Crystal structure of the external aldimine of Citrobacter freundii methionine γ-lyase with glycine provides insight in mechanisms of two stages of physiological reaction and isotope exchange of α- and β-protons of competitive inhibitors.
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.
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russia.
Svetlana V
SV
Revtovich
Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov Str. 28, Moscow 119991, Russia.
Nicolai G
NG
Faleev
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russia.
Elena A
EA
Morozova
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russia.
Natalya V
NV
Anufrieva
Institute of Protein Research, Russian Academy of Sciences, Institutskaya Str. 4, 142290 Pushchino, Moscow Region, Russia.
Alexey D
AD
Nikulin
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russia. Electronic address: tvd@eimb.ru.
Tatyana V
TV
Demidkina
D001426:Bacterial Proteins / Q000737:chemistry*; D001667:Binding, Competitive; D013437:Carbon-Sulfur Lyases / Q000737:chemistry*; D020134:Catalytic Domain; D016971:Citrobacter freundii / Q000201:enzymology*; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry; D005998:Glycine / Q000737:chemistry*; D007097:Imines / Q000737:chemistry; D008715:Methionine / Q000737:chemistry; D008958:Models, Molecular; D009570:Nitriles / Q000737:chemistry; D011485:Protein Binding
D001426:Bacterial Proteins; D004791:Enzyme Inhibitors; D007097:Imines; D009570:Nitriles; C542835:ketimine; D008715:Methionine; D013437:Carbon-Sulfur Lyases; C021558:L-methionine gamma-lyase; D005998:Glycine
Concerted mechanism; Isotopic exchange of protons; Methionine γ-lyase; Pyridoxal 5′-phosphate dependent enzyme; Stereoselectivity