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Hydrolase PDB id
2z27
Jmol
Contents
Protein chains
343 a.a. *
Ligands
DOR
NCD
Metals
_ZN ×4
Waters ×590
* Residue conservation analysis
PDB id:
2z27
Name: Hydrolase
Title: Thr109ser dihydroorotase from e. Coli
Structure: Dihydroorotase. Chain: a, b. Synonym: dhoase. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: pyrc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.87Å     R-factor:   0.148     R-free:   0.188
Authors: M.Lee,M.J.Maher,J.M.Guss
Key ref: M.Lee et al. (2007). Kinetic and Structural Analysis of Mutant Escherichia coli Dihydroorotases: A Flexible Loop Stabilizes the Transition State(,). Biochemistry, 46, 10538-10550. PubMed id: 17711307 DOI: 10.1021/bi701098e
Date:
17-May-07     Release date:   09-Oct-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05020  (PYRC_ECOLI) -  Dihydroorotase
Seq:
Struc:
348 a.a.
343 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.5.2.3  - Dihydroorotase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Pyrimidine Biosynthesis
      Reaction: (S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate
(S)-dihydroorotate
Bound ligand (Het Group name = DOR)
corresponds exactly
+ H(2)O
=
N-carbamoyl-L-aspartate
Bound ligand (Het Group name = NCD)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     pyrimidine base biosynthetic process   3 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi701098e Biochemistry 46:10538-10550 (2007)
PubMed id: 17711307  
 
 
Kinetic and Structural Analysis of Mutant Escherichia coli Dihydroorotases: A Flexible Loop Stabilizes the Transition State(,).
M.Lee, M.J.Maher, R.I.Christopherson, J.M.Guss.
 
  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.