4ADM

Crystal structure of Rv1098c in complex with meso-tartrate

PDB DOI: https://doi.org/10.2210/pdb4ADM/pdb

Classification: LYASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-12-27 Released: 2012-04-25
Deposition Author(s): Mechaly, A.E., Haouz, A., Miras, I., Weber, P., Shepard, W., Cole, S., Alzari, P.M., Bellinzoni, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 ?
R-Value Free: 0.185
R-Value Work: 0.163
R-Value Observed: 0.164

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 211.36 kDa
Atom Count: 15,056
Modelled Residue Count: 1,806
Deposited Residue Count: 1,980
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUMARATE HYDRATASE CLASS II	A, B, C, D	495	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 EC: 4.2.1.2
UniProt
Find proteins for P9WN93 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WN93 Go to UniProtKB: P9WN93
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WN93
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SRT Query on SRT Download Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C]	G [auth C], H [auth D]	S,R MESO-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-XIXRPRMCSA-N		Interactions Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain G [auth C] Focus chain H [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 ?
R-Value Free: 0.185
R-Value Work: 0.163
R-Value Observed: 0.164
Space Group: C 1 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 188.94	α = 90
b = 96.49	β = 112.44
c = 139.65	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-04-25
Type: Initial release
Version 1.1: 2012-06-06
Changes: Other
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description