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Structure of IDP00873

1.8 Angstrom Resolution Crystal Structure of Dihydroorotase (pyrc) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2.

Edit deposit information
CSGID target
IDP00873 
PDB Id
3JZE (NCBI MMDB
Authors
G.Minasov,A.Halavaty,L.Shuvalova,I.Dubrovska,J.Winsor,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Sep 23, 2009 
Release Date
Sep 29, 2009 

Annotation

Description
Dihydroorotase (DHOase) catalyzes the reversible cyclization of N-carbamyl-l-aspartate (CA-asp) to l-dihydroorotate (DHO), which is third step in the de novo biosynthesis of pyrimidine nucleotides. The pathway is subject to diverse regulatory mechanisms including allosteric inhibition and activation, phosphorylation, and perhaps changes in intracellular location. Understanding the operation and interplay of these controls in the cell remains a fascinating challenge. Modulating the pyrimidine metabolism pharmacologically has therapeutical uses. Pyrimidine synthesis inhibitors are used in active moderate to severe rheumatoid and psoriatic arthritis. Each subunit of the homodimeric enzyme folds into a TIM barrel with eight parallel beta strands in the center and alpha-helices on the outer surface of the molecule. Each subunit contains a binuclear zinc center and carboxylated Lys-103 serving as a bridging ligand between the two cations. Structural studies of apo- and different complexes with ligands and inhibitors revealed importance of the surface loop (residues 106-116), which is involved in the ligand binding.  
Functional assignment
Dihydroorotase 

Ligands

Ligand code Name Ligand type
ZN ZINC ION biological
CL CHLORIDE ION crystallization
BME crystallization
PGE crystallization
ACY crystallization
PG4 crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=50.44Å, b=79.49Å, c=180.61Å
α=90.00, β=90.35, γ=90.00 
Solvent content
43.69  
Matthews coefficient
2.18  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.83-1.80Å (1.85-1.80Å)  
Rall(%)
16.5 
Rwork(%)
16.3 (22.4) 
Rfree(%)
20.3 (27.2) 
Num. observed reflections
130156 (9284) 
Num. Rfree reflections
6507 (490) 
Completeness(%)
98.5 (95.8) 

Model parameters

Num Atoms
10988  
Num Waters
1328  
Num Hetatoms
1510  
Model mean isotropic B factor
16.320Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.516°  
Filename uploaded
3JZE.pdb (uploaded on Sep 30, 2009 1:12 PM)  
Inserted
Jul 30, 2009