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3e98

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

    Title Crystal structure of a GAF Domain with Unknown Function (NP_253966.1) from PSEUDOMONAS AERUGINOSA at 2.43 A resolution. To be published
    Site JCSG
    PDB Id 3e98 Target Id 381648
    Molecular Characteristics
    Source Pseudomonas aeruginosa pao1
    Alias Ids TPS7324,NP_253966.1, PF04340, 86819 Molecular Weight 25765.76 Da.
    Residues 233 Isoelectric Point 5.36
    Sequence mteksqeptaaldaeqvaaylsqhpeffvehdelipelriphqpgdavslverqvrllrerniemrhrl sqlmdvarendrlfdktrrlvldlldatsledvvstvedslrhefqvpyvslilfsdssvsvgrsvssa eahqaiggllsggktvcgvlrphelaflfgesdrdeigsaavvslsfqglhgvlaigspdpqhyksslg tlflgyvaevlarvlprfssplrsvr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.43 Rfree 0.270
    Matthews' coefficent 2.43 Rfactor 0.211
    Waters 75 Solvent Content 49.40

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3e98
    1. Probing designability via a generalized model of helical bundle geometry
    G Grigoryan, WF DeGrado - Journal of molecular biology, 2011 - Elsevier
     

    Protein Summary

    Gene PA5279 from Pseudomonas aeruginosa encodes the NP_253966 protein, belonging to the DUF484 (PF04340). Its genomic context shows a possible functional link (score 0.85) with dapF, a diaminopimelate epimerase, and xerC, a tyrosine recombinase.

    3e98 structure is composed of a GAF domain with a novel coiled-coil helical region which contributes to the formation of a dimer. The two dimerization regions showed very large structural differences. The ~50 residues at the N-terminal domain are disordered. Pre-SCOP classifies 3e98 in the GAF domain-like (super)family. DALI top hits are with the phosphoenolpyruvate phosphotransferase PDB:3ci6 (Zscr=12), and the YEBR protein PDB:1vhm (Z=12). Based on structural comparisons with other GAF domains (eg PDB:1f5m, Z=11; or PDB:3dba, Z=7), it appears that the cyclic nucleotide binding site is either closed or absent (figure 2). GAF domains represent a large family of cGMP (cAMP) binding regulatory domains in all kingdoms of life. The function of this protein is currently unknown.


    Figure 1. 3e98 dimer forms through a coiled-coil region 

    PU6302B-dimer.png

    Figure 2: A monomer of 3e98 superimposed with 3dba.  The cyclic nucleotide binding site seems to be closed with an alpha-helix or absent.

    figure2 (1).png

    References:

    Martinez SE, Beavo JA, Hol WG. GAF domains: two-billion-year-old molecular switches that bind cyclic nucleotides. Mol Interv. 2002 Sep;2(5):317-23.

    Hurley JH.  GAF domains: cyclic nucleotides come full circle. Sci STKE 2003 Jan 7 (164) PE1.

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     figure2 (1).png
    No description
    60.22 kB00:37, 9 Aug 2008sefcovicActions
     PU6302B-dimer.png
    Dimer of 381648
    63.74 kB17:41, 28 Jul 2008qxuActions
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