3v48 | pdb_00003v48

Crystal Structure of the putative alpha/beta hydrolase RutD from E.coli

spinqualitylabelsall models 3v48, resolution 2.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3v48 is a 2 chain structure with sequence from Ecose. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: GOL, SCN NonStd Res: MSE Gene: ECSE_1071, rutD (ECOSE) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [RUTD_ECOSE] May increase the rate of spontaneous hydrolysis of aminoacrylate to malonic semialdehyde. Required to remove a toxic intermediate produce in the pyrimidine nitrogen degradation (By similarity). Publication Abstract from PubMed The rut pathway of pyrimidine catabolism is a novel pathway that allows pyrimidine bases to serve as the sole nitrogen source in suboptimal temperatures. The rut operon in E. coli evaded detection until 2006, yet consists of seven proteins named RutA, RutB, etc. through RutG. The operon is comprised of a pyrimidine transporter and six enzymes that cleave and further process the uracil ring. Herein, we report the structure of RutD, a member of the alpha/beta hydrolase superfamily, which is proposed to enhance the rate of hydrolysis of aminoacrylate, a toxic side product of uracil degradation, to malonic semialdehyde. Although this reaction will occur spontaneously in water, the toxicity of aminoacrylate necessitates catalysis by RutD for efficient growth with uracil as a nitrogen source. RutD has a novel and conserved arrangement of residues corresponding to the alpha/beta hydrolase active site, where the nucleophile's spatial position occupied by Ser, Cys or Asp of the canonical catalytic triad is replaced by histidine. We have used a combination of crystallographic structure determination, modeling and bioinformatics, to propose a novel mechanism for this enzyme. This approach also revealed that RutD represents a previously undescribed family within the alpha/beta hydrolases. We compare and contrast RutD with PcaD, which is the closest structural homolog to RutD. PcaD is a 3-oxoadipate-enol-lactonase- with a classic arrangement of residues in the active site. We have modeled a substrate in the PcaD active site and proposed a reaction mechanism. Proteins 2012. (c) 2012 Wiley Periodicals, Inc. A multi-faceted analysis of RutD reveals a novel family of alpha/beta hydrolases.,Knapik AA, Petkowski JJ, Otwinowski Z, Cymborowski MT, Cooper DR, Majorek KA, Chruszcz M, Krajewska WM, Minor W Proteins. 2012 May 29. doi: 10.1002/prot.24122. PMID:22641504 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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