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Structure of IDP00499

1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis.

Edit deposit information
CSGID target
IDP00499 
PDB Id
3IIE (NCBI MMDB
Authors
J.Osipiuk,R.Mulligan,J.Stam,W.F.Anderson,A.Joachimiak 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jul 31, 2009 
Release Date
Aug 11, 2009 

Annotation

Description
1-deoxy-D-xylulose 5-phosphate reductoisomerases catalyze the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate (DXP) in the presence of NADPH. This reaction is the second step of the deoxyxylulose 5-phosphate/methylerythritol 4-phosphate pathway (the terpenoid biosynthesis pathway) found in many bacteria and plants. The end product, isopentenyl diphosphate, is the precursor of various isoprenoids vital to all living organisms. This pathway is not found in humans, where the mevalonate pathway is used for the formation of isopentenyl diphosphate instead. This aspect makes the reductoisomerase an excellent drug target in a number of pathogenic organisms. The family of 1-deoxy-D-xylulose 5-phosphate reductoisomerases is a member of the FAD/NAD(P)-binding Rossmann fold Superfamily. The superfamily contains redox enzymes consisting of two domains. One domain determines substrate specificity and the reaction of the enzyme. The other domain, which is common to this superfamily, is a Rossmann-fold domain and binds nicotinamide adenine dinucleotide (NAD+). 
Functional assignment
 

Ligands

Ligand code Name Ligand type
MG MAGNESIUM ION
EDO

Structure information

Unit cell parameters

Space Group
P 32 2 1  
Unit Cell

a=121.46Å, b=121.46Å, c=86.92Å
α=90.00, β=90.00, γ=120.00 
Solvent content
42.28  
Matthews coefficient
2.13  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
50.00-2.21Å (2.27-2.21Å)  
Rall(%)
18.2 
Rwork(%)
17.9 (27.3) 
Rfree(%)
24.1 (29.7) 
Num. observed reflections
39152 (2651) 
Num. Rfree reflections
1957 (124) 
Completeness(%)
99.8 (97.7) 

Model parameters

Num Atoms
5947  
Num Waters
227  
Num Hetatoms
234  
Model mean isotropic B factor
38.870Å2  
RMSD bond length
0.019Å  
RMSD bond angle
1.757°  
Filename uploaded
rcsb054449.pdb (uploaded on Aug 04, 2009 12:12 PM)  
Inserted
Aug 04, 2009