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The Open Protein Structure Annotation Network
PDB Keyword
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3gag

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of nitroreductase-like protein (NP_720799.1) from Streptococcus mutans at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3gag Target Id 394846
    Molecular Characteristics
    Source Streptococcus mutans ua159
    Alias Ids TPS20305,NP_720799.1, 3.40.109.10 Molecular Weight 23442.62 Da.
    Residues 205 Isoelectric Point 5.06
    Sequence mmndylnfldgrvsvrqfdpdavlpndlikdmlehasyapsgnnfqpwrvvvvknknkqedlkklaalq pqvatasavfllfgdenaydltwwqefhvqkgiitkdeaaaraerirqyfdlhpedketqglrldvglf amnlmqvvrvygydsvpmrgvdfdaiktyldmpnewepilmlpvgkalqagnphvrksvaefaeiie
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.70 Rfree 0.188
    Matthews' coefficent 2.19 Rfactor 0.152
    Waters 646 Solvent Content 43.80

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    SMU_346 gene from Streptococcus mutans encodes the NP_720799 protein that belongs to the nitroreductase family (PF00881). Uniprot annotates SMU_346 as a putative NADH dehydrogenase or NAD(P)H nitroreductase.  The search results from a Blast sequence alignment suggest that NP_720799 carries a conserved FMN binding domain at the N-terminus.

    Pre-SCOP classifies 3gag in the alpha+beta class, FMN-dependent nitroreducatse-like superfamily, NADH oxidase/flavin reductase family. DALI top hits are with the nitroreductase PDB:3ge6 (Z=24), the oxidoreductase PDB:3gbh (Z=24) and the ydfN nitroreductase PDB:3bem (Z=23). The SSM structural comparison reveals that 3gag is similar to PDB:1ds7 (Z=20), PDB:1kqc (Z=20) and PDB:1nox (Z=22), all containing FMN molecules in their structures.  The crystallographic interface interaction suggests that the biomolecule of 3gag is a dimer.  The conserved FMN-binding site is constructed at the interface between two subunits and it is delineated by Arg 12, Ser 14, Arg 21, Gly 158 and Gln 169.  Slightly differing from its structural partners, 3gag His192 provides extra binding interaction with the phosphate group of FMN. 

     

    394846_1.png

     

    Figure 1. 3gag structure carries a conserved FMN-Binding domain at the N-terminus.

     

    394846_2.png

     

    Figure 2. The biomolecule of 3gag is likely a dimer, based on the observed crystal interface interaction.

     

    394846_3.png

    Figure 3. 3GAG (green) is structurally similar to 1DS7(magenta), 1KQC(cyan) and 1NOX(yellow).

     

    394846_4.png

    Figure 4.  A FMN molecule, from the bacteria growth media, is found and modeled in the conserved binding site at the interface between the two subunits of the 3gag structure.

     

    References,

     

    1.    Hecht, H.J.,  Erdmann, H.,  Park, H.J.,  Sprinzl, M.,  Schmid, R.D.   (1995) Crystal structure of NADH oxidase from Thermus thermophilus.  Nat.Struct.Biol.   2: 1109-1114   
     
    2.    Parkinson, G.N.,  Skelly, J.V.,  Neidle, S.   (2000) Crystal structure of FMN-dependent nitroreductase from Escherichia coli B: a prodrug-activating enzyme.  J.Med.Chem.   43: 3624-3631
     
    3.    Haynes, C.A.,  Koder, R.L.,  Miller, A.F.,  Rodgers, D.W.   (2002) Structures of nitroreductase in three states: effects of inhibitor binding and reduction.  J.Biol.Chem.   277: 11513-11520

    Ligand Summary

     

    FMN, SO4

    Reviews

    References

     

    No references found.

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