Database accession: MF7000522
Name: Nitroreductase CinD with FMN (Lactococcus lactis)
PDB ID: 2wqf
Experimental method: X-ray (1.35 Å)
Assembly: Homodimer
Source organism: Lactococcus lactis subsp lactis
Primary publication of the structure:
Mermod M, Mourlane F, Waltersperger S, Oberholzer AE, Baumann U, Solioz M
Structure and function of CinD (YtjD) of Lactococcus lactis, a copper-induced nitroreductase involved in defense against oxidative stress.
(2010) J. Bacteriol. 192: 4172-80
PMID: 20562311
Abstract:
In Lactococcus lactis IL1403, 14 genes are under the control of the copper-inducible CopR repressor. This so-called CopR regulon encompasses the CopR regulator, two putative CPx-type copper ATPases, a copper chaperone, and 10 additional genes of unknown function. We addressed here the function of one of these genes, ytjD, which we renamed cinD (copper-induced nitroreductase). Copper, cadmium, and silver induced cinD in vivo, as shown by real-time quantitative PCR. A knockout mutant of cinD was more sensitive to oxidative stress exerted by 4-nitroquinoline-N-oxide and copper. Purified CinD is a flavoprotein and reduced 2,6-dichlorophenolindophenol and 4-nitroquinoline-N-oxide with k(cat) values of 27 and 11 s(-1), respectively, using NADH as a reductant. CinD also exhibited significant catalase activity in vitro. The X-ray structure of CinD was resolved at 1.35 A and resembles those of other nitroreductases. CinD is thus a nitroreductase which can protect L. lactis against oxidative stress that could be exerted by nitroaromatic compounds and copper.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
nucleotide binding nucleotide binding
oxidoreductase activity oxidoreductase activity
Biological process:
cellular response to oxidative stress cellular response to oxidative stress
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: Nitroreductase domain-containing protein
Source organism: Lactococcus lactis subsp lactis
Length: 202 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSFIKSLENRRTIYALGRNVQDEEKVIETIKEAVRFSPTAFNSQTGRLLILTGDAQDKLWDEIVAPELKAAMEAQGVPESAWDNTRAKLDGFKAAFGTILFFEDQAVVKNLQEQFALYADNFPVWSEQGSGIISVNVWTALAELGLGANLQHYNPLIDEAVAKEWNLPESWKLRGQLVFGSIEAPAGEKTFMDDADRFIVAK
UniProtKB AC: Q9CED0 (positions: 2-202)
Coverage: 99%
Name: Nitroreductase domain-containing protein
Source organism: Lactococcus lactis subsp lactis
Length: 202 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSFIKSLENRRTIYALGRNVQDEEKVIETIKEAVRFSPTAFNSQTGRLLILTGDAQDKLWDEIVAPELKAAMEAQGVPESAWDNTRAKLDGFKAAFGTILFFEDQAVVKNLQEQFALYADNFPVWSEQGSGIISVNVWTALAELGLGANLQHYNPLIDEAVAKEWNLPESWKLRGQLVFGSIEAPAGEKTFMDDADRFIVAK
UniProtKB AC: Q9CED0 (positions: 2-202)
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 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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