Database accession: MF7000537
Name: FMN-dependent oxidoreductase RubE7
PDB ID: 7vqk
Experimental method: X-ray (2.00 Å)
Assembly: Homodimer
Source organism: Streptomyces sp ADI95-17
Primary publication of the structure:
Yan Y, Yu Z, Zhong W, Hou X, Tao Q, Cao M, Wang L, Cai X, Rao Y, Huang SX
Characterization of Multifunctional and Non-stereoselective Oxidoreductase RubE7/IstO, Expanding the Functional Diversity of the Flavoenzyme Superfamily.
(2022) Angew. Chem. Int. Ed. Engl. 61: e202200189
PMID: 35191152
Abstract:
Flavin-dependent enzymes enable a broad range of redox transformations and generally act as monofunctional and stereoselective catalysts. Herein, we report the investigation of a multifunctional and non-stereoselective FMN-dependent oxidoreductase RubE7 from the rubrolone biosynthetic pathway. Our study outlines a single RubE7-catalysed sequential reduction of three spatially distinct bonds in a tropolone ring and a reversible double-bond reduction and dehydrogenation. The crystal structure of IstO (a RubE7 homologue) with 2.0 Å resolution reveals the location of the active site at the interface of two monomers, and the size of active site is large enough to permit both flipping and free rotation of the substrate, resulting in multiple nonselective reduction reactions. Molecular docking and site mutation studies demonstrate that His106 is oriented towards the substrate and is important for the reverse dehydrogenation reaction.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
3-hydroxypropionate dehydrogenase (NADP+) activity 3-hydroxypropionate dehydrogenase (NADP+) activity
nucleotide binding nucleotide 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: Putative malonic semialdehyde reductase RutE
Source organism: Streptomyces sp ADI95-17
Length: 199 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAGHPLALDEAAQDLLFREARTANTFAPTHIGDEHIEAIYDLVKWGPTSMNQQPMRVVLVRSDESRRALLQHVLEGNRDKVASAPLVAVLAADLSFPDTLPRLFPHAPNARHAYADENARRESAVFNTALQLGYFIIGIRAGGLAAGPIAGFDPEGVHKEFFPGEPVLVTSIVNIGYPGPDAFSARLPRLGYREVVRSV
UniProtKB AC: A0A3N6GWZ7 (positions: 5-199)
Coverage: 97%
Name: Putative malonic semialdehyde reductase RutE
Source organism: Streptomyces sp ADI95-17
Length: 199 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAGHPLALDEAAQDLLFREARTANTFAPTHIGDEHIEAIYDLVKWGPTSMNQQPMRVVLVRSDESRRALLQHVLEGNRDKVASAPLVAVLAADLSFPDTLPRLFPHAPNARHAYADENARRESAVFNTALQLGYFIIGIRAGGLAAGPIAGFDPEGVHKEFFPGEPVLVTSIVNIGYPGPDAFSARLPRLGYREVVRSV
UniProtKB AC: A0A3N6GWZ7 (positions: 5-199)
Coverage: 97%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Nitroreductase family
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
Authors claim that the homodimeric NAD(P)H nitroreductase is a highly intertwined dimer with the FMN binding site lying at the dimer interface (PMID:18241886). Other structures belonging to the nitroreductase family also have an extensive interaction surface wherein a large hydrophobic solvent-accessible surface becomes buried upon dimer formation, suggesting that the monomers would be unstable on their own (PMID:16229462, PMID:19436071). Domain-swapping is also typical, where the extended C-terminal region extensively interacts with the core domain of the neighbouring monomer, forming an interlocked dimer (PMID:34473996, PMID:19436071, PMID:8885832).
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)
Download this entry's JSON file (.json)
