3b1e | pdb_00003b1e

Crystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: alpha-Aminoacrylate form

spinqualitylabelsall models 3b1e, resolution 1.78Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3b1e is a 4 chain structure with sequence from "streptococcus_anginosus"_andrewes_and_horder_1906 "streptococcus anginosus" andrewes and horder 1906. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ACT, EPE, NA, P1T Related: 3b1c, 3b1d Gene: lcd ("Streptococcus anginosus" Andrewes and Horder 1906) Activity: Cystathionine beta-lyase, with EC number 4.4.1.8 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Hydrogen sulfide (H(2) S) is a causative agent of oral malodor and may play an important role in the pathogenicity of oral bacteria such as Streptococcus anginosus. In this microorganism, H(2) S production is associated with betaC-S lyase (Lcd) encoded by lcd gene, which is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the alpha,beta-elimination of sulfur-containing amino acids. When Lcd acts on L-cysteine, H(2) S is produced along with pyruvate and ammonia. To understand the H(2) S-producing mechanism of Lcd in detail, we determined the crystal structures of substrate-free Lcd (internal aldimine form) and two reaction intermediate complexes (external aldimine and alpha-aminoacrylate forms). The formation of intermediates induced little changes in the overall structure of the enzyme and in the active site residues, with the exception of Lys234, a PLP-binding residue. Structural and mutational analyses highlighted the importance of the active site residues Tyr60, Tyr119, and Arg365. In particular, Tyr119 forms a hydrogen bond with the side chain oxygen atom of L-serine, a substrate analog, in the external aldimine form suggesting its role in the recognition of the sulfur atom of the true substrate (L-cysteine). Tyr119 also plays a role in fixing the PLP cofactor at the proper position during catalysis through binding with its side chain. Finally, we partly modified the catalytic mechanism known for cystalysin, a betaC-S lyase from Treponema denticola, and proposed an improved mechanism, which seems to be common to the betaC-S lyases from oral bacteria. Proteins 2012. (c) 2012 Wiley Periodicals, Inc. Structural insights into catalysis by betaC-S lyase from Streptococcus anginosus.,Kezuka Y, Yoshida Y, Nonaka T Proteins. 2012 Jun 6. doi: 10.1002/prot.24129. PMID:22674431 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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