6CQS

Sediminispirochaeta smaragdinae SPS-1 metallo-beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Noncanonical Metal Center Drives the Activity of the Sediminispirochaeta smaragdinae Metallo-beta-lactamase SPS-1.

Cheng, Z.VanPelt, J.Bergstrom, A.Bethel, C.Katko, A.Miller, C.Mason, K.Cumming, E.Zhang, H.Kimble, R.L.Fullington, S.Bretz, S.L.Nix, J.C.Bonomo, R.A.Tierney, D.L.Page, R.C.Crowder, M.W.

(2018) Biochemistry 57: 5218-5229

  • DOI: 10.1021/acs.biochem.8b00728

  • PubMed Abstract: 
  • In an effort to evaluate whether a recently reported putative metallo-β-lactamase (MβL) contains a novel MβL active site, SPS-1 from Sediminispirochaeta smaragdinae was overexpressed, purified, and characterized using spectroscopic and crystallograph ...

    In an effort to evaluate whether a recently reported putative metallo-β-lactamase (MβL) contains a novel MβL active site, SPS-1 from Sediminispirochaeta smaragdinae was overexpressed, purified, and characterized using spectroscopic and crystallographic studies. Metal analyses demonstrate that recombinant SPS-1 binds nearly 2 equiv of Zn(II), and steady-state kinetic studies show that the enzyme hydrolyzes carbapenems and certain cephalosporins but not β-lactam substrates with bulky substituents at the 6/7 position. Spectroscopic studies of Co(II)-substituted SPS-1 suggest a novel metal center in SPS-1, with a reduced level of spin coupling between the metal ions and a novel Zn 1 metal binding site. This site was confirmed with a crystal structure of the enzyme. The structure shows a Zn 2 site that is similar to that in NDM-1 and other subclass B1 MβLs; however, the Zn 1 metal ion is coordinated by two histidine residues and a water molecule, which is held in position by a hydrogen bond network. The Zn 1 metal is displaced nearly 1 Å from the position reported in other MβLs. The structure also shows extended helices above the active site, which create a binding pocket that precludes the binding of substrates with large, bulky substituents at the 6/7 position of β-lactam antibiotics. This study reveals a novel metal binding site in MβLs and suggests that the targeting of metal binding sites in MβLs with inhibitors is now more challenging with the identification of this new MβL.


    Organizational Affiliation

    Molecular Biology Consortium, Beamline 4.2.2, Advanced Light Source , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Research Service , Louis Stokes Cleveland Department of Veterans Affairs Medical Center , Cleveland , Ohio 44106 , United States.,Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics, and Bioinformatics and CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology , Case Western Reserve University , Cleveland , Ohio 44106 , United States.,Department of Chemistry and Biochemistry , Miami University , 651 East High Street, 160 Hughes Laboratories , Oxford , Ohio 45056 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
246Sediminispirochaeta smaragdinae (strain DSM 11293 / JCM 15392 / SEBR 4228)Mutation(s): 0 
EC: 3.5.2.6
Find proteins for E1R245 (Sediminispirochaeta smaragdinae (strain DSM 11293 / JCM 15392 / SEBR 4228))
Go to UniProtKB:  E1R245
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.176 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 73.601α = 90.00
b = 73.601β = 90.00
c = 108.784γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM111926

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-05
    Type: Data collection, Database references
  • Version 1.2: 2018-09-12
    Type: Data collection, Database references