic form. The isotopic exchange of β-protons, which is observed for amino acids bearing longer side groups, may be effected by two catalytic groups: Lys210 in its basic form, and Tyr113 acting as a general acid. PubMed: 24463191DOI: 10.1016/j.biochi.2014.01.007 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.45 Å) |
Structure validation
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