Database accession: MF7000467
Name: FosB with Zn and Fosfomycin (Bacillus cereus)
PDB ID: 4jh3
Experimental method: X-ray (1.50 Å)
Assembly: Homodimer
Source organism: Bacillus cereus
Primary publication of the structure:
Thompson MK, Keithly ME, Harp J, Cook PD, Jagessar KL, Sulikowski GA, Armstrong RN
Structural and chemical aspects of resistance to the antibiotic fosfomycin conferred by FosB from Bacillus cereus.
(2013) Biochemistry 52: 7350-62
PMID: 24004181
Abstract:
The fosfomycin resistance enzymes, FosB, from Gram-positive organisms, are M(2+)-dependent thiol tranferases that catalyze nucleophilic addition of either L-cysteine (L-Cys) or bacillithiol (BSH) to the antibiotic, resulting in a modified compound with no bacteriacidal properties. Here we report the structural and functional characterization of FosB from Bacillus cereus (FosB(Bc)). The overall structure of FosB(Bc), at 1.27 Å resolution, reveals that the enzyme belongs to the vicinal oxygen chelate (VOC) superfamily. Crystal structures of FosB(Bc) cocrystallized with fosfomycin and a variety of divalent metals, including Ni(2+), Mn(2+), Co(2+), and Zn(2+), indicate that the antibiotic coordinates to the active site metal center in an orientation similar to that found in the structurally homologous manganese-dependent fosfomycin resistance enzyme, FosA. Surface analysis of the FosB(Bc) structures show a well-defined binding pocket and an access channel to C1 of fosfomycin, the carbon to which nucleophilic addition of the thiol occurs. The pocket and access channel are appropriate in size and shape to accommodate L-Cys or BSH. Further investigation of the structures revealed that the fosfomycin molecule, anchored by the metal, is surrounded by a cage of amino acids that hold the antibiotic in an orientation such that C1 is centered at the end of the solvent channel, positioning the compound for direct nucleophilic attack by the thiol substrate. In addition, the structures of FosB(Bc) in complex with the L-Cys-fosfomycin product (1.55 Å resolution) and in complex with the bacillithiol-fosfomycin product (1.77 Å resolution) coordinated to a Mn(2+) metal in the active site have been determined. The L-Cys moiety of either product is located in the solvent channel, where the thiol has added to the backside of fosfomycin C1 located at the end of the channel. Concomitant kinetic analyses of FosB(Bc) indicated that the enzyme has a preference for BSH over L-Cys when activated by Mn(2+) and is inhibited by Zn(2+). The fact that Zn(2+) is an inhibitor of FosB(Bc) was used to obtain a ternary complex structure of the enzyme with both fosfomycin and L-Cys bound.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
magnesium ion binding magnesium ion binding
transferase activity, transferring alkyl or aryl (other than methyl) groups transferase activity, transferring alkyl or aryl (other than methyl) groups
Biological process:
response to antibiotic response to antibiotic
Cellular component:
cytoplasm cytoplasm
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Metallothiol transferase FosB
Source organism: Bacillus cereus
Length: 138 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMLNGINHLCFSVSNLEDSIEFYEKVLEGELLVRGRKLAYFNICGVWVALNEEIHIPRNEIYQSYTHIAFSVEQKDFESLLQRLEENDVHILKGRERDVRDCESIYFVDPDGHKFEFHSGTLQDRLNYYREDKPHMTFY
UniProtKB AC: Q739M9 (positions: 1-138)
Coverage: 100%
Name: Metallothiol transferase FosB
Source organism: Bacillus cereus
Length: 138 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMLNGINHLCFSVSNLEDSIEFYEKVLEGELLVRGRKLAYFNICGVWVALNEEIHIPRNEIYQSYTHIAFSVEQKDFESLLQRLEENDVHILKGRERDVRDCESIYFVDPDGHKFEFHSGTLQDRLNYYREDKPHMTFY
UniProtKB AC: Q739M9 (positions: 1-138)
Coverage: 100%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
The VOC superfamily of metalloenzymes is characterized by a three-dimensional domain-swapped arrangement of tandem βαβββ-motifs (PMID:24447055). The original gene duplication event led to the βαβββ tandem structure, which appears to require dimerization for stability. Two different forms of domain-swapped dimers may coexist in solution (PMID:12121648) in which both subunits of the homodimer participate in coordination of each metal ion and formation of the U-shaped active sites in the enzyme (PMID:24004181). The complex is predominantly dimeric in solution (gel filtration) (PMID:12121648).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
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