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Structure of IDP01071

Crystal structure of the Salmonella typhimurium FadA 3-ketoacyl-CoA thiolase

Edit deposit information
CSGID target
IDP01071 
PDB Id
3GOA (NCBI MMDB
Authors
S.M.Anderson,T.Skarina,O.Onopriyenko,Z.Wawrzak,L.Papazisi,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Spencer Anderson 
Responsible lab
Northwestern University 
Deposition Date
Mar 18, 2009 
Release Date
Mar 31, 2009 

Annotation

Description
3-ketoacyl-CoA thiolase is part of a complex of enzymes that work together to catabolize fatty acids. The protein catalyzes the final step of the beta-oxidation cycle by reversibly splitting the 3-ketoacyl-CoA substrate into acetyl-CoA and acyl-CoA. The acyl-CoA product is reduced in length by 2 carbons and is free to enter another fatty acid beta-oxidation cycle. 3-ketoacyl-CoA thiolase is an alpha and beta protein with a thiolase-like fold. The entire enzyme complex composed of 3-ketoacyl-CoA thiolase, 2-Enoyl-CoA hydratase and L-3-Hydroxyacyl-CoA dehydrogenase has been crystallized from Pseudomonas fragi in complex with Acetyl CoA and NAD+ (1WDK). 3-ketoacyl-CoA thiolase from P. fragi has 61% identity and 1.1Å RMSD with the current Salmonella typhimurium structure. The part of the molecule that is in contact with 2-Enoyl-CoA hydratase in the enzyme complex forms an alpha-helix, but is completely disordered in this structure. Although Acetyl-CoA was added to the mother liquor, there is no ordered electron density for it and the catalytic triad of Cys91, Cys373, and His343 are only in contact with ordered water. Other structures of 3-ketoacyl-CoA thiolase include those from Thermus thermophilus (1ULQ), Homo sapiens (1WL4) and Zoogloea ramigera (1M1T). Ishikawa, M., Tsuchiya, D., Oyama, T., Tsunaka, Y., Morikawa, K. (2004) Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex Embo J. 23: 2745-2754 Kim J.P., Battaile K.P. (2002) Burning fat: the structural basis of fatty acid beta-oxidation. Curr Opin Struct Biol 12: 721–728  
Functional assignment
 

Ligands

Ligand code Name Ligand type
CA
CL CHLORIDE ION
NA Sodium ion
MSE modified residue

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=73.00Å, b=64.50Å, c=74.40Å
α=90.00, β=104.50, γ=90.00 
Solvent content
39.09  
Matthews coefficient
2.02  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
30.00-1.70Å (1.74-1.70Å)  
Rall(%)
14.5 
Rwork(%)
14.2 (21.8) 
Rfree(%)
19.2 (29.2) 
Num. observed reflections
77669 (5049) 
Num. Rfree reflections
3883 (237) 
Completeness(%)
99.3 (92.6) 

Model parameters

Num Atoms
5422  
Num Waters
976  
Num Hetatoms
1326  
Model mean isotropic B factor
17.000Å2  
RMSD bond length
0.014Å  
RMSD bond angle
1.443°  
Filename uploaded
rcsb052109.pdb (uploaded on Mar 27, 2009 2:52 PM)  
Inserted
Mar 27, 2009