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Structure of IDP01002

Structure of IDP01002, a putative oxidoreductase from and essential gene of Salmonella typhimurium

Edit deposit information
CSGID target
IDP01002 
PDB Id
3ERP (NCBI MMDB
Authors
A.U.Singer,G.Minasov,E.Evdokimova,J.S.Brunzelle,M.Kudritska,A.M.Edwards,W.F.Anderson,A.Savchenko,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Alexander Singer 
Responsible lab
University of Calgary 
Deposition Date
Oct 02, 2008 
Release Date
Nov 04, 2008 

Annotation

Description
Oxidoreductases are implicated in a number of pathways and no specific role has been yet associated to STM2406 from S. typhimurium, although it has been determined to be an essential gene of this organism. It shares 58% sequence identity to YghZ, an alpha-aldo-ketoreductase for the toxic metabolic bi-product methylglyoxyl (FEMS Microbiol Lett. 2003 Jan 21;218(1):93-9). In addition YghZ could also be a more promiscuous aldo-ketoreductase; a recent paper has pointed to the possibility that YghZ could catalyze the stereospecific, NADPH-dependent reduction of l-glyceraldehyde 3-phosphate and thus provide another route to synthesis of dihydroxyacetone phosphate as a way to bipass Triose phosphate isomerase (Biochemistry. 2008 Aug 5; 47(31):7983-5). The fold is characteristic of this group of enzymes and comprises a parallel beta/alpha-barrel. A catalytic quartet of residues was found: Tyr-66, His-138, Lys-97 and Asp-61. 
Functional assignment
Oxidoreductase 

Ligands

Ligand code Name Ligand type
CAC cacodylate ion
CL
EDO
NA Sodium ion
ZN

Structure information

Unit cell parameters

Space Group
I 4  
Unit Cell

a=127.10Å, b=127.10Å, c=120.49Å
α=90.00, β=90.00, γ=90.00 
Solvent content
59.69  
Matthews coefficient
3.05  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.96-1.55Å (1.59-1.55Å)  
Rall(%)
15.5 
Rwork(%)
15.3 (25.8) 
Rfree(%)
17.8 (27.0) 
Num. observed reflections
132729 (7590) 
Num. Rfree reflections
6769 (410) 
Completeness(%)
96.8 (75.4) 

Model parameters

Num Atoms
5559  
Num Waters
844  
Num Hetatoms
977  
Model mean isotropic B factor
23.404Å2  
RMSD bond length
0.014Å  
RMSD bond angle
1.517°  
Filename uploaded
validate12.pdb (uploaded on Oct 27, 2008 4:11 PM)  
Inserted
Oct 27, 2008