3m5y | pdb_00003m5y

Crystal structure of the mutant V182A,V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum

spinqualitylabelsall models 3m5y, resolution 1.46Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3m5y is a 2 chain structure with sequence from Methanothermobacter thermautotrophicus str. delta h. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: FMT, GOL Related: 3g18, 3m5z, 3m5x, 3m47, 3m44, 3m43, 3m41, 3m1z Gene: pyrF, MTH_129 (Methanothermobacter thermautotrophicus str. Delta H) Activity: Orotidine-5'-phosphate decarboxylase, with EC number 4.1.1.23 Resources: FirstGlance, OCA, RCSB, PDBsum Function [PYRF_METTH] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A] 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 The structural factors responsible for the extraordinary rate enhancement ( approximately 10(17)) of the reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) have not been defined. Catalysis requires a conformational change that closes an active site loop and "clamps" the orotate base proximal to hydrogen-bonded networks that destabilize the substrate and stabilize the intermediate. In the OMPDC from Methanobacter thermoautotrophicus, a "remote" structurally conserved cluster of hydrophobic residues that includes Val 182 in the active site loop is assembled in the closed, catalytically active conformation. Substitution of these residues with Ala decreases k(cat)/K(m) with a minimal effect on k(cat), providing evidence that the cluster stabilizes the closed conformation. The intrinsic binding energies of the 5'-phosphate group of orotidine 5'-monophosphate for the mutant enzymes are similar to that for the wild type, supporting this conclusion. Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.,Wood BM, Amyes TL, Fedorov AA, Fedorov EV, Shabila A, Almo SC, Richard JP, Gerlt JA Biochemistry. 2010 May 4;49(17):3514-6. PMID:20369850 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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