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Structure of IDP00577

1.84 Angstrom resolution crystal structure of 3-oxoacyl-(acyl carrier protein) synthase I (fabB) from Yersinia pestis CO92

Edit deposit information
CSGID target
IDP00577 
PDB Id
3OYT (NCBI MMDB
Authors
A.S.Halavaty,Z.Wawrzak,O.Onopriyenko,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
Sep 23, 2010 
Release Date
Jan 12, 2011 

Annotation

Description
Beta-ketoacyl-acyl carrier protein (ACP) synthase enzymes join short carbon units to construct fatty acyl chains by a three-step Claisen condensation reaction. The reaction starts with a trans thioesterification of the acyl primer substrate from ACP to the enzyme. Subsequently, the donor substrate malonyl-ACP is decarboxylated to form a carbanion intermediate, which in the third step attacks C1 of the primer substrate giving rise to an elongated acyl chain. The IDP00577 protein, 3-oxoacyl-(acyl carrier protein) synthase I from Yersinia pestis CO92, was co-crystallized with CoA, however, there was no ligand bound in the final Se-Met structure (PDB ID code 3OYT). Nevertheless, the catalytic Cys164 in chain A seems to be covalently modified with an unknown ligand, which was not modeled because of its noncontinuous electron density. This ligand is solvent oriented, whereas caprylic acid in the homologous 3-oxoacyl-(acyl carrier protein) synthase I structure from E.coli (PDB ID code 2BUI), which covalently bound to Cys163, is embedded into a narrow strongly hydrophobic pocket of the protein. Phe393 (in our structure) and Phe392 (2BUI) might function as a gate residue allowing the relocation of covalently bound product from the solvent side, i.e. from the substrate-binding site to the protein's core. The Phe393 in chain B has alternative side chain conformations, which shows close and open state of the aforementioned pocket. Moreover, Met139 in the 3OYT structure adopts alternative side chain conformations in response to the position of Phe393 side chain. The stretch of residues 268 through 275 in the Y. pestis fabB structure adopts a loop conformation. The loop hides a possible area of fabB that is used by the protein’s substrate(s) for interaction. The loop is ordered in chain A and flexible in chain B, indicating that the mobility of this secondary structure element might be a requirement for the productive complex formation between fabB and its substrate(s). The C-alpha atom of Val271 in the loop is 4.8 A from the C-alpha atom of aforementioned Phe393.  
Functional assignment
Transferase 

Ligands

Ligand code Name Ligand type
PO4 PHOSPHATE ION crystallization
MSE modified residue
PG4 crystallization
K crystallization
EDO crystallization
PEG crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 21 21 2  
Unit Cell

a=109.65Å, b=114.61Å, c=59.16Å
α=90.00, β=90.00, γ=90.00 
Solvent content
41.65  
Matthews coefficient
2.11  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.58-1.84Å (1.89-1.84Å)  
Rall(%)
15.7 
Rwork(%)
15.5 (21.4) 
Rfree(%)
19.3 (27.6) 
Num. observed reflections
64318 (4199) 
Num. Rfree reflections
3280 (201) 
Completeness(%)
99.0 (89.1) 

Model parameters

Num Atoms
5693  
Num Waters
651  
Num Hetatoms
1116  
Model mean isotropic B factor
19.040Å2  
RMSD bond length
0.014Å  
RMSD bond angle
1.659°  
Filename uploaded
3OYT.pdb (uploaded on Sep 28, 2011 11:09 AM)  
Inserted
Sep 23, 2010