4yza | pdb_00004yza

C. bescii Family 3 pectate lyase double mutant K108A/Q111A in complex with trigalacturonic acid

spinqualitylabelsall models 4yza, resolution 1.25Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4yza is a 2 chain structure with sequence from Caldicellulosiruptor bescii DSM 6725. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.25Å Ligands: ADA, CA, GTR, IMD, MPD, MRD, X1X Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function B9MKT4_CALBD Publication Abstract from PubMed The unique active site of the Caldicellulosiruptor bescii family 3 pectate lyase (PL3) enzyme has been thoroughly characterized using a series of point mutations, X-ray crystallography, pK(a) calculations and biochemical assays. The X-ray structures of seven PL3 active-site mutants, five of them in complex with intact trigalacturonic acid, were solved and characterized structurally, biochemically and computationally. The results confirmed that Lys108 is the catalytic base, but there is no clear candidate for the catalytic acid. However, the reaction mechanism can also be explained by an antiperiplanar trans-elimination reaction, in which Lys108 abstracts a proton from the C5 atom without the help of simultaneous proton donation by an acidic residue. An acidified water molecule completes the anti beta-elimination reaction by protonating the O4 atom of the substrate. Both the C5 hydrogen and C4 hydroxyl groups of the substrate must be orientated in axial configurations, as for galacturonic acid, for this to be possible. The wild-type C. bescii PL3 displays a pH optimum that is lower than that of Bacillus subtilis PL1 according to activity measurements, indicating that C. bescii PL3 has acquired a lower pH optimum by utilizing lysine instead of arginine as the catalytic base, as well as by lowering the pK(a) of the catalytic base in a unique active-site environment. The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase.,Alahuhta M, Taylor LE 2nd, Brunecky R, Sammond DW, Michener W, Adams MW, Himmel ME, Bomble YJ, Lunin V Acta Crystallogr D Biol Crystallogr. 2015 Sep;71(Pt 9):1946-54. doi:, 10.1107/S1399004715013760. Epub 2015 Aug 25. PMID:26327384 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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