Database accession: MF7000239
Name: YdjA (Escherichia coli)
PDB ID: 3bm1
Experimental method: X-ray (2.00 Å)
Assembly: Homodimer
Source organism: Escherichia coli
Primary publication of the structure:
Choi JW, Lee J, Nishi K, Kim YS, Jung CH, Kim JS
Crystal structure of a minimal nitroreductase, ydjA, from Escherichia coli K12 with and without FMN cofactor.
(2008) J. Mol. Biol. 377: 258-67
PMID: 18241886
Abstract:
Nitroreductases (NTR) are enzymes that reduce hazardous nitroaromatic compounds and are of special interest due to their potential use in bioremediation and their activation of prodrugs in directed anticancer therapies. We elucidated the crystal structures of ydjA from Escherichia coli (Ec_ydjA), one of the smallest NTRs, in its flavin mononucleotide (FMN)-bound and cofactor-free forms. The alpha+beta mixed monomeric Ec_ydjA forms a homodimeric structure through the interactions of the long central helices and the extended regions at both termini. Two FMN molecules are bound at the dimeric interface. The absence of the 30 internal amino acids in Ec_ydjA, which forms two helices and restricts the cofactor and substrate binding in other NTR family members, creates a wider and more flexible active site. Unlike the bent FMN ring structures present in most NTR complexes currently known, the flavin system in the Ec_ydjA structure maintains a flat ring conformation, which is sandwiched between a Trp and a His residue from each monomer. The analysis of our Ec_ydjA structure explains its specificity for larger substrates and provides structural information for the rational design of novel prodrugs with the ability to reduce nitrogen-containing hazardous molecules.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
FMN binding FMN binding
oxidoreductase activity oxidoreductase activity
protein homodimerization activity protein homodimerization activity
Biological process: not assigned
Cellular component:
cytosol cytosol
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: Putative NAD(P)H nitroreductase YdjA
Source organism: Escherichia coli
Length: 183 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMDALELLINRRSASRLAEPAPTGEQLQNILRAGMRAPDHKSMQPWHFFVIEGEGRERFSAVLEQGAIAAGSDDKAIDKARNAPFRAPLIITVVAKCEENHKVPRWEQEMSAGCAVMAMQMAAVAQGFGGIWRSGALTESPVVREAFGCREQDKIVGFLYLGTPQLKASTSINVPDPTPFVTYF
UniProtKB AC: P0ACY1 (positions: 1-183)
Coverage: 100%
Name: Putative NAD(P)H nitroreductase YdjA
Source organism: Escherichia coli
Length: 183 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMDALELLINRRSASRLAEPAPTGEQLQNILRAGMRAPDHKSMQPWHFFVIEGEGRERFSAVLEQGAIAAGSDDKAIDKARNAPFRAPLIITVVAKCEENHKVPRWEQEMSAGCAVMAMQMAAVAQGFGGIWRSGALTESPVVREAFGCREQDKIVGFLYLGTPQLKASTSINVPDPTPFVTYF
UniProtKB AC: P0ACY1 (positions: 1-183)
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 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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