3V48

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

A multi-faceted analysis of RutD reveals a novel family of alpha / beta hydrolases.

Knapik, A.A.Petkowski, J.J.Otwinowski, Z.Cymborowski, M.T.Cooper, D.R.Majorek, K.A.Chruszcz, M.Krajewska, W.M.Minor, W.

(2012) Proteins 80: 2359-2368

  • DOI: 10.1002/prot.24122

  • 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 ...

    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.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22903, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative aminoacrylate hydrolase RutD
A, B
268Escherichia coli (strain SE11)Mutation(s): 0 
Gene Names: rutD
EC: 3.5.1.-
Find proteins for B6I985 (Escherichia coli (strain SE11))
Go to UniProtKB:  B6I985
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download SDF File 
Download CCD File 
A, B
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 79.597α = 90.00
b = 79.597β = 90.00
c = 161.753γ = 90.00
Software Package:
Software NamePurpose
HKL-3000phasing
SOLVEphasing
ARP/wARPmodel building
MD2data collection
DMphasing
HKL-2000data reduction
DMmodel building
CCP4model building
CCP4phasing
SHELXEmodel building
MLPHAREphasing
SHELXCDphasing
RESOLVEmodel building
HKL-2000data scaling
REFMACrefinement
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-01-04
    Type: Initial release
  • Version 1.1: 2012-02-22
    Type: Database references, Structure summary
  • Version 1.2: 2012-06-06
    Type: Database references
  • Version 1.3: 2012-06-20
    Type: Database references
  • Version 1.4: 2013-08-28
    Type: Database references
  • Version 1.5: 2017-11-08
    Type: Refinement description