.
The Open Protein Structure Annotation Network
PDB Keyword
.

3g68

    Title Crystal structure of double-SIS domain protein (YP_001089791.1) from Clostridium difficile 630 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3g68 Target Id 391665
    Molecular Characteristics
    Source Clostridium difficile 630
    Alias Ids TPS14649,YP_001089791.1, 3.40.50.10490, 289345 Molecular Weight 39743.61 Da.
    Residues 351 Isoelectric Point 5.77
    Sequence mtiqdymletpvrmreiisnadslfnevkrtnlkkiiitgsgtsyhsgvqvqpylqnlldidvvkmypf mitedtfkfdnentlvvgvsqggssystynamklaedkgckiasmagcknalideisdyiltvncgeek sgaktkgyyctklnlmllglqiarekgiissekyneeinkildainrfeavyklskqwiernkeklvns keiriighsdiygdtleaalklletmripvtgyefeefihgiynainsdstifildtgkeprvtkmidv lsgwtenvfaigrdvtendknlkiditdnpyyqtfnfivpiqlicgeiptlrgvdpsvpkdtrfhmklg skklnk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.80 Rfree 0.194
    Matthews' coefficent 2.12 Rfactor 0.159
    Waters 629 Solvent Content 42.08

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3g68
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Ligands in crystal structures that aid in functional characterization
    AE Speers, BF Cravatt - Acta Crystallographica Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    The CD3275 (YP_001089791.1) gene from Clostridium difficile 630 encodes a putative phosphosugar isomerase and belongs to PFAM PF01380. These domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. Presumably the SIS domains bind to the end-product of the pathway.

    There are many structural homologs of this protein as identified by DALI and SSM searches. All of these proteins have SIS domain.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 2aml 43.8 2.0 343 366 27 SIS DOMAIN PROTEIN
    2 2v4m 39.7 2.5 330 352 20 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE
    3 2j6h 39.1 2.5 337 609 20 GLUCOSAMINE-FRUCTOSE-6-PHOSPHATE
    4 2bpj 39.1 2.5 338 609 20 GLUCOSAMINE-FRUCTOSE-6-PHOSPHATE
    5 2bpl 39.0 2.5 338 608 19 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE
    6 2puv 38.4 2.4 326 348 21 ISOMERASE DOMAIN OF GLUTAMINE-FRUCTOSE-6-
    7 1jxa 38.3 2.5 334 608 19 GLUCOSAMINE 6-PHOSPHATE SYNTHASE
    8 2poc 38.2 2.5 327 352 21 ISOMERASE DOMAIN OF GLUTAMINE-FRUCTOSE-6-
    9 1mos 38.2 2.5 336 367 20 GLUCOSAMINE 6-PHOSPHATE SYNTHASE
    10 1mor 38.2 2.5 336 366 20 GLUCOSAMINE 6-PHOSPHATE SYNTHASE
    SSM Structural Homologs
    N PDB Q-score RMSD TITLE
    1 2aml 0.5766 1.763 LMO0035 PROTEIN (46906266) FROM LISTERIA MONOCYTOGENES 4B F2365 AT 1.50 A RESOLUTION
    2 1j5x 0.5133 2.151 GLUCOSAMINE-6-PHOSPHATE DEAMINASE (TM0813) FROM THERMOTOGA MARITIMA AT 1.8 A RESOLUTION

     

     

    A superposition of the above structures are shown below. Some of these proteins have an extra domain and are shown separately on the right panel.

    all_1.png           all_2.png

    Color scheme: YP_001089791.1 (green), 1j5x (cyan), 1jxa (lightmagenta), 1mos (yellow), 2aml (salmon), 2bpj (lightgrey), 2bpl (slate), 2j6h (orange), 2poc (lime), 2puv (deepteal), 2v4m (hotpink).
     

    The monomer structure is shown below. A citrate molecule binds in the active site of the protein, as shown in stick representation in the top center portion of the protein.

    mol1.png

    The citrate molecule occupies the same position as various sugars in structural  homologs, shown below in the left panel. The right panel shows a zoomed in view.

    citrate_1.png        citrate_zoom.png

     

     

    The protein occurs most likely as a dimer, shown below.

    dimer.png

     

     

     

    References

    1. Teplyakov A, Obmolova G, Badet-Denisot MA, Badet B, Polikarpov I; , Structure 1998;6:1047-1055.: Involvement of the C terminus in intramolecular nitrogen channeling in glucosamine 6-phosphate synthase: evidence from a 1.6 A crystal structure of the isomerase domain. PUBMED:9739095

    2. Bateman A; , Trends Biochem Sci 1999;24:94-95.: The SIS domain: a phosphosugar-binding domain. PUBMED:10203754


     
    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    • No tags
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch