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3ezu

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

    Title Crystal structure of multidomain protein of unknown function with GGDEF-domain (NP_951600.1) from GEOBACTER SULFURREDUCENS at 1.95 A resolution. To be published
    Site JCSG
    PDB Id 3ezu Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS18293,NP_951600.1, 1.20.1260.10, 85497
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.40 Rfactor 0.184
    Waters
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    Solvent Content 48.72

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3ezu
    1. Biosynthesis of the Pseudomonas aeruginosa extracellular polysaccharides, alginate, Pel, and Psl
    MJ Franklin, DE Nivens, JT Weadge - Frontiers in , 2011 - ncbi.nlm.nih.gov
     
    2. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    3. Functional Insights from Computational Modeling of Orphan Proteins Expressed in a Microbial Community
    KE Wheeler, A Zemla, Y Jiao - J Proteomics , 2010 - omicsonline.org
     

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    Protein Summary

    NP_951600.1 contains a GGDEF domain at the C-terminus. The N-terminal domain (187-341) forms a 6-helix bundle which seems to have novel features. One of the function is to mediate dimerization (~5000 total buried surface area through the N-terminal domain).There are only two sequence homologs of the full length protein, both in Geobacter. Another protein, gb|EDZ63080.1 from Campylobacterales bacterium GD 1, have sequence similarity beyond the GGDEF domain.


    NP_951600.1 contains a similar GGDEF motif at 260-DGDEF-264. A loop at this region, 227-233, is disordered. The GGDEF domain is homologous the adenylyl cyclase catalytic domain. Many proteins with this domain are involved in cell signaling in bacteria. Dali search identified NP_951600.1 is most similar to 3bre, 1w25, 2v0n. However, the similarity is restricted to the GGDEF domain. A second Dali search with only the first domain, suggests that the N-terminal domain is partially similar to 1vjx, 2gs4, 2gyq etc.

    Figure 1. Monomer of NP_951600.1, DGDEF residues are shown in sticks.

    monomer.png

    Figure 2. Dimer of NP_951600.1 through the N-terminal helical domain

    dimer1.png

     

    The region between N-terminal (ferritin-like) and C-terminal (GGDEF-domain) part of this protein contains two alpha helices. A wide range of signaling proteins contain a conserved helical segment. Some proteins with GGDEF-domain contain signaling helix (S-helix), but there is no sequence similarity between NP_951600 and known S-helix domains.

    References:

     Pei J, Grishin NV; , Proteins 2001;42:210-216.: GGDEF domain is homologous to adenylyl cyclase.  PUBMED:11119645

     

    Ligand Summary

    A UNL ligand is present in a hydrophic pocket near the dimer interface.

    Reviews

    References

     

    No references found.

    Tag page

    Files (2)

    FileSizeDateAttached by 
     dimer1.png
    dimer of NP_951600.1
    158.44 kB22:27, 16 Oct 2008qxuActions
     monomer.png
    monomer with domain definition
    103.36 kB22:22, 16 Oct 2008qxuActions
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