Structure Report for: 3V48

The structure of RutD, a member of the alpha/beta hydrolase superfamily, and a putative aminoacrylate hydrolytic enzyme of the rut uracil degradation pathway in E.coli Knapik, A.A., Petkowski, J.J., Otwinowski, Z, Cymborowski, M.T., Cooper, D.G., Chruszcz, M., Porebski, P.J., Niedzialkowska, E., Krajewska, W.M., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Title: 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
Ref: Proteins, 80:2359, 2012 : PubMed
Abstract


ESTHER: Knapik_2012_Proteins_80_2359
PubMedSearch: Knapik 2012 Proteins 80 2359
PubMedID: 22641504
Gene_locus related to this paper: ecoli-rutD

Abstract

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.