Thr109Ser dihydroorotase from E. coli

Experimental Data Snapshot

  • Resolution: 1.87 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


Kinetic and Structural Analysis of Mutant Escherichia coli Dihydroorotases: A Flexible Loop Stabilizes the Transition State

Lee, M.Maher, M.J.Christopherson, R.I.Guss, J.M.

(2007) Biochemistry 46: 10538-10550

  • DOI: https://doi.org/10.1021/bi701098e
  • Primary Citation of Related Structures:  
    2Z24, 2Z25, 2Z26, 2Z27, 2Z28, 2Z29, 2Z2A, 2Z2B

  • PubMed Abstract: 

    Dihydroorotase (DHOase) catalyzes the reversible cyclization of N-carbamyl-l-aspartate (CA-asp) to l-dihydroorotate (DHO) in the de novo biosynthesis of pyrimidine nucleotides. Two different conformations of the surface loop (residues 105-115) were found in the dimeric Escherichia coli DHOase crystallized in the presence of DHO (PDB code 1XGE). The loop asymmetry reflected that of the active site contents of the two subunits: the product, DHO, was bound in the active site of one subunit and the substrate, CA-asp, in the active site of the other. In the substrate- (CA-asp-) bound subunit, the surface loop reaches in toward the active site and makes hydrogen bonds with the bound CA-asp via two threonine residues (Thr109 and Thr110), whereas the loop forms part of the surface of the protein in the product- (DHO-) bound subunit. To investigate the relationship between the structural states of this loop and the catalytic mechanism of the enzyme, a series of mutant DHOases including deletion of the flexible loop were generated and characterized kinetically and structurally. Disruption of the hydrogen bonds between the surface loop and the substrate results in significant loss of catalytic activity. Furthermore, structures of these mutants with low catalytic activity have no interpretable electron density for parts of the flexible loop. The structure of the mutant (Delta107-116), in which the flexible loop is deleted, shows only small differences in positions of other substrate binding residues and in the binuclear zinc center compared with the native structure, yet the enzyme has negligible activity. The kinetic and structural analyses suggest that Thr109 and Thr110 in the flexible loop provide productive binding of substrate and stabilize the transition-state intermediate, thereby increasing catalytic activity.

  • Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, New South Wales 2006, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
347Escherichia coliMutation(s): 1 
Gene Names: PYRC
Find proteins for P05020 (Escherichia coli (strain K12))
Explore P05020 
Go to UniProtKB:  P05020
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05020
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.87 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.378α = 90
b = 78.521β = 90
c = 180.221γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection