Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 103.83 kDa 
• Atom Count: 6940 
• Modelled Residue Count: 738 
• Deposited Residue Count: 934 
• Unique protein chains: 1

1XRT

The Crystal Structure of a Novel, Latent Dihydroorotase from Aquifex Aeolicus at 1.7 A Resolution

• PDB DOI: 10.2210/pdb1XRT/pdb

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-15 Released: 2005-07-05 
• Deposition Author(s): Martin, P.D., Purcarea, C., Zhang, P., Vaishnav, A., Sadecki, S., Guy-Evans, H.I., Evans, D.R., Edwards, B.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.208 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

The crystal structure of a novel, latent dihydroorotase from Aquifex aeolicus at 1.7A resolution

Martin, P.D., Purcarea, C., Zhang, P., Vaishnav, A., Sadecki, S., Guy-Evans, H.I., Evans, D.R., Edwards, B.F.

(2005) J Mol Biol 348: 535-547

• PubMed: 15826652 
• DOI: 10.1016/j.jmb.2005.03.015
• Primary Citation of Related Structures:  
  1XRF, 1XRT


• PubMed Abstract: 
  

Dihydroorotases (EC 3.5.2.3) catalyze the reversible cyclization of carbamoyl aspartate to form dihydroorotate in de novo pyrimidine biosynthesis. The X-ray structures of Aquifex aeolicus dihydroorotase in two space groups, C222(1) and C2, were determined at a resolution of 1.7A. These are the first structures of a type I dihydroorotase, a class of molecules that includes the dihydroorotase domain of mammalian CAD. The type I enzymes are more ancient and larger, at 45 kDa, than the type II enzymes exemplified by the 38 kDa Escherichia coli dihydroorotase. Both dihydroorotases are members of the metallo-dependent hydrolase superfamily, whose members have a distorted "TIM barrel" domain containing the active site. However, A.aeolicus dihydroorotase has a second, composite domain, which the E.coli enzyme lacks and has only one of the two zinc atoms present in the E.coli enzyme. A.aeolicus dihydroorotase is unique in exhibiting significant activity only when complexed with aspartate transcarbamoylase, whereas the E.coli dihydroorotase and the CAD dihydroorotase domain are active as free proteins. The latency of A.aeolicus dihydroorotase can be related to two differences between its structure and that of E.coli dihydroorotase: (1) the monoclinic structure has a novel cysteine ligand to the zinc that blocks the active site and possibly functions as a "cysteine switch"; and (2) active site residues that bind the substrate in E.coli dihydroorotase are located in disordered loops in both crystal structures of A.aeolicus dihydroorotase and may function as a disorder-to-order "entropy switch".

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Organizational Affiliation: 

Wayne State University School of Medicine, Department of Biochemistry and Molecular Biology, 540 E. Canfield, Detroit, MI 48201, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotase	A, B	467	Aquifex aeolicus	Mutation(s): 0  Gene Names: pyrC EC: 3.5.2.3
UniProt
Find proteins for O66990 (Aquifex aeolicus (strain VF5)) Explore O66990  Go to UniProtKB:  O66990

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.208 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.201	α = 90
b = 91.235	β = 93.15
c = 61.183	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-15 
• Released Date: 2005-07-05 
Deposition Author(s): Martin, P.D., Purcarea, C., Zhang, P., Vaishnav, A., Sadecki, S., Guy-Evans, H.I., Evans, D.R., Edwards, B.F.

Revision History  

• Version 1.0: 2005-07-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance