Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.91 kDa 
• Atom Count: 2,097 
• Modelled Residue Count: 264 
• Deposited Residue Count: 275 
• Unique protein chains: 1

 7UHN

Time-Resolved Structure of Metallo Beta-Lactamase L1 in a Complex with Cleaved Moxalactam (300 ms Snapshot)

• PDB DOI:  https://doi.org/10.2210/pdb7UHN/pdb

• Classification: HYDROLASE
• Organism(s): Stenotrophomonas maltophilia K279a
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-03-27 Released: 2022-04-13 
• Deposition Author(s): Wilamowski, M., Kim, Y., Sherrell, D.A., Lavens, A., Henning, R., Maltseva, N., Endres, M., Babnigg, G., Srajer, V., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Time-resolved beta-lactam cleavage by L1 metallo-beta-lactamase.

Wilamowski, M., Sherrell, D.A., Kim, Y., Lavens, A., Henning, R.W., Lazarski, K., Shigemoto, A., Endres, M., Maltseva, N., Babnigg, G., Burdette, S.C., Srajer, V., Joachimiak, A.

(2022) Nat Commun 13: 7379-7379

• PubMed: 36450742 
• DOI: https://doi.org/10.1038/s41467-022-35029-3
• Primary Citation of Related Structures:  
  7L91, 7UHH, 7UHI, 7UHJ, 7UHK, 7UHL, 7UHM, 7UHN, 7UHO, 7UHP, 7UHQ, 7UHR, 7UHS, 7UHT


• PubMed Abstract: 
  

Serial x-ray crystallography can uncover binding events, and subsequent chemical conversions occurring during enzymatic reaction. Here, we reveal the structure, binding and cleavage of moxalactam antibiotic bound to L1 metallo-β-lactamase (MBL) from Stenotrophomonas maltophilia. Using time-resolved serial synchrotron crystallography, we show the time course of β-lactam hydrolysis and determine ten snapshots (20, 40, 60, 80, 100, 150, 300, 500, 2000 and 4000 ms) at 2.20 Å resolution. The reaction is initiated by laser pulse releasing Zn ²⁺ ions from a UV-labile photocage. Two metal ions bind to the active site, followed by binding of moxalactam and the intact β-lactam ring is observed for 100 ms after photolysis. Cleavage of β-lactam is detected at 150 ms and the ligand is significantly displaced. The reaction product adjusts its conformation reaching steady state at 2000 ms corresponding to the relaxed state of the enzyme. Only small changes are observed in the positions of Zn ²⁺ ions and the active site residues. Mechanistic details captured here can be generalized to other MBLs.

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Organizational Affiliation: 

Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)	A	275	Stenotrophomonas maltophilia K279a	Mutation(s): 0  Gene Names: Smlt2667 EC: 3.5.2.6
UniProt
Find proteins for B2FTM1 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FTM1  Go to UniProtKB:  B2FTM1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XQP (Subject of Investigation/LOI)	D [auth A]	(2R)-2-[(R)-carboxy{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}methoxymethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-oxazine-4-carboxylic acid C20 H22 N6 O10 S BNVHAJAUCCPJNC-WYAVIUHXSA-N
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.853	α = 90
b = 105.853	β = 90
c = 99.1	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOLREP	phasing
Precognition	data reduction
Epinorm	data scaling

Structure Validation

Currently 7UHN does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-13 
Deposition Author(s): Wilamowski, M., Kim, Y., Sherrell, D.A., Lavens, A., Henning, R., Maltseva, N., Endres, M., Babnigg, G., Srajer, V., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2022-04-13
  Type: Initial release
  
• Version 1.1: 2023-02-08
  Changes: Database references