3BM1

Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor

Summary for 3BM1

• Entry DOI: 10.2210/pdb3bm1/pdb
• Related: 3BM2
• Descriptor: Protein ydjA, FLAVIN MONONUCLEOTIDE (3 entities in total)
• Functional Keywords: ydja, nitroreductase, oxidoreductase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 41076.66

Authors

Choi, J.W.,Kim, J.S. (deposition date: 2007-12-12, release date: 2008-01-01, Last modification date: 2023-11-01)

Primary citation

Choi, J.-W.,Lee, J.,Nishi, K.,Kim, Y.-S.,Jung, C.-H.,Kim, J.-S.
Crystal structure of a minimal nitroreductase, ydjA, from Escherichia coli K12 with and without FMN cofactor
J.Mol.Biol., 377:258-267, 2008

PubMed 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.

PubMed: 18241886
DOI: 10.1016/j.jmb.2008.01.004

Experimental method

X-RAY DIFFRACTION (2 Å)