3V48

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

Summary for 3V48

• Entry DOI: 10.2210/pdb3v48/pdb
• Descriptor: Putative aminoacrylate hydrolase RutD, GLYCEROL, THIOCYANATE ION, ... (4 entities in total)
• Functional Keywords: structural genomics, psi-biology, new york structural genomics research consortium, nysgrc, hydrolase
• Biological source: Escherichia coli SE11
• Total number of polymer chains: 2
• Total formula weight: 59349.90

Authors

Knapik, A.A.,Petkowski, J.J.,Otwinowski, Z.,Cymborowski, M.T.,Cooper, D.R.,Chruszcz, M.,Porebski, P.J.,Niedzialkowska, E.,Almo, S.C.,Minor, W.,New York Structural Genomics Research Consortium (NYSGRC) (deposition date: 2011-12-14, release date: 2012-01-04, Last modification date: 2024-11-06)

Primary citation

Knapik, A.A.,Petkowski, J.J.,Otwinowski, Z.,Cymborowski, M.T.,Cooper, D.R.,Majorek, K.A.,Chruszcz, M.,Krajewska, W.M.,Minor, W.
A multi-faceted analysis of RutD reveals a novel family of alpha / beta hydrolases.
Proteins, 80:2359-2368, 2012

PubMed 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 α/β 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 α/β 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 α/β 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.

PubMed: 22641504
DOI: 10.1002/prot.24122

Experimental method

X-RAY DIFFRACTION (2.1 Å)