6cqs | pdb_00006cqs
Sediminispirochaeta smaragdinae SPS-1 metallo-beta-lactamase
Structural highlights
Publication Abstract from PubMedIn an effort to evaluate whether a recently reported putative metallo-beta-lactamase (MbetaL) contains a novel MbetaL 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 beta-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 Zn1 metal binding site. This site was confirmed with a crystal structure of the enzyme. The structure shows a Zn2 site that is similar to that in NDM-1 and other subclass B1 MbetaLs; however, the Zn1 metal ion is coordinated by two histidine residues and a water molecule, which is held in position by a hydrogen bond network. The Zn1 metal is displaced nearly 1 A from the position reported in other MbetaLs. 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 beta-lactam antibiotics. This study reveals a novel metal binding site in MbetaLs and suggests that the targeting of metal binding sites in MbetaLs with inhibitors is now more challenging with the identification of this new MbetaL. 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 RL, Fullington S, Bretz SL, Nix JC, Bonomo RA, Tierney DL, Page RC, Crowder MW Biochemistry. 2018 Aug 21. doi: 10.1021/acs.biochem.8b00728. PMID:30106565[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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