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The Open Protein Structure Annotation Network
PDB Keyword
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3hj9

    Title Crystal structure of oxidoreductase (YP_295443.1) from RALSTONIA EUTROPHA JMP134 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3hj9 Target Id 391221
    Molecular Characteristics
    Source Ralstonia eutropha jmp134
    Alias Ids TPS20209,YP_295443.1, 3.40.109.10, 87430 Molecular Weight 24342.62 Da.
    Residues 222 Isoelectric Point 6.97
    Sequence mndlkrlpyepvkgllprpavgtservitlpepdrtsgmplmgtlwlrkstrefdqqplplkqlsellw aaagvnrslgggrtapspygetvidvyvalpaglyrydpvhhclelkraadlrsmtgyqdfvgmapldl vfvanhgrmqemppklretfsaaaagamaenaylycasaglgavvrgwlnrrqlaehmslnedeepils qtigraashvtttqa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.00 Rfree 0.208
    Matthews' coefficent 2.47 Rfactor 0.174
    Waters 287 Solvent Content 50.13

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hj9
    1. Mechanism for the Alteration of the Substrate Specificities of Template-Independent RNA Polymerases
    Y Toh, D Takeshita, T Nagaike, T Numata, K Tomita - Structure, 2011 - Elsevier
     

    Protein Summary

    Gene Reut_A1228 from Ralstonia eutropha jmp134 encodes the protein YP_295443.1 that belongs to a family of nitroreductases (PF00881). Members of this family utilise FMN as a cofactor and are often found to be homodimers, both of which are shown to be true in this protein.

     

    SCOP classifies 3hj9 in the alpha+beta class, FMN-dependent nitroreductase-like superfamily, NADH oxidase/flavin reductase family. The 3hj9 monomer structure is a typical FMN binding protein, as shown below.

    MG8761L_mon.png

    3hj9 assembles as a dimer in the crystal lattice which is also its likley biological state.

    MG8761L_dimer.png

    The FMN interacts with both chains (cyan and green) of the 3hj9 dimer and makes numerous contacts, as shown below.

    MG8761L_FMN.png

    An unbiased (DM) density at 1 sigma level above the mean has been contoured  around the FMN molecule. An acetate ion (shown in grey and red stick representation) is observed right above the flavin ring of FMN.

     

    There are several structural highly similar to 3hj9, mostly nitroreductases.

    Top ten DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3ge5 15.5 2.1 146 176 17 PUTATIVE NAD(P)HFMN OXIDOREDUCTASE
    2 3gbh 15.4 2.3 151 211 17 NAD(P)H-FLAVIN OXIDOREDUCTASE
    3 3e10 15.2 2.3 140 167 26 PUTATIVE NADH OXIDASE
    4 3ge6 15.0 2.4 149 210 16 NITROREDUCTASE
    5 3eo7 15.0 3.3 189 487 19 PUTATIVE NITROREDUCTASE
    6 2bkj 14.8 2.5 149 230 21 FLAVIN REDUCTASE
    7 1bkj 14.8 2.4 149 230 21 NADPH-FLAVIN OXIDOREDUCTASE
    8 3g14 14.7 2.2 147 179 18 NITROREDUCTASE FAMILY PROTEIN
    9 3e39 14.6 2.1 143 175 20 PUTATIVE NITROREDUCTASE
    10 1zch 14.5 2.1 148 249 24 HYPOTHETICAL OXIDOREDUCTASE YCND

    Some of these proteins are shown superimposed on 3hj9 below

    MG8761L_all.png

    3hj9 (green), 1bkj (cyan), 1nox (lightmagenta), 1zch (yellow), 2b67 (salmon), 2bkj (lightgrey), 2fre (slate), 3bm1 (orange), 3e10 (lime), 3e39 (deepteal), 3g14 (yelloworange), 3gbh (violetpurple), 3ge5 (grey70), 3ge6 (marine)
     

     

    Literature references

    1. Hecht HJ, Erdmann H, Park HJ, Sprinzl M, Schmid RD , Nat Struct Biol 1995;2:1109-1114.: Crystal structure of NADH oxidase from Thermus thermophilus. PUBMED:8846223

    2. de Oliveira IM, Henriques JA, Bonatto D; , Biochem Biophys Res Commun. 2007;355:919-925.: In silico identification of a new group of specific bacterial and fungal nitroreductases-like proteins. PUBMED:17331467

    Ligand Summary

    FMN

    Reviews

    References

     

    No references found.

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