3g7k

Crystal Structure of Methylitaconate-delta-isomerase

spinqualitylabelsall models 3g7k, resolution 2.70Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3g7k is a 4 chain structure with sequence from "inflabilis_barati"_(sic)_prevot_1938 "inflabilis barati" (sic) prevot 1938. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Related: 2pwz, 2pw0, 2gkj, 1w61, 1xua Gene: Mii ("Inflabilis barati" (sic) Prevot 1938) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [MII_EUBBA] Catalyzes the reversible isomerization of (R)-3-methylitaconate to 2,3-dimethylmaleate. Has very low isomerase activity with itaconate. 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 3-Methylitaconate-Delta-isomerase (Mii) participates in the nicotinate fermentation pathway of the anaerobic soil bacterium Eubacterium barkeri (order Clostridiales) by catalyzing the reversible conversion of (R)-3-methylitaconate (2-methylene-3-methylsuccinate) to 2,3-dimethylmaleate. The enzyme is also able to catalyze the isomerization of itaconate (methylenesuccinate) to citraconate (methylmaleate) with ca 10-fold higher K(m) but > 1000-fold lower k(cat). The gene mii from E. barkeri was cloned and expressed in Escherichia coli. The protein produced with a C-terminal Strep-tag exhibited the same specific activity as the wild-type enzyme. The crystal structure of Mii from E. barkeri has been solved at a resolution of 2.70 A. The asymmetric unit of the P2(1)2(1)2(1) unit cell with parameters a = 53.1 A, b = 142.3 A, and c = 228.4 A contains four molecules of Mii. The enzyme belongs to a group of isomerases with a common structural feature, the so-called diaminopimelate epimerase fold. The monomer of 380 amino acid residues has two topologically similar domains exhibiting an alpha/beta-fold. The active site is situated in a cleft between these domains. The four Mii molecules are arranged as a tetramer with 222 symmetry for the N-terminal domains. The C-terminal domains have different relative positions with respect to the N-terminal domains resulting in a closed conformation for molecule A and two distinct open conformations for molecules B and D. The C-terminal domain of molecule C is disordered. The Mii active site contains the putative catalytic residues Lys62 and Cys96, for which mechanistic roles are proposed based on a docking experiment of the Mii substrate complex. The active sites of Mii and the closely related PrpF, most likely a methylaconitate Delta-isomerase, have been compared. The overall architecture including the active-site Lys62, Cys96, His300, and Ser17 (Mii numbering) is similar. This positioning of (R)-3-methylitaconate allows Cys96 (as thiolate) to deprotonate C-3 and (as thiol) to donate a proton to the methylene carbon atom of the resulting allylic carbanion. Interestingly, the active site of isopentenyl diphosphate isomerase type I also contains a cysteine that cooperates with glutamate rather than lysine. It has been proposed that the initial step in this enzyme is a protonation generating a tertiary carbocation intermediate. Crystal structure and putative mechanism of 3-methylitaconate-delta-isomerase from Eubacterium barkeri.,Velarde M, Macieira S, Hilberg M, Broker G, Tu SM, Golding BT, Pierik AJ, Buckel W, Messerschmidt A J Mol Biol. 2009 Aug 21;391(3):609-20. Epub 2009 Jun 24. PMID:19559030 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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