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2q83

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

    Title Genomics, evolution, and crystal structure of a new family of bacterial spore kinases. Proteins 78 1470-1482 2010
    Site JCSG
    PDB Id 2q83 Target Id 362376
    Molecular Characteristics
    Source Bacillus subtilis subsp. subtilis str. 168
    Alias Ids TPS1470,2635576 Molecular Weight 39874.68 Da.
    Residues 345 Isoelectric Point 5.22
    Sequence eegnsselplsaedakkltelaenvlqgwdvqaekidviqgnqmalvwkvhtdsgavclkrihrpekka lfsifaqdylakkgmnvpgilpnkkgslyskhgsflfvvydwiegrpfeltvkqdlefimkgladfhta svgyqppngvpiftklgrwpnhytkrckqmetwklmaeaekedpfsqlylqeidgfiedglrikdrllq styvpwteqlkkspnlchqdygtgntllgeneqiwvidldtvsfdlpirdlrkmiiplldttgvwddet fnvmlnayesraplteeqkqvmfidmlfpyelydvirekyvrksalpkeelesafeyerikanalrqli
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.50 Rfree 0.210
    Matthews' coefficent Rfactor 0.198
    Waters 187 Solvent Content

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2q83
    1. Genomics, evolution, and crystal structure of a new family of bacterial spore kinases
    ED Scheeff, HL Axelrod, MD Miller - Proteins: Structure, , 2010 - Wiley Online Library
     

    Protein Summary

    Pfam Update : This target protein hits  APH (PF01636), Phosphotransferase enzyme, family with a high degree of certainty. There are other structures for this family.
     

     

    ytaA of Bacillus subtilis is a member of a novel class of of CAK (Choline and Aminoglycosidase Kinase) kinases, which adopt a protein kinase-like (PKL) fold, but are predicted to phosphorylate small molecules (Kannan et al, 2007, Kannan and Neuwald, 2005). The CAKs span a wide sequence and phylogenetic space, of which just two subclasses, which act on the lipid choline, or on aminoglycosidase antibiotics, have been both functionally and structurally characterized.

    ytaA is a paralog and close chromosomal neighbor of cotS, a defined component of the bacterial endospore, whose expression is under the control of spore-specific sigma factors, and whose only known function is in the expression and packaging of another spore component, CotSA; (Takamatsu et al., 1998; for review, see Driks, 2002). Members of the CotS subfamily of CAKs are restricted to spore-producing firmicutes, but are not present in all firmicute genomes, suggesting that they are not critical components of all spores. Other genomes also have multiple CotS paralogs, and it is not clear which are spore proteins. Analysis of key catalytic residues suggests that ytaA is an active kinase, but CotS, and many other homologs, are catalytically inactive, indicating that kinase activity is not be required for sporulation.

    The ytaA structure confirms it to adopt a Protein Kinase-Like fold and to be most similar to published CAK structures from the aminoglycosidase phosphotransferase (APH) and Choline Kinase subfamilies. It is more distantly related to other PKLs such as the eukaryotic Protein Kinase (ePK) member, PKA (Fig 1) [Kannan: can you add in structural alignment scores here?]



    The YTAA gene product is a CotS like protein that also belongs to the CAK family. Indeed, the crystal structure of YTAA reveals strikingly similarity to choline kinases and aminoglycoside kinases (APH) (Fig 1) that phosphorylate lipids and antibiotics, respectively. Although the physiological substrates of YTAA and CotS are currently unknown, structural analysis (see below) suggests that YTAA and CotS are also small molecule kinases.

     

    Conserved core and variable substrate binding regions: ytaA contains a Protein Kinase-Like catalytic fold similar to those of other CAKs (APH, Choline Kinase: Fig 1) and ePKs (PKA). The catalytic domain binds ATP and contains conserved residues that catalyze the transfer of the gamma phosphate from ATP to a hydroxyl group in a protein or small molecule substrate. These catalytic residues in ytaA are shown in Fig 2.

     
    ytaA also contains a alpha helical sub-domain (shown in cyan). Unlike the catalytic core, the alpha [rename?-GM] sub-domain is strikingly different between ePKs and ELKs (Fig 1). In ePKs, the alpha sub-domain serves a docking site for proteins, while in ELKs it forms as a docking site for small molecules [Is this true for all ELKs or is this specific to CAKs? How is this subdomain named in ePKs?] . The observed structural similarity in the alpha helical sub-domain of YTAA and APH (Fig 1) suggests that YTAA may use the alpha helical sub-domain to dock small molecules.

    A characteristic feature of ytaA is a long insert segment (residues 152-233), which structurally bridges the catalytic core and alpha sub-domain. This insert is present in most CAK family members, but absent in ePKs such as PKA (Fig 1). ePK's, however, conserve a flexible regulatory loop (activation loop), which structurally links the ATP and substrate binding regions (Fig 1). [This paragraph is a general comparison of ePKs and CAKs and is probably not relevant to this report - GM]
     


     

    Ligand Summary



    References

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