Database accession: MF7000519
Name: Hypothetical oxidoreductase YcnD (Bacillus subtilis)
PDB ID: 1zch
Experimental method: X-ray (1.85 Å)
Assembly: Homodimer
Source organism: Bacillus subtilis
Primary publication of the structure:
Morokutti A, Lyskowski A, Sollner S, Pointner E, Fitzpatrick TB, Kratky C, Gruber K, Macheroux P
Structure and function of YcnD from Bacillus subtilis, a flavin-containing oxidoreductase.
(2005) Biochemistry 44: 13724-33
PMID: 16229462
Abstract:
YcnD from the gram-positive bacterium Bacillus subtilis is a member of a family of bacterial proteins that act as NADH- and/or NADPH-dependent oxidoreductases. Here, we report for the first time on the biochemical characterization of the purified protein, demonstrating that YcnD is an FMN-containing enzyme that can be reduced by NADH or NADPH (Km = 6.4 and 4.4 microM, respectively). In the presence of free FMN as the electron-accepting substrate, the latter reductant showed a ping-pong Bi-Bi reaction mechanism, whereas utilization of NADH is competitively inhibited by this substrate. This finding suggests that NADPH is the physiological reductant of the enzyme. We also show that YcnD reduces nitro-organic compounds, chromate, and a series of azo dyes. The reduction of azo dyes appears to be mediated by free reduced FMN because the reaction is considerably slower in its absence. Structure determination by X-ray crystallography revealed that YcnD folds into a three layer alpha-beta-alpha sandwich strongly resembling the topology of the NADH oxidase superfamily. Similar to homologous bacterial oxidoreductase, YcnD forms homodimers with an extended dimer interface. The biochemical data and the structure are discussed in light of the putative physiological function of YcnD as an oxidoreductase delivering reduced FMN to enzymes that require the reduced cofactor for activity.
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 (NADH) activity FMN reductase (NADH) activity
FMN reductase (NADPH) activity FMN reductase (NADPH) activity
Biological process:
aromatic compound catabolic process obsolete aromatic compound catabolic process
response to toxic substance response to toxic substance
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: FMN reductase [NAD(P)H]
Source organism: Bacillus subtilis
Length: 249 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNEVIKSLTDHRSIRSYTDEPVAQEQLDQIIEAVQSAPSSINGQQVTVITVQDKERKKKISELAGGQPWIDQAPVFLLFCADFNRAKIALEDLHDFKMEITNGLESVLVGAVDAGIALGTATAAAESLGLGTVPIGAVRGNPQELIELLELPKYVFPLSGLVIGHPADRSAKKPRLPQEAVNHQETYLNQDELTSHIQAYDEQMSEYMNKRTNGKETRNWSQSIASYYERLYYPHIREMLEKQGFKVEK
UniProtKB AC: P94424 (positions: 1-249)
Coverage: 100%
Name: FMN reductase [NAD(P)H]
Source organism: Bacillus subtilis
Length: 249 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNEVIKSLTDHRSIRSYTDEPVAQEQLDQIIEAVQSAPSSINGQQVTVITVQDKERKKKISELAGGQPWIDQAPVFLLFCADFNRAKIALEDLHDFKMEITNGLESVLVGAVDAGIALGTATAAAESLGLGTVPIGAVRGNPQELIELLELPKYVFPLSGLVIGHPADRSAKKPRLPQEAVNHQETYLNQDELTSHIQAYDEQMSEYMNKRTNGKETRNWSQSIASYYERLYYPHIREMLEKQGFKVEK
UniProtKB AC: P94424 (positions: 1-249)
Coverage: 100%
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)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
