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    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 390844
    Molecular Characteristics
    Source Geobacter sulfurreducens pca
    Alias Ids TPS18293,NP_951600.1, 1.20.1260.10, 85497 Molecular Weight 37659.59 Da.
    Residues 341 Isoelectric Point 5.07
    Sequence msgdilndivaaclelerkassvfkmfaahagsdearrfwetvadetrhhsavyerlqerggrenlpii iykpaetleelemigksideqveryteapsseaacllgfrlqlyllhpafaslcrltrdasgedlpdig ygrylrrfidgigscglataetellgealfrlwnearqlaaqshfdaltgvmtragffktvgslayaaq rsgsnvgimlidldyfklvgdnyghqtgdrilqlvaetitshlrrsdvvgrydgdefvvylspvepasl rtvaenlrrsieeesarmvpvtasigvaqgilgtdvdggieelvrladeclmqakytgknkvvvk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.95 Rfree 0.232
    Matthews' coefficent 2.40 Rfactor 0.184
    Waters 201 Solvent Content 48.72

    Ligand Information


    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

    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.


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



    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.


     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.




    No references found.

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    Files (2)

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