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Structure of IDP90587

2.00 Angstrom resolution crystal structure of a catalytic subunit of an aspartate carbamoyltransferase (pyrB) from Yersinia pestis CO92

Edit deposit information
CSGID target
IDP90587 
PDB Id
3LXM (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,I.Dubrovska,J.Winsor,L.Shuvalova,S.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Feb 25, 2010 
Release Date
Mar 16, 2010 

Annotation

Description
The enzyme aspartate carbamoyltransferase (ATCase) catalyzes the first step in the pyrimidine biosynthetic pathway. Crystal structure of a catalytic (C) subunit of the Yersinia pestis CO92 ATCase was solved by molecular replacement using the structure of the unregulated, N-phosphonacetyl-L-aspartate (PALA)-bound C subunit of ATCase from Escherichia coli (PDB ID 1EKX) as a model. Both proteins share 84 % sequence identity, are trimeric in the crystal and have 1.6 Å root-mean-square deviation (rmsd) of the C-alpha atoms. The structural discrepancy between two proteins is due to the greater overall flexibility and disorder in loops containing active-site residues of the ligand-free Y. pestis C trimer. In contrast, the E.coli PALA-free C trimer (PDB ID 3CSU) has 0.5 Å rmsd of the C-alpha atoms with its Y. pestis homolog. This indicates that binding of a substrate (substrate analog) alters structural perturbations. In order to understand the regulation mechanism of the Y. pestis ATCase, conformational states that account for allosteric structural changes in catalytic activity should be defined. 
Functional assignment
Transferase 

Ligands

Ligand code Name Ligand type
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=67.62Å, b=120.41Å, c=126.70Å
α=90.00, β=90.00, γ=90.00 
Solvent content
46.57  
Matthews coefficient
2.3  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
30.00-2.00Å (2.05-2.00Å)  
Rall(%)
18.1 
Rwork(%)
17.9 (23.7) 
Rfree(%)
21.7 (29.1) 
Num. observed reflections
70860 (5080) 
Num. Rfree reflections
3543 (240) 
Completeness(%)
99.7 (98.1) 

Model parameters

Num Atoms
6731  
Num Waters
448  
Num Hetatoms
465  
Model mean isotropic B factor
45.810Å2  
RMSD bond length
0.015Å  
RMSD bond angle
1.674°  
Filename uploaded
3LXM.pdb (uploaded on Sep 17, 2010 6:08 PM)  
Inserted
Feb 25, 2010