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Structure of IDP00355

2.23 Angstrom resolution crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) from Listeria monocytogenes EGD-e

Edit deposit information
CSGID target
IDP00355 
PDB Id
3R38 (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,L.Shuvalova,I.Dubrovska,J.Winsor,S.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Mar 15, 2011 
Release Date
Mar 23, 2011 

Annotation

Description
The UDP-N-acetylglucosamine enolpyruvyl transferase (MurA; EC 2.5.1.7) enzyme catalyzes transfer of enolpyruvate from phosphoenolpyruvate to UDP-N-acetylglucosamine to form enolpyruvyl-UDP-N-acetylglucosamine. This is the first step of the first stage of the biosynthetic pathway of peptidoglycan that occurs in the cytoplasm. The X-ray structure of the MurA from Listeria monocytogenes EGD-e was solved by molecular replacement using the crystal structure of the MurA from Haemophilus influenzae (PDB ID code: 2RL2) as a model. Both proteins possess two large almost globular domains, which create an active site area between them. The two proteins share 49 % sequence identity and have 1.4 A r.m.s.d. in the positions of their Cα atoms. Larger structural differences are seen in the area of active site loop, which is in open conformation in the L. monocytogenes apo-MurA structure. The position of the loop is partially determined by its crystal contacts with the intact purification tag of the symmetry-related molecule. This loop is in closed state in the binary UDP-N-acetylglucosamine-bound 2RL2 structure. The distance between the Cα atoms of the active cysteine residues of the loop, in both structures Cys117, is 5.7 A. A sulfate ion was modeled in the active site of the L. monocytogenes MurA mimicking the α-phosphate group of the UDP-N-acetylglucosamine in the 2RL2 structure 
Functional assignment
Transferase 

Ligands

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

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=144.58Å, b=51.92Å, c=78.18Å
α=90.00, β=110.95, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.11-2.23Å (2.29-2.23Å)  
Rall(%)
19.8 
Rwork(%)
19.6 (38.6) 
Rfree(%)
23.9 (35.4) 
Num. observed reflections
26363 (1631) 
Num. Rfree reflections
1318 (78) 
Completeness(%)
98.7 (83.4) 

Model parameters

Num Atoms
3346  
Num Waters
184  
Num Hetatoms
236  
Model mean isotropic B factor
38.980Å2  
RMSD bond length
0.007Å  
RMSD bond angle
1.328°  
Filename uploaded
3R38.pdb (uploaded on Apr 04, 2011 7:00 PM)  
Inserted
Mar 24, 2011