4APB

Crystal structure of Mycobacterium tuberculosis fumarase (Rv1098c) S318C in complex with fumarate

• PDB DOI: https://doi.org/10.2210/pdb4APB/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-03-31 Released: 2012-04-25 
• Deposition Author(s): Bellinzoni, M., Haouz, A., Mechaly, A.E., Alzari, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.174 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 

Starting Model: experimental

Literature

Conformational Changes Upon Ligand Binding in the Essential Class II Fumarase Rv1098C from Mycobacterium Tuberculosis.

Mechaly, A.E., Haouz, A., Miras, I., Barilone, N., Weber, P., Shepard, W., Alzari, P.M., Bellinzoni, M.

(2012) FEBS Lett 586: 1606

• PubMed: 22561013 
• DOI: https://doi.org/10.1016/j.febslet.2012.04.034
• Primary Citation of Related Structures:  
  4ADL, 4ADM, 4APA, 4APB


• PubMed Abstract: 
  

  rv1098c, an essential gene in Mycobacterium tuberculosis, codes for a class II fumarase. We describe here the crystal structure of Rv1098c in complex with l-malate, fumarate or the competitive inhibitor meso-tartrate. The models reveal that substrate binding promotes the closure of the active site through conformational changes involving the catalytic SS-loop and the C-terminal domain, which likely represents a general feature of this enzyme superfamily. Analysis of ligand-enzyme interactions as well as site-directed mutagenesis suggest Ser318 as one of the two acid-base catalysts.

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Organizational Affiliation: 

Institut Pasteur, Unité de Microbiologie Structurale and CNRS-UMR3528, 25 rue du Dr. Roux, 75724 Paris cedex 15, France.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 201.12 kDa 
• Atom Count: 15,229 
• Modelled Residue Count: 1,842 
• Deposited Residue Count: 1,896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUMARATE HYDRATASE CLASS II	A, B, C, D	474	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  EC: 4.2.1.2
UniProt
Find proteins for P9WN93 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WN93  Go to UniProtKB:  P9WN93

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUM	E [auth A], G [auth B], I [auth C], J [auth D]	FUMARIC ACID C4 H4 O4 VZCYOOQTPOCHFL-OWOJBTEDSA-N
CA	F [auth A], H [auth B], K [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.174 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.997	α = 90
b = 98.736	β = 90
c = 188.171	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Bellinzoni, M., Haouz, A., Mechaly, A.E., Alzari, P.M.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2012-06-06
  Changes: Other
• Version 1.2: 2012-07-18
  Changes: Atomic model, Derived calculations, Non-polymer description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other
• Version 2.1: 2023-12-20
  Changes: Refinement description