5NJ2 | pdb_00005nj2

Crystal structure of BlaC from Mycobacterium tuberculosis bound to phosphate

PDB DOI: https://doi.org/10.2210/pdb5NJ2/pdb

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

Deposited: 2017-03-27 Released: 2017-11-15
Deposition Author(s): Tassoni, R., Pannu, N.S., Ubbink, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free:
0.190 (Depositor), 0.195 (DCC)
R-Value Work:
0.167 (Depositor), 0.176 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Phosphate Promotes the Recovery of Mycobacterium tuberculosis beta-Lactamase from Clavulanic Acid Inhibition.

Elings, W., Tassoni, R., van der Schoot, S.A., Luu, W., Kynast, J.P., Dai, L., Blok, A.J., Timmer, M., Florea, B.I., Pannu, N.S., Ubbink, M.

(2017) Biochemistry 56: 6257-6267

PubMed: 29087696 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.7b00556
Primary Citation Related Structures:
5NJ2, 5OYO

PubMed Abstract:
The rise of multi- and even totally antibiotic resistant forms of Mycobacterium tuberculosis underlines the need for new antibiotics. The pathogen is resistant to β-lactam compounds due to its native serine β-lactamase, BlaC. This resistance can be circumvented by administration of a β-lactamase inhibitor. We studied the interaction between BlaC and the inhibitor clavulanic acid. Our data show hydrolysis of clavulanic acid and recovery of BlaC activity upon prolonged incubation. The rate of clavulanic acid hydrolysis is much higher in the presence of phosphate ions. A specific binding site for phosphate is identified in the active site pocket, both in the crystalline state and in solution. NMR spectroscopy experiments show that phosphate binds to this site with a dissociation constant of 30 mM in the free enzyme. We conclude that inhibition of BlaC by clavulanic acid is reversible and that phosphate ions can promote the hydrolysis of the inhibitor.

Organizational Affiliation

Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands.

Macromolecule Content

Total Structure Weight: 59.95 kDa
Atom Count: 4,416
Modeled Residue Count: 537
Deposited Residue Count: 548
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	274	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: blaC, ERS027646_02769 EC: 3.5.2.6
UniProt
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKD3 Go to UniProtKB: P9WKD3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WKD3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AE4 Query on AE4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL C₁₂ H₂₆ O₆ NJRFAMBTWHGSDE-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
ETE Query on ETE Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₉ H₂₀ O₅ ZNYRFEPBTVGZDN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], G [auth B], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	D [auth A], E [auth A], F [auth A], I [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free: 0.190 (Depositor), 0.195 (DCC)
R-Value Work: 0.167 (Depositor), 0.176 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.591	α = 101.28
b = 41.683	β = 90.11
c = 76.841	γ = 90.43

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-11-15

Deposition Author(s):

Tassoni, R.

Pannu, N.S.

Ubbink, M.

Revision History (Full details and data files)

Version 1.0: 2017-11-15
Type: Initial release
Version 1.1: 2017-12-06
Changes: Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description