6N14 | pdb_00006n14

Phosphoserine BlaC, Class A serine beta-lactamase from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb6N14/pdb

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


• Deposited: 2018-11-08 Released: 2019-08-28 
• Deposition Author(s): Moural, T.W., White, D.S., Choy, C.J., Kang, C., Berkman, C.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Phosphoserine BlaC fromMycobacterium tuberculosisInactivated by Bis(Benzoyl) Phosphate.

Moural, T.W., White, D.S., Choy, C.J., Kang, C., Berkman, C.E.

(2019) Int J Mol Sci 20

• PubMed: 31269656 
• DOI: https://doi.org/10.3390/ijms20133247
• Primary Citation Related Structures: 
  6N14


• PubMed Abstract: 
  

  Mycobacterium tuberculosis , the pathogen responsible for tuberculosis (TB), is the leading cause of death from infectious disease worldwide. The class A serine β-lactamase BlaC confers Mycobacterium tuberculosis resistance to conventional β-lactam antibiotics. As the primary mechanism of bacterial resistance to β-lactam antibiotics, the expression of a β-lactamase by Mycobacterium tuberculosis results in hydrolysis of the β-lactam ring and deactivation of these antibiotics. In this study, we conducted protein X-ray crystallographic analysis of the inactivation of BlaC, upon exposure to the inhibitor bis(benzoyl) phosphate. Crystal structure data confirms that serine β-lactamase is phosphorylated at the catalytic serine residue (Ser-70) by this phosphate-based inactivator. This new crystallographic evidence suggests a mechanism for phosphorylation of BlaC inhibition by bis(benzoyl) phosphate over acylation. Additionally, we confirmed that bis(benzoyl) phosphate inactivated BlaC in a time-dependent manner.

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Organizational Affiliation: 
• Department of Chemistry, Washington State University, Pullman, WA 99164, USA.
Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
Department of Chemistry, Washington State University, Pullman, WA 99164, USA. [e-mail].
Department of Chemistry, Washington State University, Pullman, WA 99164, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 32.89 kDa 
• Atom Count: 2,328 
• Modeled Residue Count: 265 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	307	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.84	α = 90
b = 68.037	β = 90
c = 75.454	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Moural, T.W., White, D.S., Choy, C.J., Kang, C., Berkman, C.E.

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary