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The Open Protein Structure Annotation Network
PDB Keyword
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3hmz

    Title Crystal structure of FMN-binding domain of flavin reductases-like enzyme (YP_001049024.1) from Shewanella baltica OS155 at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3hmz Target Id 375054
    Molecular Characteristics
    Source Shewanella baltica os155
    Alias Ids TPS24217,YP_001049024.1, 2.30.110.10, 92234 Molecular Weight 21856.79 Da.
    Residues 198 Isoelectric Point 5.88
    Sequence mhhqrkthvdnniaavelakayrllnhgptvlvsarsqgidnvmaaawccaldfappkltvvldkmtkt refieqsgmfviqvptvaqlqlthrvgsqsladdankllncgvelfemaghdlpfvagcsawlacklip epnnqlqydlfiaevigawadtqvfnhghwhfdtapadkrslhyiaggqfyaigesfnad
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.50 Rfree 0.150
    Matthews' coefficent 2.69 Rfactor 0.129
    Waters 224 Solvent Content 54.22

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    The gene Sbal_0626 from Shewanella baltica OS155 translates into the YP_001049024 protein, a FMN binding flavin reductase domain. It belongs to PFAM PF01613 which is a family of enzymes known to be flavin reductases as well as components of various oxidoreductases and monooxygenases.

    Pre-SCOP classifies 3hmz in the all beta class, FMN binding split barrel superfamily, NAD:FMN oxidoreductase-like family. The 3hmz monomer structure folds into a typical FMN binding domain shown below.

    FB10609B.png

    The 3hmz crystal structure carries a FMN molecule bound to the protein, as shown in stick representation in the above figure. The crystal packing analysis suggests that the functional oligomeric state of the protein is a dimer, shown below, as it is the case with most proteins in this family.

    FB10609B_dimer.png

    3hmz structure is very similar to many other reductases as observed by DALI and SSM searches.

    DALI Structures Similar to 3HMZ
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3e4v 24.6 1.8 171 179 26 NADHFMN OXIDOREDUCTASE LIKE PROTEIN
    2 1usf 20.8 1.8 158 178 22 PUTATIVE STYRENE MONOOXYGENASE SMALL COMPONENT
    3 1usc 20.8 1.8 158 178 22 PUTATIVE STYRENE MONOOXYGENASE SMALL COMPONENT
    4 2r6v 20.4 1.9 160 182 24 UNCHARACTERIZED PROTEIN PH0856
    5 3bnk 19.9 2.1 161 186 23 FLAVOREDOXIN
    6 1eje 19.8 1.8 162 192 17 FMN-BINDING PROTEIN
    7 3fge 19.7 2.0 161 198 16 PUTATIVE FLAVIN REDUCTASE WITH SPLIT BARREL
    8 2d5m 19.3 2.1 160 183 24 FLAVOREDOXIN
    9 3bpk 18.9 1.9 158 196 18 NITRILOTRIACETATE MONOOXYGENASE COMPONENT B
    10 1rz1 17.2 1.9 135 153 21 PHENOL 2-HYDROXYLASE COMPONENT B

     

    A superposition of these proteins on this target reveals the conservation of the core domain.

    FB10609B_all1.png

    However, there are some differences in the orientation of the N-terminus in these structures.

    FB10609B_all2.png

    FB10609B_3e4v.png

    3hmz (green) and 3e4v (deepteal; another JCSG structure) are very similar.                                         

         FB10609B_all3.png

    However, 1eje (cyan), 1rz1 (lightmagenta), 1usc (yellow), 1usf (salmon), 2d5m (lightgrey), 2r6v (slate), 3bnk (orange), 3bpk (lime), 3fge (hotpink) have their N-terminus oriented in the opposite direction.

     

    Literature references
    1. Blanc V, Lagneaux D, Didier P, Gil P, Lacroix P, Crouzet J; , J Bacteriol 1995;177:5206-5214.: Cloning and analysis of structural genes from Streptomyces pristinaespiralis encoding enzymes involved in the conversion of pristinamycin IIB to pristinamycin IIA (PIIA): PIIA synthase and NADH:riboflavin 5'-phosphate oxidoreductase. PUBMED:7665509

    2. Parry RJ, Li W; , J Biol Chem 1997;272:23303-23311.: An NADPH:FAD oxidoreductase from the valanimycin producer, Streptomyces viridifaciens. Cloning, analysis, and overexpression. PUBMED:9287340

    Ligand Summary

    Reviews

    References

     

    No references found.

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