Database accession: MF7000485
Name: Fosfomycin resistance protein (Klebsiella pneumoniae)
PDB ID: 5v91
Experimental method: X-ray (1.30 Å)
Assembly: Homodimer
Source organism: Klebsiella pneumoniae 30660/NJST258_1
Primary publication of the structure:
Klontz EH, Tomich AD, Günther S, Lemkul JA, Deredge D, Silverstein Z, Shaw JF, McElheny C, Doi Y, Wintrode PL, MacKerell AD, Sluis-Cremer N, Sundberg EJ
Structure and Dynamics of FosA-Mediated Fosfomycin Resistance in Klebsiella pneumoniae and Escherichia coli.
(2017) Antimicrob. Agents Chemother. 61:
PMID: 28874374
Abstract:
Fosfomycin exhibits broad-spectrum antibacterial activity and is being reevaluated for the treatment of extensively drug-resistant pathogens. Its activity in Gram-negative organisms, however, can be compromised by expression of FosA, a metal-dependent transferase that catalyzes the conjugation of glutathione to fosfomycin, rendering the antibiotic inactive. In this study, we solved the crystal structures of two of the most clinically relevant FosA enzymes: plasmid-encoded FosA3 from Escherichia coli and chromosomally encoded FosA from Klebsiella pneumoniae (FosAKP). The structure, molecular dynamics, catalytic activity, and fosfomycin resistance of FosA3 and FosAKP were also compared to those of FosA from Pseudomonas aeruginosa (FosAPA), for which prior crystal structures exist. E. coli TOP10 transformants expressing FosA3 and FosAKP conferred significantly greater fosfomycin resistance (MIC, >1,024 μg/ml) than those expressing FosAPA (MIC, 16 μg/ml), which could be explained in part by the higher catalytic efficiencies of the FosA3 and FosAKP enzymes. Interestingly, these differences in enzyme activity could not be attributed to structural differences at their active sites. Instead, molecular dynamics simulations and hydrogen-deuterium exchange experiments with FosAKP revealed dynamic interconnectivity between its active sites and a loop structure that extends from the active site of each monomer and traverses the dimer interface. This dimer interface loop is longer and more extended in FosAKP and FosA3 than in FosAPA, and kinetic analyses of FosAKP and FosAPA loop-swapped chimeric enzymes highlighted its importance in FosA activity. Collectively, these data yield novel insights into fosfomycin resistance that could be leveraged to develop new strategies to inhibit FosA and potentiate fosfomycin activity.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
metal ion binding metal ion binding
Biological process: not assigned
Cellular component: not assigned
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: Fosfomycin resistance protein
Source organism: Klebsiella pneumoniae 30660/NJST258_1
Length: 139 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMLSGLNHLTLAVSQLAPSVAFYQQLLGMTLHARWDSGAYLSCGDLWLCLSLDPQRRVTPPEESDYTHYAFSISEADFASFAARLEAAGVAVWKLNRSEGASHYFLDPDGHKLELHVGSLAQRLAACREQPYKGMVFFEQ
UniProtKB AC: A0A0E1CQ35 (positions: 1-138)
Coverage: 99%
Name: Fosfomycin resistance protein
Source organism: Klebsiella pneumoniae 30660/NJST258_1
Length: 139 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMLSGLNHLTLAVSQLAPSVAFYQQLLGMTLHARWDSGAYLSCGDLWLCLSLDPQRRVTPPEESDYTHYAFSISEADFASFAARLEAAGVAVWKLNRSEGASHYFLDPDGHKLELHVGSLAQRLAACREQPYKGMVFFEQ
UniProtKB AC: A0A0E1CQ35 (positions: 1-138)
Coverage: 99%
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)
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