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1j5u

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

    Title Crystal structure of archease, possible chaperone (TM1083) from Thermotoga maritima at 2.0 A resolution. To be published
    Site JCSG
    PDB Id 1j5u Target Id 282950
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1259,TM1083, 282149, 84769, 84770, 282147 Molecular Weight 14664.90 Da.
    Residues 124 Isoelectric Point 4.85
    Sequence mrkpiehtadiayeisgnsyeelleearnilleeegivldteekekmypleetedaffdtvndwileis kgwapwrikregnelkvtfrkirkkegteikaltyhllkferdgdvlktkvvfdt
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.271
    Matthews' coefficent 2.93 Rfactor 0.212
    Waters 118 Solvent Content 57.74

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    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1j5u
    1. Distinguishing structural and functional restraints in evolution in order to identify interaction sites
    V Chelliah, L Chen, TL Blundell, SC Lovell - Journal of molecular biology, 2004 - Elsevier
     
    2. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species
    SB Conners, EF Mongodin, MR Johnson - FEMS microbiology , 2006 - Wiley Online Library
     
    3. Finding functional sites in structural genomics proteins
    A Stark, A Shkumatov, RB Russell - Structure, 2004 - Elsevier
     
    4. Prediction of active sites for protein structures from computed chemical properties
    J Ko, LF Murga, Y Wei, MJ Ondrechen - Bioinformatics, 2005 - Oxford Univ Press
     
    5. Faster data-collection strategies for structure determination using anomalous dispersion
    A Gonzalez - Acta Crystallographica Section D: Biological , 2003 - scripts.iucr.org
     
    6. Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins
    R Page, AM Deacon, SA Lesley - Journal of structural and , 2005 - Springer
     
    7. The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies
    V Anantharaman, L Aravind - Proteins: Structure, Function, and , 2004 - Wiley Online Library
     
    8. Predicted role for the archease protein family based on structural and sequence analysis of TM1083 and MTH1598, two proteins structurally characterized through
    JM Canaves - Proteins: Structure, Function, and Bioinformatics, 2004 - Wiley Online Library
     
    9. Application of long_range order to predict unfolding rates of two_state proteins
    B Harihar, S Selvaraj - Proteins: Structure, Function, and , 2011 - Wiley Online Library
     
    10. IOPscience-Local and non-local native topologies reveal the underlying folding landscape of proteins
    T Zou, SB Ozkan - Physical Biology, 2011 - iopscience.iop.org
     
    11. Integrated prediction of protein folding and unfolding rates from only size and structural class
    D De Sancho, V Muoz - Phys. Chem. Chem. Phys., 2011 - xlink.rsc.org
     
    12. Carbohydrate utilization pathway analysis in the hyperthermophile Thermotoga maritima
    SB Conners - 2006 - repository.lib.ncsu.edu
     

    Protein Summary

    The TM1083 gene from Thermotoga maritima encodes a protein of unkown function (DUF101 (PF01951), COG1371). The family has a wide phylogenetic distribution, encountered in archaea, viruses, fungi, insects (moth, mosquito, fruit fly), nematodes, fish and mammals including humans. The TM1083 structure adopts a novel fold termed MTH1598-like fold and shows strong similarity (2.6 Å main-chain rmsd over 112 residues with 20% sequence identity; Dali Zscr=10) to another DUF101 homolog from Methanothermobacter thermoautotrophicus (PDB id: 1jw3) from which the fold takes its name. Both structures comprise a single domain with two helices in the center flanked by short beta-sheets at both ends. This arrangement is reminiscent of BTB/POZ domains which have been described in a wide range of organisms as protein-protein interactions modules (Perez-Torrado 2006) with a role in the regulation of DNA transcription. Structural analysis of 1jw3 shows similarity to heat-shock protein 33 (PDB id: 1i7f; Dali Z=4) and suggests a function in RNA binding (Yee 2002) with bioinformatics analysis predicting a role as chaperone or modulators of proteins involved in DNA or RNA processing (Canaves 2004).

    The genetic neighborhood of TM1083 shows with a high probability a functional association with a LexA repressor (EC 3.4.21.88), DNA gyrase subunit A (EC 5.99.1.3), a putative anti-sigma factor antagonist (TM1081), a methionyl-tRNA synthetase (EC 6.1.1.10) and a ribosomal protein L11 methyltransferase, suggesting an involvement in regulation of DNA transcription. A similar neighborhood is observed for MTH1598 and shows cooccurrence with a DNA polymerase sliding clamp.

    RNA interference experiments have shown the C. elegans DUF101 homolog to be implicated in larval arrest and genitalia development. Yeast-two-hybrid experiments in the D. melanogaster DUF101 homolog have shown physical interactions with a stress-response chaperone (DnaJ-1), proteins involved in translation-elongation and ribosomes (Ef1-gamma, RpS7, SnrB) and a protein located on the germline ring canal involved in germ-line cyst encapsulation (cher).

     

     

    [Any data on whether or not 1j5u forms a dimer in solution?]

    [electrostatics? look for hydrophobic patch that might indicate area of protein-protein interactions]

    [Describe structural differences between 1j5u and 1jw3, including conformational change in the presence of calcium.]

    Ligand Summary



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