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3lwx

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

    Title Crystal structure of Na(+)-translocating NADH-quinone reductase subunit C (YP_001302508.1) from Parabacteroides distasonis ATCC 8503 at 1.10 A resolution. To be published
    Site JCSG
    PDB Id 3lwx Target Id 405115
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS31029,YP_001302508.1, BIG_537, 332259 Molecular Weight 21599.03 Da.
    Residues 198 Isoelectric Point 5.27
    Sequence qslrsfqkqnedndkrqqilrsinvnvssseaetkynelikeaflvnengekvegdafatdvvkaateh qypvfvanvdgqpkyimalhgaglwgplwgyisvdsdkntiygadfshqgetpglgaeiskpvfsnefk gkkifmsgefksvavvkpgksvagqdyvdgisggtitskgvdemlfnslsgyvkfltsqn
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.10 Rfree 0.138
    Matthews' coefficent 2.15 Rfactor 0.116
    Waters 411 Solvent Content 42.92

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3lwx
    1. Low-resolution structure determination of Na+-translocating NADH: ubiquinone oxidoreductase from Vibrio cholerae by ab initio phasing and electron microscopy
    VY Lunin, NL Lunina, MS Casutt, K Knoops - Section D: Biological , 2012 - scripts.iucr.org
     

    Protein Summary

    Comments from Pfam: This is part of FMN_bind family in Pfam. Looks like you already solved another structure in this family: PDB 3dcz. Will be interesting to see if new structure has FMN covalently bound as first structure did not.

     

    The structure of target ID 405115 was determined by single wavelength Se-SAD at a resolution of 1.1 Angstroms from an orthorhombic crystal form. The construct used for expression of this targets contains residues 73-270 of the full length construct (residues 1-270). Residues 164-262 at the C-terminal end of the structure belongs to the FMD_bind(PF04205) Pfam family. This family is associated with the regulatory domain of the Na(+) translocating NADH:ubiquinone oxidoreductase from Vibrio cholerae that contains a covalently bound FMN. The Na(+) translocating NADH:ubiquinone oxidoreductases (NQR)  are typically composed of six subunits, Nqr A-F, part of an nqr operon Target ID 405115 in Parabacteroides distasonis is associated with the Nqr C subunit. Nqr is couples the oxidation of NADH and reduction of ubiquinone to the transfer of sodium ions from the cytoplasmic to the periplasmic space. The resulting transmembrane Na+ electrochemical potential is used for a variety of other cellular processes including ATP synthesis, altered virulence gene regulation in Vibrio cholerae, and regulation of alginate sunthesis in Azotobacter vinelandii.

    Full protein from Parabacteroides distasonis consitsts of rubredoxin domain, TM-helix and FMN binding domain (this structure is described here). Such combination of domains is present only in few bacteria from human gut microbiome. Its homologs in most bacteria contain only FMN binding domain and TM helix.

    monomer.png

    A ribbon representation of target ID 405115 is shown above color coded with the N-terminal end in blue and the C-terminal end in red. The table below lists the reuslts of  a DALI structural similarity search for target ID 405115.

    PDB ID DALI Z-Score rmds (Angstroms) length of alignment total residues in target % sequence id Description
    3dcz 9.6 3.3 137 170 13 Putative Rnfg subunit of electron tranport complex TM0426 from Thermotoga maritima
    3a7a 6.4 2.9 97 337 8  E. coli lipoate-protein ligase A in complex with octyl-AMP and APOH-protein
    1r9p 6.0 5.3 112 134 14  Solution NMR structure of the Haemophilus influenzae Fe-S assembly protein U (Iscu) with zinc bound at the active site
    1wfz 5.5 3.0 100 130 16  Solution structure of Fe-S cluser protein U (Iscu)
    1fo4 5.5 3.7 110 1299 6  Xanthine dehyrogenase isolated from bovine milk
    1vdv 5.4 3.8 110 1299 6  Bovine milk xanthine dehydrogenase Y-700 form

     

     

    The image below shows a suerpositing of the structures of target id 405115(blue) and PDB ID 3dcz(yellow), the Thermotoga ortholog,

     

    3dcz_overlap.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     3dcz_overlap.png
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    236.16 kB16:33, 14 Feb 2010haxelrodActions
     monomer.png
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    158.33 kB03:16, 14 Feb 2010haxelrodActions
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