Database accession: MF7000507
Name: NADPH:FMN oxidoreductase (Vibrio harveyi)
PDB ID: 1bkj
Experimental method: X-ray (1.80 Å)
Assembly: Homodimer
Source organism: Vibrio harveyi
Primary publication of the structure:
Tanner JJ, Lei B, Tu SC, Krause KL
Flavin reductase P: structure of a dimeric enzyme that reduces flavin.
(1996) Biochemistry 35: 13531-9
PMID: 8885832
Abstract:
We report the structure of an NADPH:FMN oxidoreductase (flavin reductase P) that is involved in bioluminescence by providing reduced FMN to luciferase. The 1.8 A crystal structure of flavin reductase P from Vibrio harveyi was solved by multiple isomorphous replacement and reveals that the enzyme is a unique dimer of interlocking subunits, with 9352 A2 of surface area buried in the dimer interface. Each subunit comprises two domains. The first domain consists of a four-stranded antiparallel beta-sheet flanked by helices on either side. The second domain reaches out from one subunit and embraces the other subunit and is responsible for interlocking the two subunits. Our structure explains why flavin reductase P is specific for FMN as cofactor. FMN is recognized and tightly bound by a network of 16 hydrogen bonds, while steric considerations prevent the binding of FAD. A flexible loop containing a Lys and an Arg could account for the NADPH specificity. The structure reveals information about several aspects of the catalytic mechanism. For example, we show that the first step in catalysis, which is hydride transfer from C4 of NADPH to cofactor FMN, involves addition to the re face of the FMN, probably at the N5 position. The limited accessibility of the FMN binding pocket and the extensive FMN-protein hydrogen bond network are consistent with the observed ping-pong bisubstrate--biproduct reaction kinetics. Finally, we propose a model for how flavin reductase P might shuttle electrons between NADPH and luciferase.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
FMN reductase (NAD(P)H) activity FMN reductase (NAD(P)H) activity
FMN reductase (NADPH) activity FMN reductase (NADPH) activity
Biological process:
bioluminescence bioluminescence
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: NADPH-flavin oxidoreductase
Source organism: Vibrio harveyi
Length: 240 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNNTIETILAHRSIRKFTAVPITDEQRQTIIQAGLAASSSSMLQVVSIVRVTDSEKRNELAQFAGNQAYVESAAEFLVFCIDYQRHATINPDVQADFTELTLIGAVDSGIMAQNCLLAAESMGLGGVYIGGLRNSAAQVDELLGLPENSAVLFGMCLGHPDQNPEVKPRLPAHVVVHENQYQELNLDDIQSYDQTMQAYYASRTSNQKLSTWSQEVTGKLAGESRPHILPYLNSKGLAKR
UniProtKB AC: Q56691 (positions: 2-240)
Coverage: 99%
Name: NADPH-flavin oxidoreductase
Source organism: Vibrio harveyi
Length: 240 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNNTIETILAHRSIRKFTAVPITDEQRQTIIQAGLAASSSSMLQVVSIVRVTDSEKRNELAQFAGNQAYVESAAEFLVFCIDYQRHATINPDVQADFTELTLIGAVDSGIMAQNCLLAAESMGLGGVYIGGLRNSAAQVDELLGLPENSAVLFGMCLGHPDQNPEVKPRLPAHVVVHENQYQELNLDDIQSYDQTMQAYYASRTSNQKLSTWSQEVTGKLAGESRPHILPYLNSKGLAKR
UniProtKB AC: Q56691 (positions: 2-240)
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: 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)
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