2PFC | pdb_00002pfc

Structure of Mycobacterium tuberculosis Rv0098

• PDB DOI: https://doi.org/10.2210/pdb2PFC/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-04-04 Released: 2008-04-08 
• Deposition Author(s): Wang, F., Sacchettini, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.273 (Depositor) 
• R-Value Work: 
  0.235 (Depositor) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Identification of a type III thioesterase reveals the function of an operon crucial for Mtb virulence.

Wang, F., Langley, R., Gulten, G., Wang, L., Sacchettini, J.C.

(2007) Chem Biol 14: 543-551

• PubMed: 17524985 
• DOI: https://doi.org/10.1016/j.chembiol.2007.04.005
• Primary Citation Related Structures: 
  2PFC


• PubMed Abstract: 
  

  Rv0098 is part of an operon, Rv0096-Rv0101, from Mycobacterium tuberculosis (Mtb) that is essential for Mtb's survival in mouse macrophages. This operon also contains an acyl carrier protein and one of the only two nonribosomal peptide synthases in Mtb. Rv0098 is annotated in the genome as a hypothetical protein and was proposed to be an acyl-coenzyme A (CoA) dehydratase. The structure of Rv0098, together with subsequent biochemical analysis, indicated that Rv0098 is a long-chain fatty acyl-CoA thioesterase (FcoT). However, FcoT lacks a general base or a nucleophile that is always found in the catalytic site of type II and type I thioesterases, respectively. The active site of Mtb FcoT reveals the structural basis for its substrate specificity for long-chain acyl-CoA and allows us to propose a catalytic mechanism for the enzyme. The characterization of Mtb FcoT provides a putative function of this operon that is crucial for Mtb pathogenicity.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.81 kDa 
• Atom Count: 1,310 
• Modeled Residue Count: 160 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein Rv0098/MT0107	A	183	Mycobacterium tuberculosis	Mutation(s): 0  EC: 3.1.2.2 (UniProt), 4.3.2.11 (UniProt), 3.1.2 (UniProt)
UniProt
Find proteins for P9WM67 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WM67  Go to UniProtKB:  P9WM67

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM	B [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.273 (Depositor) 
• R-Value Work:  0.235 (Depositor) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.767	α = 90
b = 101.767	β = 90
c = 101.767	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-08 
Deposition Author(s): Wang, F., Sacchettini, J.C.

Revision History  

• Version 1.0: 2008-04-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary