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PDB Keyword
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3mcr

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

    Title Crystal structure of NADH dehydrogenase subunit C (Tfu_2693) from THERMOBIFIDA FUSCA YX-ER1 at 2.65 A resolution. To be published
    Site JCSG
    PDB Id 3mcr Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS6568,YP_290749.1, PF00329
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.85 Rfactor 0.207
    Waters
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    Solvent Content 56.89

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3mcr
    1. Evaluation of indigenous anaerobic microorganisms from Mexican carbonate reservoirs with potential MEOR application
    G Castorena-Corts, I Zapata-Peasco - Journal of Petroleum , 2012 - Elsevier
     

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    Protein Summary

    The gene Tfu_2693 from the moderate thermophilic bacterium (growth temperature 55 C) Thermobifida fusca translates into the YP_290749 protein that belongs to the group Complex1_30KDa (PF00329).  This Pfam group includes those proteins that are the 30-kilodalton subunits of NADH:ubiquionone oxidoreductase (complex 1). 

    The crystal structure of 3mcr was determined at a resolution of 2.65 Angstroms using the structure of PDB ID 2fug (Chain N) as a search model. Shown below is a ribbons representation of the structure of 3mcr color-coded with the N-terminal end in blue and the C-terminal end in red. Complex I, a large membrane-associated mitochondrial pigment-protein complex, performs the first step in the aerobic electron transfer electron transfer chain. This complex catalyzed the transfer of two electrons from NADH to quinone and results in the pumping of two protons across the membrane, thus providing some of the proton-motive force for ATP synthesis. The structure of the hydrophilic domain of complex I, consisting of 14-subunits, has been determined by Sazanov and Hinchliffe. The 30-kilodalton subunit (Nqo5) is part of this hydrophilic domain, and this subunit is believed to be important for stabilizing the complex. 

    PC00329C_monomer.png

     

    The 3mcr structure belongs to the Nqo-like SCOP fold. A DALI search reveals that 3mcr has structural similarity to the following.

     

    PDB ID
    DALI Z-Score
    rmsd (Ang)
    length of alignment (residues)
    number of residues in PDB ID
    % Sequence Identity
    Description
    3ias-chain N 14.4 2.3 123 196 23 Hydrophilic domain of respiratory complex I from Thermus thermophilus, 4 mol/asymm unit, oxidized at 3.15 Ang.
    3i9v-chain 5 14.2 2.3 123 196 23 Hydrophilic domain of respiratory complex I from Thermus thermophilus, 2 mol/asymm unit,
    3iam-chain 5 13.3 2.3 123 196 23
    Hydrophophilic domain of respiratory complex I from Thermus thermophilus, reduced, 2 mol/asymm unit with bound NADH.
    2fug-chain N 12.5 2.5 119 191 13 Structure of hydrophilic domain  of respiratory complex I from Thermus thermophilus.

     

     References

    Hinchliffe, P. and Sazanov, L.A. (2005) "Organization of the Iron-Sulfur Clusters in Respiratory Complex I" Science Vol 309 pp. 771-774.

    Sazanov, L.A. and Hinchliffe, P. (2006) "Structure of the Hydrophilic Domain of Respiratory Complex I from Thermus thermophilusScience Vol 311 pp. 1430-1436.

    Berrisford, J.M. and Sazanov, L.A. "Structural Basis for the Mechanism of Respiratory Complex I (2009). J. Biol. Chem. Vol 284, No 43, pp. 29773-29783.

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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    96.75 kB17:29, 8 Mar 2010haxelrodActions
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