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Structure of IDP01038

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium.

Edit deposit information
CSGID target
IDP01038 
PDB Id
3GHZ (NCBI MMDB
Authors
J.Osipiuk,M.Gu,S.Peterson,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 04, 2009 
Release Date
Mar 17, 2009 

Annotation

Description
2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase from Salmonella typhimurium, ispF gene product, takes part in biosynthesis of the isomers isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate, which are universal five-carbon precursors of isoprenoids. The enzyme is involved in the non-mevalonate pathway of isoprenoid synthesis which is essential in all organisms. The non-mevolanate route is used by many bacteria and human pathogens. This route appears to involve seven enzymes. MECDP synthetases, ispF and YgbB proteins, catalyze the fifth stage of the pathway. They convert 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate into MECDP and CMP. The enzyme is a homotrimer with three active sites located in a cleft lined by residues from two subunits. Each active site binds a Zn2+ ion and the ribose and diphosphate of CDP. The non-mevalonate pathway is present in many bacteria, some algae, certain protozoa, and in the plastids of higher plants, but not in mammals or archaea. Therefore, these enzymes have been recognised as promising drug targets. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
MG crystallization
POP pyrophosphate 2- biological
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
I 2 3  
Unit Cell

a=143.97Å, b=143.97Å, c=143.97Å
α=90.00, β=90.00, γ=90.00 
Solvent content
48.97  
Matthews coefficient
2.41  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
46.00-2.03Å (2.08-2.03Å)  
Rall(%)
16.8 
Rwork(%)
16.6 (22.0) 
Rfree(%)
20.5 (25.4) 
Num. observed reflections
33851 (2369) 
Num. Rfree reflections
1726 (128) 
Completeness(%)
99.9 (99.8) 

Model parameters

Num Atoms
3591  
Num Waters
198  
Num Hetatoms
232  
Model mean isotropic B factor
32.010Å2  
RMSD bond length
0.018Å  
RMSD bond angle
1.644°  
Filename uploaded
rcsb051883.pdb (uploaded on Mar 09, 2009 5:42 PM)  
Inserted
Mar 09, 2009