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2gjg

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

    Title Crystal structure of hypothetical protein (NP_746511.1) from Pseudomonas putida KT2440 at 2.25 A resolution. To be published
    Site JCSG
    PDB Id 2gjg Target Id 360827
    Molecular Characteristics
    Source Pseudomonas putida kt2440
    Alias Ids TPS1455,NP_746511.1, PF07317, PF07238, 432970 Molecular Weight 28447.61 Da.
    Residues 247 Isoelectric Point 6.23
    Sequence mfnesdapqppkvlstpleiaanlrqlqeshdpliitfhdrshrfqsyvvhvdresntlaldemiprdg ekfiengehfrvegfhdgvriawecdhalkisevdghrcysgplpqevtyhqrrnafraalklsqlvdi ildgahlkgngamrgklldisatgcklrfegnvedrlqlgqvyerfkagnplglvdtmvelrhlhyeer inttfagvrfhnlsgqaqrkiesfvyqlqrearrfdkddy
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.25 Rfree 0.275
    Matthews' coefficent 2.11 Rfactor 0.206
    Waters 137 Solvent Content 41.22

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2gjg
    1. The structural basis of cyclic diguanylate signal transduction by PilZ domains
    J Benach, SS Swaminathan, R Tamayo - The EMBO , 2007 - nature.com
     
    2. Structure of PP4397 reveals the molecular basis for different c-di-GMP binding modes by Pilz domain proteins
    J Ko, KS Ryu, H Kim, JS Shin, JO Lee - Journal of molecular , 2010 - Elsevier
     
    3. The role of PilZ domain proteins in the virulence of Xanthomonas campestris pv. campestris
    Y Mccarthy, RP RYAN, K O'DONOVAN - Molecular plant , 2008 - Wiley Online Library
     
    4. PILZ protein structure and interactions with PILB and the FIMX EAL domain: implications for control of type IV pilus biogenesis
    CR Guzzo, RK Salinas, MO Andrade - Journal of molecular , 2009 - Elsevier
     
    5. XC1028 from Xanthomonas campestris adopts a PilZ domain_like structure without ac_di_GMP switch
    TN Li, KH Chin, JH Liu, AHJ Wang - Structure, Function, and , 2009 - Wiley Online Library
     
    6. Structural characterization reveals that a PilZ domain protein undergoes substantial conformational change upon binding to cyclic dimeric guanosine monophosphate
    JS Shin, KS Ryu, J Ko, A Lee, BS Choi - Protein Science, 2011 - Wiley Online Library
     
    7. A Novel Tetrameric PilZ Domain Structure from Xanthomonads
    TN Li, KH Chin, KM Fung, MT Yang, AHJ Wang - PloS one, 2011 - dx.plos.org
     
    8. Top (Index), File: 18034161. pdf
    C Sensitive, J Benach - The EMBO , 2007 - www-tsujii.is.su-tokyo.ac.jp
     
    9. XC6012 from Xanthomonas campestris Adopts a Novel Tetrameric PilZ Domain Structure Stabilized by a Central Parallel Four-Stranded Coiled-Coil
    TN Li, KH Chin, HJW Andrew - __________, 2009 - research.nchu.edu.tw
     

    Protein Summary

    Protein NP_746511.1 from Pseudomonas putida is a two domain protein. The N-terminal domain belongs to the YcgR family (PF07317), hypothesized to be involved in the flagellar motor function and may be a part of the flagellar regulon (Ko M, Park C; , J Mol Biol 2000;303:371-382.: Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli. PUBMED:11031114).
    The C-terminal domain has a weak, below significance threshold, sequence similarity to proteins of the 'PilZ' family (PF07238). This similarity is confirmed by structure analysis.

    The NP_746511.1 protein shares the same genomic neighborhood as hypothetical protein PP4396, Negative regulator of flagellin synthesis FlgM  PP4395, and Flagella basal body P-ring formation protein FlgA PP4394, according to the STRING database, supporting its involvement in the flagellar motor function.

    NP_746511.1 is distantly homologous to the VCA0042 protein from Vibrio cholerae O1, solved by the Midwest Structural Genomics center and deposited in PDB as 1yln, but the sequence similarity is extremely low (~10% sequence id). Structure of Pseudomonas aeruginosa protein PA4608, which is homolgous (also with very low sequence similarity of ~13%) to a C-terminal of NP_746511.1, was solved by the NorthEast Structural Genomics Center and deposited in PDB as 1ywu.

    Structure of NP_746511.1 consists of two domains, both belonging to the FMN-binding split barrel fold and classified by pre-SCOP as a member of the new 'PilZ' superfamily of the (FMN-binding) split-barrel fold.

    Analysis of the crystallographic packing of the protein using the PQS server indicates that a dimer is the biologically relevant form.


    Ligand Summary



    References

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