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2ka5

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

    Title Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites. Acta Crystallogr.,Sect.F 66 1393-1405 2010
    Site JCSG
    PDB Id 2ka5 Target Id 282948
    Related PDB Ids 3f43 
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS2208,TM1081, 289486 Molecular Weight 12972.43 Da.
    Residues 113 Isoelectric Point 5.40
    Sequence mfpykivddvvilmpnkelnienahlfkkwvfdeflnkgynkiflvlsdvesidsfslgvivnilksis ssggffalvspnekvervlsltnldrivkiydtiseameevrrk
      BLAST   FFAS

    Structure Determination
    Method NMR Chains 1

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2ka5
    1. Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites
    P Serrano, B Pedrini, M Geralt, K Jaudzems - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    Gene TM1081 from Thermotoga maritima encodes a small protein (NP_228887), which belongs to the anti-sigma-factor antagonist family and has sequence similarity to the STAS (after Sulphate Transporter and AntiSigma factor antagonist) family (PF01740) from Pfam. By similarity, it is speculated that in the phosphorylated form on a serine residue, the protein could act as an anti-anti-sigma factor that counteracts an anti-sigma factor and thus release a sigma factor from inhibition. The phosphorylation site (Ser 55) is shown as dots in the figure below.

     monomer_96990.png

    Pre-SCOP clasifies 3f43 in the alpha/beta class, SpoIIaa-like fold, anti-sigma factor antagonist SpoIIaa (super)family. A DALI search with the 3f43 structure shows its similarity with many other anti sigma F factors. They include several structures of the Bacillus anti-sigma factor SpoIIAB in complex with the anti-anti-sigma SpoIIAA (see reference #1, PDB codes: PDB:1th8, PDB:1thn, PDB:1tid, PDB:1til which have a rmsd 1.5A for 110 aligned Ca, 25% seq id, Z=18); next is the TM1442 protein from Thermotoga maritima (see reference #2, PDB code: PDB:1vc1, rmsd 1.7A for 105 aligned Ca, 36% seq id, Z=17), the anti-sigma factor antagonist SPOIIAA in its unphosphorylated form (see reference #3, PDB code: PDB:1h4y, PDB:1h4x (rmsd 1.7A for 108 aligned Ca, 19% seq id, Z=16). The superposition of 3f43 with the above structures is shown below. 3f43 (green), 1h4x (yellow), 1th8 (orange) and 1vc1 (grey).  All of the similar structures are in the anti-sigma factor antagonist SPOIIAA family from SCOP.

    super_96990.png

    The interface calculation suggests that the biomolecule of 3f43 is a dimer.

    dimer_96990.png

     

    References: 

    1. Masuda, S.,  Murakami, K.S.,  Wang, S.,  Olson, C.A.,  Donigian, J.,  Leon, F.,  Darst, S.A.,  Campbell, E.A. (2004) Crystal Structures of the ADP and ATP Bound Forms of the Bacillus Anti-sigma Factor SpoIIAB in Complex with the Anti-anti-sigma SpoIIAA. J.Mol.Biol. 340: 941-956
    2. Lee, J.Y.,  Ahn, H.J.,  Ha, K.S.,  Suh, S.W. (2004) Crystal structure of the TM1442 protein from Thermotoga maritima, a homolog of the Bacillus subtilis general stress response anti-anti-sigma factor RsbV Proteins 56: 176-179
    3. Seavers, P.R.,  Lewis, R.J.,  Brannigan, J.A.,  Verschueren, K.H.,  Murshudov, G.N.,  Wilkinson, A.J. (2001) Structure of the Bacillus cell fate determinant SpoIIAA in phosphorylated and unphosphorylated forms. Structure 9: 605-614

    Ligand Summary

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