The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of Putative Nitroreductase in Complex with FMN (YP_387283.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3e39 Target Id 390745
    Molecular Characteristics
    Source Desulfovibrio desulfuricans g20
    Alias Ids TPS14547,YP_387283.1,, 85746 Molecular Weight 19383.16 Da.
    Residues 177 Isoelectric Point 5.96
    Sequence mltenpvlqairqrrsirrytdeavsdeavrlileagiwapsglnnqpcrflviraddprcdilaahtr yghivrgakviilvfldreamynevkdhqaagaavqnmllaahalqlgavwlgeiinqaatllpalald parlsfeaaiaaghpaqngsssrrplaellleepfpqpe
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.201
    Matthews' coefficent 2.07 Rfactor 0.165
    Waters 385 Solvent Content 40.46

    Ligand Information


    Google Scholar output for 3e39

    Protein Summary

    The gene Dde_0787 (YP_387283.1) from Desulfovibrio desulfuricans st G20 is annotated as a nitroreductase family protein belonging to Pfam PF00881 whose members use FMN as cofactor. There are 1907 proteins in this group from 566 species with 10 unique crystal structures. Members of this family are primarily bacterial proteins, but some eukaryotic homologs have been found in C. elegans, D. melanogaster, mouse and human (InterPro entry).

    The Conserved Domain Database indicates that YP_387283 belongs to the Nitro_FMN_Reductase superfamily, and specifically to NADPH_oxidoreductase_1. This superfamily includes Nitro_FMN_reductase, Nitroreductase_3, Arsenite_oxidase, NfsA_FRP, Nitroreductase_2, NADPH_oxidoreductase_2, NADH_nitroreductase, Nitroreductase_1, Nitroreductase, NADH_oxidase, BluB, NfsB_like_nitroreductase, iodotyrosine_dehalogenase, Nitroreductase, NfnB, PRK10765, PRK05365, Nitroreductase_5, PRK10828 and mcbC-like_oxidoreductase.

    Pre-SCOP classifies 3e39 structure in the alpha+beta class, FMN-dependent nitroreductase-like superfamily, NADH oxidase/flavin reductase family. 3e39 was selected for structure detemination as a CATH mega-family target (CATH, NADH oxidase homologous superfamily). The closest structure to 3e39 is 3E10 and 3KWK (Dali Z=21; Blast e-value=2e-10; seq.id. 35%). Another close structure is that of 1NOX.pdb (Ref1) with Dali Z-score 18, Blast exp=2e-05 and sequence identity of ~30%. 

    3e39 crystallizes as a dimer in the structure and crystal packing analysis suggests that this oligomeric state forms in solution.

    Fig1_MG0383I (1).png


    Superposition of 3e39 structure with 1NOX (magenta) shows that the FMN is bound in the same cleft in both structures (red in 3e39, grey in 1NOX), at the interface of the dimer. The low B-factors of the FMN molecule compared to that of the surrounding protein residues indicates that the cofactor is tightly bound to the protein. The conformation of the cofactor is also very similar and this is different from what is usually seen in FMN flavodoxins (Ref1):


    Inspection of the  FMN binding site reveals that the phosphate moiety of the FMN in 3e39 is stabilized by interaction with Arg14 and Arg15 (white), similar to that seen in the 1NOX structure. The Trp47 that is present near and parallel to the flavin moiety in 1NOX (blue) is not present in 3e39. Instead Trp120 on the opposite site in this protein (green) appears to be within interaction distance of the bound FMN:



    Another similar protein structure from this CATH and Pfam family has been solved recently at the JCSG, NP_348178 from Clostridium acetobutylicum, PDB id 3e10. Interestingly, an estimation of the active site volume of 3e39 is ~274A3 compared to ~486A3 for 3e10.



    1) Hecht HJ, Erdmann H, Park HJ, Sprinzl M, Schmid RD. Crystal structure of NADH oxidase from Thermus thermophilus.Nat Struct Biol. 1995 Dec;2(12):1109-14

    Ligand Summary




    No references found.

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