7PA5 | pdb_00007pa5

Complex between the beta-lactamase CMY-2 with an inhibitory nanobody

• PDB DOI: https://doi.org/10.2210/pdb7PA5/pdb

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


• Deposited: 2021-07-29 Released: 2022-11-16 
• Deposition Author(s): Frederic Cawez, F.C., Frederic Kerff, F.K., Moreno Galleni, M.G., Raphael Herman, R.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free: 
  0.250 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Models: experimental

Literature

Development of Nanobodies as Theranostic Agents against CMY-2-Like Class C beta-Lactamases.

Cawez, F., Mercuri, P.S., Morales-Yanez, F.J., Maalouf, R., Vandevenne, M., Kerff, F., Guerin, V., Mainil, J., Thiry, D., Saulmont, M., Vanderplasschen, A., Lafaye, P., Ayme, G., Bogaerts, P., Dumoulin, M., Galleni, M.

(2023) Antimicrob Agents Chemother 67: e0149922-e0149922

• PubMed: 36892280 
• DOI: https://doi.org/10.1128/aac.01499-22
• Primary Citation Related Structures: 
  7PA5


• PubMed Abstract: 
  

  Three soluble single-domain fragments derived from the unique variable region of camelid heavy-chain antibodies (VHHs) against the CMY-2 β-lactamase behaved as inhibitors. The structure of the complex VHH cAb _CMY-2 (254)/CMY-2 showed that the epitope is close to the active site and that the CDR3 of the VHH protrudes into the catalytic site. The β-lactamase inhibition pattern followed a mixed profile with a predominant noncompetitive component. The three isolated VHHs recognized overlapping epitopes since they behaved as competitive binders. Our study identified a binding site that can be targeted by a new class of β-lactamase inhibitors designed on the sequence of the paratope. Furthermore, the use of mono- or bivalent VHH and rabbit polyclonal anti-CMY-2 antibodies enables the development of the first generation of enzyme-linked immunosorbent assay (ELISA) for the detection of CMY-2 produced by CMY-2-expressing bacteria, irrespective of resistotype.

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Organizational Affiliation: 
• InBioS, Center for Protein Engineering, Biological Macromolecules, Department of Life Sciences, University of Liège, Liège, Belgium.
InBioS, Center for Protein Engineering, NEPTUNS, Department of Life Sciences, University of Liège, Liège, Belgium.
ALPANANO, Center for Protein Engineering & FARAH, University of Liège, Liège, Belgium.
InBios, Center for Protein Engineering, ROBOTEIN, Department of Life Sciences, University of Liège, Liège, Belgium.
InBioS, Center for Protein Engineering, Department of Life Sciences, University of Liège, Liège, Belgium.
Bacteriology, FARAH and Faculty of Veterinary Medicine, Department of Infectious and Parasitic Diseases, University of Liège, Liège, Belgium.
Regional Animal Health and Identification Association (ARSIA), Ciney, Belgium.
Immunology-Vaccinology, FARAH and Faculty of Veterinary Medicine, Department of Infectious and Parasitic Diseases, University of Liège, Liège, Belgium.
Institut Pasteur, Université Paris Cité, CNRS UMR 328, Paris, France.
National Reference Center for Antibiotic-Resistant Gram-Negative Bacilli, Department of Clinical Microbiology, CHU UCL Namur, Yvoir, Belgium.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.29 kDa 
• Atom Count: 3,773 
• Modeled Residue Count: 481 
• Deposited Residue Count: 490 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	361	Escherichia coli	Mutation(s): 0  Gene Names:  bla CMY-2, ampC, blaCMY-2, blaCMY-2-1, CMY-2, A9819_28690, AM333_27370, AM464_28260, APX88_19125, BB545_24720, BHS81_30845, BIQ87_27420, BIU72_25045, BK248_14575, BK292_11440, BK375_28010, BWI89_23710, CWM24_03220, D2184_22885, D2185_19815, D2188_23590, D9D43_21375, D9D43_30790, DS732_29990, E2129_13225, EAN77_15185, ED648_23630, ED648_28285, EJC75_03830, EJC75_22930, ELT58_15290, EO241_21750, FKC84_16435, HMQ05_23325, HMQ05_27045, HND23_22080, HND23_27950, HVX28_23930, HVZ20_24300, HVZ21_14455, KPCE_053, pAPEC1990_61_74, pAR060302_0084, pAR060302_81, peH4H_0073, pESCR_00001, WR15_23065 EC: 3.5.2.6
UniProt
Find proteins for Q53TY8 (Escherichia coli) Explore Q53TY8  Go to UniProtKB:  Q53TY8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody	B	129	Camelidae	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free:  0.250 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.12	α = 90
b = 95.12	β = 90
c = 242.94	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Frederic Cawez, F.C., Frederic Kerff, F.K., Moreno Galleni, M.G., Raphael Herman, R.H.

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary