5X2W
Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-methionine intermediates
Summary for 5X2W
| Entry DOI | 10.2210/pdb5x2w/pdb |
| Related | 5X2V 5X2X 5X2Y 5X2Z 5X30 |
| Descriptor | L-methionine gamma-lyase, (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-(methylsulfanyl)but-2-enoic acid (3 entities in total) |
| Functional Keywords | pyridoxal 5'-phosphate, lyase |
| Biological source | Pseudomonas putida |
| Total number of polymer chains | 4 |
| Total formula weight | 172207.82 |
| Authors | Shiba, T.,Sato, D.,Harada, S. (deposition date: 2017-02-02, release date: 2017-04-12, Last modification date: 2023-11-22) |
| Primary citation | Sato, D.,Shiba, T.,Yunoto, S.,Furutani, K.,Fukumoto, M.,Kudou, D.,Tamura, T.,Inagaki, K.,Harada, S. Structural and mechanistic insights into homocysteine degradation by a mutant of methionine gamma-lyase based on substrate-assisted catalysis Protein Sci., 26:1224-1230, 2017 Cited by PubMed Abstract: Methionine γ-lyse (MGL) catalyzes the α, γ-elimination of l-methionine and its derivatives as well as the α, β-elimination of l-cysteine and its derivatives to produce α-keto acids, volatile thiols, and ammonia. The reaction mechanism of MGL has been characterized by enzymological studies using several site-directed mutants. The Pseudomonas putida MGL C116H mutant showed drastically reduced degradation activity toward methionine while retaining activity toward homocysteine. To understand the underlying mechanism and to discern the subtle differences between these substrates, we analyzed the crystal structures of the reaction intermediates. The complex formed between the C116H mutant and methionine demonstrated that a loop structure (Ala51-Asn64) in the adjacent subunit of the catalytic dimer cannot approach the cofactor pyridoxal 5'-phosphate (PLP) because His116 disrupts the interaction of Asp241 with Lys240, and the liberated side chain of Lys240 causes steric hindrance with this loop. Conversely, in the complex formed between C116H mutant and homocysteine, the thiol moiety of the substrate conjugated with PLP offsets the imidazole ring of His116 via a water molecule, disrupting the interaction of His116 and Asp241 and restoring the interaction of Asp241 with Lys240. These structural data suggest that the Cys116 to His mutation renders the enzyme inactive toward the original substrate, but activity is restored when the substrate is homocysteine due to substrate-assisted catalysis. PubMed: 28329912DOI: 10.1002/pro.3158 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.7 Å) |
Structure validation
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