4EMN | pdb_00004emn

Crystal structure of RpfB catalytic domain in complex with benzamidine

PDB DOI: https://doi.org/10.2210/pdb4EMN/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-12 Released: 2013-02-27
Deposition Author(s): Ruggiero, A., Marchant, J., Squeglia, F., Makarov, V., De Simone, A., Berisio, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.17 Å
R-Value Free:
0.188 (Depositor), 0.199 (DCC)
R-Value Work:
0.127 (Depositor)
R-Value Observed:
0.129 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Molecular determinants of inactivation of the resuscitation promoting factor B from Mycobacterium tuberculosis.

Ruggiero, A., Marchant, J., Squeglia, F., Makarov, V., De Simone, A., Berisio, R.

(2013) J Biomol Struct Dyn 31: 195-205

PubMed: 22831279 Search on PubMed
DOI: https://doi.org/10.1080/07391102.2012.698243
Primary Citation Related Structures:
4EMN

PubMed Abstract:
Inactivation of revival of Mycobacterium tuberculosis from dormancy is one of the main goals of the WHO Global Plan to stop tuberculosis (TB) 2011-2015, given the huge reservoir of latently infected individuals. This process requires a group of secreted proteins, denoted as resuscitation-promoting factors (Rpfs). Of these, RpfB is the sole member indispensable for resuscitation in vivo. The first class of inhibitors of RpfB was identified among 2-nitrophenylthiocyanates. However, their inactivation mechanism is hitherto not known. To gain insight into the inactivation mechanism of one of the most promising RpfB inhibitors, 4-benzoyl-2-nitrophenyl thiocyanate, NPT7, we have performed replica exchange molecular dynamics (REMD) simulations, starting from the crystal structure of RpfB catalytic domain, derived in this study. We validated our results by resuscitation experiments of M. tuberculosis cultures. The atomic resolution crystal structure of RpfB catalytic domain identified the potential of the enzyme catalytic cleft to bind benzene rings. REMD simulations, 48 replicas, identified the key interactions for the binding of NPT7 to RpfB catalytic site. Of these, an important role is played by the thiocyanate group of NPT7. Consistently, we prove that the substitution of this group implies a complete loss of RpfB inactivation. Our results provide valuable information for modifications of NPT7 structure to enhance its binding affinity to RpfB, with the final aim of developing second-generation inhibitors of therapeutic interest in TB eradication strategy.

Organizational Affiliation

Institute of Biostructure and Bioimaging, CNR, Naples, Italy.

Macromolecule Content

Total Structure Weight: 35.28 kDa
Atom Count: 3,033
Modeled Residue Count: 322
Deposited Residue Count: 324
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable resuscitation-promoting factor rpfB	A, B, C, D	81	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: MT1038, rpfB, Rv1009 EC: 3
UniProt
Find proteins for P9WG29 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG29 Go to UniProtKB: P9WG29
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WG29
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEN Query on BEN Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.17 Å
R-Value Free: 0.188 (Depositor), 0.199 (DCC)
R-Value Work: 0.127 (Depositor)
R-Value Observed: 0.129 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.545	α = 90
b = 50.733	β = 104.09
c = 66.421	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-02-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-27
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary