6CQS

Sediminispirochaeta smaragdinae SPS-1 metallo-beta-lactamase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    6CQS

  • 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 crystallographic studies ...

    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: 

    Department of Chemistry and Biochemistry , Miami University , 651 East High Street, 160 Hughes Laboratories , Oxford , Ohio 45056 , United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamaseA246Sediminispirochaeta smaragdinae DSM 11293Mutation(s): 0 
Gene Names: Spirs_2827
EC: 3.5.2.6
UniProt
Find proteins for E1R245 (Sediminispirochaeta smaragdinae (strain DSM 11293 / JCM 15392 / SEBR 4228))
Explore E1R245 
Go to UniProtKB:  E1R245
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1R245
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.601α = 90
b = 73.601β = 90
c = 108.784γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM111926

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence