3NY4 | pdb_00003ny4

Crystal Structure of BlaC-K73A bound with Cefamandole

• PDB DOI: https://doi.org/10.2210/pdb3NY4/pdb

• Classification: HYDROLASE/ANTIBIOTIC
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-07-14 Released: 2010-11-24 
• Deposition Author(s): Tremblay, L.W., Blanchard, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.178 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Structures of the Michaelis Complex (1.2 A) and the Covalent Acyl Intermediate (2.0 A) of Cefamandole Bound in the Active Sites of the Mycobacterium tuberculosis beta-Lactamase K73A and E166A Mutants.

Tremblay, L.W., Xu, H., Blanchard, J.S.

(2010) Biochemistry 49: 9685-9687

• PubMed: 20961112 
• DOI: https://doi.org/10.1021/bi1015088
• Primary Citation Related Structures: 
  3N8S, 3NY4


• PubMed Abstract: 
  

  The genome of Mycobacterium tuberculosis (TB) contains a gene that encodes a highly active β-lactamase, BlaC, that imparts TB with resistance to β-lactam chemotherapy. The structure of covalent BlaC-β-lactam complexes suggests that active site residues K73 and E166 are essential for acylation and deacylation, respectively. We have prepared the K73A and E166A mutant forms of BlaC and have determined the structures of the Michaelis complex of cefamandole and the covalently bound acyl intermediate of cefamandole at resolutions of 1.2 and 2.0 Å, respectively. These structures provide insight into the details of the catalytic mechanism.

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Organizational Affiliation: 
• Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States.

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: 30.62 kDa 
• Atom Count: 2,419 
• Modeled Residue Count: 265 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	265	Mycobacterium tuberculosis	Mutation(s): 1  Gene Names: blaA, blaC, Rv2068c, MT2128, MTCY49.07c 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SMX	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	(6R,7R)-7-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-3-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid C18 H18 N6 O5 S2 OLVCFLKTBJRLHI-AXAPSJFSSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free:  0.178 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.804	α = 90
b = 67.915	β = 90
c = 75.524	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-24 
Deposition Author(s): Tremblay, L.W., Blanchard, J.S.

Revision History  

• Version 1.0: 2010-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-05-23
  Changes: Non-polymer description
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations