Database accession: MF7000508
Name: NADPH:FMN oxidoreductase with NAD+ (Vibrio harveyi)
PDB ID: 2bkj
Experimental method: X-ray (2.08 Å)
Assembly: Homodimer
Source organism: Vibrio harveyi
Primary publication of the structure:
Tanner JJ, Tu SC, Barbour LJ, Barnes CL, Krause KL
Unusual folded conformation of nicotinamide adenine dinucleotide bound to flavin reductase P.
(1999) Protein Sci. 8: 1725-32
PMID: 10493573
Abstract:
The 2.1 A resolution crystal structure of flavin reductase P with the inhibitor nicotinamide adenine dinucleotide (NAD) bound in the active site has been determined. NAD adopts a novel, folded conformation in which the nicotinamide and adenine rings stack in parallel with an inter-ring distance of 3.6 A. The pyrophosphate binds next to the flavin cofactor isoalloxazine, while the stacked nicotinamide/adenine moiety faces away from the flavin. The observed NAD conformation is quite different from the extended conformations observed in other enzyme/NAD(P) structures; however, it resembles the conformation proposed for NAD in solution. The flavin reductase P/NAD structure provides new information about the conformational diversity of NAD, which is important for understanding catalysis. This structure offers the first crystallographic evidence of a folded NAD with ring stacking, and it is the first enzyme structure containing an FMN cofactor interacting with NAD(P). Analysis of the structure suggests a possible dynamic mechanism underlying NADPH substrate specificity and product release that involves unfolding and folding of NADP(H).
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)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
