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Structure of IDP02325

1.99 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor'

Edit deposit information
CSGID target
IDP02325 
PDB Id
3IMF (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,T.Skarina,O.Onopriyenko,E.Gordon,S.Peterson,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Aug 10, 2009 
Release Date
Aug 18, 2009 

Annotation

Description
The apo-structure of the B. anthracis short-chain dehydrogenase/reductase (SCD/R) has been determined. The protein of unknown specificity shares ~44 % sequence identity with the human mitochondrial 2,4-dienoyl-CoA reductase (PDB IDs: 1W73, 1W8D and 1W6U). Except for the N- and C-terminal extensions of the human enzyme, both proteins exhibit identical fold, which is a single alpha/beta domain with the dinucleotide binding “Rossmann” fold, characteristic for the SCD/R family. The rmsd of their C-alpha positions is 1.3-1.6 Å. The human homolog catalyzes the reduction of 2,4-dienoyl-CoA to enoyl-CoA, which then enters the beta-oxidation cycle. Interestingly, known bacterial 2,4-dienoyl-CoA reductase from E. coli (PDB ID 1PS9) is structurally unrelated to two mentioned proteins and binds a different set of cofactors, FAD, FMN and 4Fe-4S cluster. Homologous SCD/Rs are homotetramers in the crystal lattice with their coenzyme- and substrate-binding sites being almost entirely exposed to the solvent. This is one of the reasons why there are not big structural perturbations upon association of NADP, binding and processing of the substrate. Indeed, pairwise structural alignment of 3IMF and 1W8D/1W6U indicates that structural changes due to association of the ligands are small in magnitude. However, co-crystallization of the Bacillus homolog with NADP and its structure determination are required to confirm these observations. Identical distortion of the active site region spanning residues (190-200 in 3IMF; 245-255 in 1W8D) may reflect broad substrate specificity of the human and perhaps bacterial SCD/R. Identification of potential substrate(s) of the bacterial enzyme is desired.  
Functional assignment
short-chain dehydrogenase/reductase 

Ligands

Ligand code Name Ligand type
MSE selenomethionine modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=174.24Å, b=89.56Å, c=71.78Å
α=90.00, β=111.60, γ=90.00 
Solvent content
46.3  
Matthews coefficient
2.29  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
30.00-1.99Å (2.05-1.99Å)  
Rall(%)
16.8 
Rwork(%)
16.6 (16.9) 
Rfree(%)
20.6 (21.7) 
Num. observed reflections
69189 (4749) 
Num. Rfree reflections
3459 (240) 
Completeness(%)
98.8 (91.8) 

Model parameters

Num Atoms
7356  
Num Waters
592  
Num Hetatoms
982  
Model mean isotropic B factor
17.700Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.376°  
Filename uploaded
3IMF.pdb (uploaded on Sep 17, 2010 6:59 PM)  
Inserted
Aug 10, 2009