Database accession: MF7000103
Name: FosX (Listeria monocytogenes, hexagonal form)
PDB ID: 2p7k
Experimental method: X-ray (3.30 Å)
Assembly: Homodimer
Source organism: Listeria monocytogenes serovar 1/2a
Primary publication of the structure:
Fillgrove KL, Pakhomova S, Schaab MR, Newcomer ME, Armstrong RN
Structure and mechanism of the genomically encoded fosfomycin resistance protein, FosX, from Listeria monocytogenes.
(2007) Biochemistry 46: 8110-20
PMID: 17567049
Abstract:
The fosfomycin resistance protein, FosX, catalyzes the hydration of the antibiotic fosfomycin, (1R,2S)-epoxypropylphosphonic acid. Genes encoding the enzyme are found in several pathogenic microorganisms. The structure and mechanism of action of the genomically encoded FosX enzyme from Listeria monocytogenes (FosXLMATCC) obtained from the American Type Culture Collection are reported. The gene harbors 31 point mutations, and as a consequence, the protein differs in 10 amino acid residues from the previously reported FosX encoded in the genome of the EGD strain of L. monocytogenes (FosXLMEGD). The FosXLMATCC enzyme is shown to catalyze the addition of water to the C1 position of the antibiotic with inversion of configuration at C1. The reaction involves Mn(II) activation of the oxirane oxygen and E44 acting as a general base. The structure of the enzyme has been determined from six different crystal forms of the protein. The structures of the enzyme without metal bound are similar but differ in the loop regions. Perhaps the most informative structure is the one with the product bound. This structure shows that the phosphonate group of the product is bound in an orientation that is different than that of fosfomycin bound to the related enzyme, FosA. The implication is that the substrate may also be bound in a different orientation in FosX. A high-resolution structure (1.44 A resolution) of the enzyme reveals a unique conformation in which the C-terminal tail of the protein coordinates to the Mn(II) center via the carboxylate of E126. The kinetic characterization of the E126Q mutant indicates that this conformation of the protein is probably not relevant to the function of the enzyme. Kinetic analysis of mutants of active site residue E44 is consistent with its proposed roll as a general base catalyst in the addition of water to the antibiotic.
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:
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: Fosfomycin resistance protein FosX
Source organism: Listeria monocytogenes serovar 1/2a
Length: 133 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMISGLSHITLIVKDLNKTTTFLREIFNAEEIYSSGDQTFSLSKEKFFLIAGLWICIMEGDSLQEQTYNHIAFRIQSEEVDEYIERIKSLGVEIKPERPRVEGEGRSIYFYDFDNHLFELHAGTLEERLKRYHE
UniProtKB AC: Q8Y6I2 (positions: 1-128)
Coverage: 96%
Name: Fosfomycin resistance protein FosX
Source organism: Listeria monocytogenes serovar 1/2a
Length: 133 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMISGLSHITLIVKDLNKTTTFLREIFNAEEIYSSGDQTFSLSKEKFFLIAGLWICIMEGDSLQEQTYNHIAFRIQSEEVDEYIERIKSLGVEIKPERPRVEGEGRSIYFYDFDNHLFELHAGTLEERLKRYHE
UniProtKB AC: Q8Y6I2 (positions: 1-128)
Coverage: 96%
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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