Database accession: MF7000841
Name: Peroxide resistance protein (Xylella fastidiosa)
PDB ID: 1zb9
Experimental method: X-ray (1.80 Å)
Assembly: Homodimer
Source organism: Xylella fastidiosa
Primary publication of the structure:
Oliveira MA, Guimarães BG, Cussiol JR, Medrano FJ, Gozzo FC, Netto LE
Structural insights into enzyme-substrate interaction and characterization of enzymatic intermediates of organic hydroperoxide resistance protein from Xylella fastidiosa.
(2006) J. Mol. Biol. 359: 433-45
PMID: 16631787
Abstract:
Organic hydroperoxide resistance proteins (Ohr) belong to a family of proteins that possess thiol-dependent peroxidase activity endowed by reactive cysteine residues able to reduce peroxides. The crystal structure of Ohr from Xylella fastidiosa in complex with polyethylene glycol, providing insights into enzyme-substrate interactions is described herein. In addition, crystallographic studies, molecular modeling and biochemical assays also indicated that peroxides derived from long chain fatty acids could be the biological substrates of Ohr. Because different oxidation states of the reactive cysteine were present in the Ohr structures from X. fastidiosa, Pseudomonas aeruginosa and Deinococcus radiodurans it was possible to envisage a set of snapshots along the coordinate of the enzyme-catalyzed reaction. The redox intermediates of X. fastidiosa Ohr observed in the crystals were further characterized in solution by electrospray ionization mass spectrometry and by biochemical approaches. In this study, the formation of an intramolecular disulfide bond and oxidative inactivation through the formation of a sulfonic acid derivative was unequivocally demonstrated for the first time. Because Ohr proteins are exclusively present in bacteria, they may represent promising targets for therapeutical drugs. In this regard, the structural and functional analyses of Ohr presented here might be very useful.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.Molecular function: not assigned
Biological process:
response to oxidative stress response to oxidative stress
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: Organic hydroperoxide resistance protein
Source organism: Xylella fastidiosa
Length: 143 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNSLEKVLYTAIVTATGGRDGSVVSSDNVLNVKLSVPQGLGGPGGSGTNPEQLFAAGYSACFIGALKFVANKEKVDLPAEPRVEGRVGIGEIPGGFGLVVELRIAVSGMERSMLQTLVDKAHRVCPYSNATRGNIDVVLILID
UniProtKB AC: Q9PCF4 (positions: 2-143)
Coverage: 99%
Name: Organic hydroperoxide resistance protein
Source organism: Xylella fastidiosa
Length: 143 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNSLEKVLYTAIVTATGGRDGSVVSSDNVLNVKLSVPQGLGGPGGSGTNPEQLFAAGYSACFIGALKFVANKEKVDLPAEPRVEGRVGIGEIPGGFGLVVELRIAVSGMERSMLQTLVDKAHRVCPYSNATRGNIDVVLILID
UniProtKB AC: Q9PCF4 (positions: 3-143)
Coverage: 98%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: OsmC-like protein
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
Ohr is a tightly folded homodimer with a large buried hydrophobic surface area. The two monomers are tightly wrapped around each other in a head-to-tail orientation. Dimerization is dominated by helix–helix packing interactions of two long helices at the center of the hydrophobic core of the dimeric enzyme. Also, each β-sheet is composed of six strands, three from one monomer and three from the other (beta sheet augmentation). The hydrophobic core, as well as the surrounding β-sheets, are generated by combining elements of both monomers, therefore, it is clear that the two polypeptide chains have to fold together to form active Ohr, and that each monomer would individually be unstable. The two active sites are also located at the dimer interface (PMID:12485986).
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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