3r6v | pdb_00003r6v

Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate

spinqualitylabelsall models 3r6v, resolution 2.60Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3r6v is a 8 chain structure with sequence from Bacillus sp. ym55-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ASP, CA Related: 3r6q, 3r6y Gene: aspB (Bacillus sp. YM55-1) Activity: Aspartate ammonia-lyase, with EC number 4.3.1.1 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Aspartate ammonia lyases (or aspartases) catalyze the reversible deamination of l-aspartate into fumarate and ammonia. The lack of crystal structures of complexes with substrate, product, or substrate analogues so far precluded determination of their precise mechanism of catalysis. Here, we report crystal structures of AspB, the aspartase from Bacillus sp. YM55-1, in an unliganded state and in complex with l-aspartate at 2.4 and 2.6 A resolution, respectively. AspB forces the bound substrate to adopt a high-energy, enediolate-like conformation that is stabilized, in part, by an extensive network of hydrogen bonds between residues Thr101, Ser140, Thr141, and Ser319 and the substrate's beta-carboxylate group. Furthermore, substrate binding induces a large conformational change in the SS loop (residues G(317)SSIMPGKVN(326)) from an open conformation to one that closes over the active site. In the closed conformation, the strictly conserved SS loop residue Ser318 is at a suitable position to act as a catalytic base, abstracting the Cbeta proton of the substrate in the first step of the reaction mechanism. The catalytic importance of Ser318 was confirmed by site-directed mutagenesis. Site-directed mutagenesis of SS loop residues, combined with structural and kinetic analysis of a stable proteolytic AspB fragment, further suggests an important role for the small C-terminal domain of AspB in controlling the conformation of the SS loop and, hence, in regulating catalytic activity. Our results provide evidence supporting the notion that members of the aspartase/fumarase superfamily use a common catalytic mechanism involving general base-catalyzed formation of a stabilized enediolate intermediate. Structural basis for the catalytic mechanism of aspartate ammonia lyase.,Fibriansah G, Veetil VP, Poelarends GJ, Thunnissen AM Biochemistry. 2011 Jul 12;50(27):6053-62. Epub 2011 Jun 20. PMID:21661762 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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