Database accession: MF7000506
Name: NADH oxidase (Thermus thermophilus)
PDB ID: 1nox
Experimental method: X-ray (1.59 Å)
Assembly: Homodimer
Source organism: Thermus thermophilus
Primary publication of the structure:
Hecht HJ, Erdmann H, Park HJ, Sprinzl M, Schmid RD
Crystal structure of NADH oxidase from Thermus thermophilus.
(1995) Nat. Struct. Biol. 2: 1109-14
PMID: 8846223
Abstract:
The crystal structures of the flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) containing isoforms of NADH oxidase from Thermus thermophilus have been determined by isomorphous and molecular replacement and refined to 2.3 A and 1.6 A resolution with R-values of 18.5% and 18.6% respectively. The structure of the homodimeric enzyme consists of a central 4-stranded antiparallel beta-sheet covered by helices, a more flexible domain formed by two helices, and a C-terminal excursion connecting the subunits. The active sites are located in a deep cleft between the subunits. The binding site of the flavin cofactor lacks the common nucleotide binding fold and is different from the FMN binding site found in flavodoxins.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
NADH dehydrogenase (ubiquinone) activity NADH dehydrogenase (ubiquinone) activity
Biological process: not assigned
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: NADH dehydrogenase
Source organism: Thermus thermophilus
Length: 205 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMEATLPVLDAKTAALKRRSIRRYRKDPVPEGLLREILEAALRAPSAWNLQPWRIVVVRDPATKRALREAAFGQAHVEEAPVVLVLYADLEDALAHLDEVIHPGVQGERREAQKQAIQRAFAAMGQEARKAWASGQSYILLGYLLLLLEAYGLGSVPMLGFDPERVRAILGLPSHAAIPALVALGYPAEEGYPSHRLPLERVVLWR
UniProtKB AC: Q60049 (positions: 6-205)
Coverage: 97%
Name: NADH dehydrogenase
Source organism: Thermus thermophilus
Length: 205 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMEATLPVLDAKTAALKRRSIRRYRKDPVPEGLLREILEAALRAPSAWNLQPWRIVVVRDPATKRALREAAFGQAHVEEAPVVLVLYADLEDALAHLDEVIHPGVQGERREAQKQAIQRAFAAMGQEARKAWASGQSYILLGYLLLLLEAYGLGSVPMLGFDPERVRAILGLPSHAAIPALVALGYPAEEGYPSHRLPLERVVLWR
UniProtKB AC: Q60049 (positions: 6-205)
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 A-2:
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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