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1uwd

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

    Title NMR Structure of the Conserved Hypothetical Protein Tm0487 from Thermotoga Maritima: Implications for 216 Homologous Duf59 Proteins. Protein Sci. 14 2880-2886 2005
    Site JCSG
    PDB Id 1uwd Target Id 282360
    Related PDB Ids 1wcj 
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1911,TM0487, 84914 Molecular Weight 11637.98 Da.
    Residues 104 Isoelectric Point 4.39
    Sequence mpmskkvtkedvlnalknvidfelgldvvslglvydiqiddqnnvkvlmtmttpmcplagmilsdaeea ikkiegvnnveveltfdppwtpermspelrekfgv
      BLAST   FFAS

    Structure Determination
    Method NMR Chains 1

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    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1uwd
    1. Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests
    S O_dziej, C Czaplewski, A Liwo - Proceedings of the , 2005 - National Acad Sciences
     
    2. Protein structure prediction based on the sliced lattice model
    CC Wang, CB Yang, HY Ann - 2008 Conference on , 2005 - etd.lib.nsysu.edu.tw
     
    3. The mammalian DUF59 protein Fam96a forms two distinct types of domain-swapped dimer
    KE Chen, AA Richards, JK Ariffin, IL Ross - Section D: Biological , 2012 - scripts.iucr.org
     
    4. Prediction of Protein Backbone Based on the Sliced Lattice Model
    CC Wang, CB Yang, HY Ann, HY Chang - 2008 - csie.npu.edu.tw
     

    Protein Summary

    The gene TM0487 from Thermotoga maritima encodes the NP_228297 protein of unknown function from the DUF59 group PF01883.  SCOP classifies 1uwd inthe alpha+beta class, Fe-S cluster superfamily, PaaD-like family. 1uwd DALI top hits are with the uncharacterized proteins 3lno (Z=13), TTHB138 3cq2 (Z=12), and the dTDP-4-keto-L-rhamnose reductase-related protein 2cu6 (Z=11). Based on structural similarity with nitrogen fixation proteins (NifU, PDB id: 1XHJ, HHPred, P-value 1.6E-07, probability 96.4%, 21% identities; Z=3) and sequence homology with the same (HHPred P-value 9.6E-05 with PF0116 over 71 residues), we propose an involvement of this family in Fe-S cluster biosynthesis. This hypothesis finds further support in an analysis of the genome context of TM0487, where with a probability of 0.87, an association is found with the NifU-like protein, HemK [TM0488].

     

    The BLAST alignment indicates 53% sequence identity to a putative dTDP-4-keto-l-rhamnose reductase  RELATED protein EC:1.1.1.133 from Pyrococcus abyssi GE5 COG1091.  The structure comparison of 1uwd with the structurally similar proteins from Thermus thermophilus HB8, 2CU6 3CQ1 (Z=11), also suggests that 1uwd is most probably a dTDP-4-keto-l-rhamnose reductase-RELATED protein.  The enzyme (2GGS) catalyzes the following reaction: dTDP-6-deoxy-L-mannose + NADP(+) <=> dTDP-4-dehydro-6-deoxy-L-mannose + NADPH.  The enzyme participates in 3 metabolic pathways: nucleotide sugars metabolism, streptomycin biosynthesis, and polyketide sugar unit biosynthesis.

     

    Annotation of "putative dTDP-4-keto-l-rhamnose reductase" does not match TM0487 either in terms of structure (rmsd  4.5 Å over 56 residues between TM0487 and PDB id: 2GGS) or sequence homology. The folds of the two proteins are different, alpha-lytic protease prodomain like (Fe-S cluster assembly domain like superfamily) for TM0487 and NAD(P)-binding Rossmann fold-like for 2GGS and there's no indication of dTDP binding in TM0487 (the NDP observed in 2GGS clashes sterically with TM0487 loops).

    Ligand Summary


    References

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    References

     

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