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The Open Protein Structure Annotation Network
PDB Keyword
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3odp

    Title Crystal structure of a putative tagatose-6-phosphate ketose/aldose isomerase (NT01CX_0292) from CLOSTRIDIUM NOVYI NT at 2.35 A resolution. To be published
    Site JCSG
    PDB Id 3odp Target Id 391683
    Molecular Characteristics
    Source Clostridium novyi nt
    Alias Ids TPS14656,YP_878790.1, 3.40.50.10490, 85711 Molecular Weight 44028.94 Da.
    Residues 392 Isoelectric Point 5.25
    Sequence mknllgysedylkerkgyitakeicnqpklwretyeiilsqreklksfldnfakkpnakivitgagssa fvgnsvvsylnakenikieaiattdivshpfyylkkdeptlliscarsgnspestaavtlaekivddis hliitcnsegklalhakrnynsflllmpeesndkgfamtgsfstmllscllifnldklesigkqiesis mqgekvlvnnvelmkkivgekfkrtvylgaanafglakesalkvleltagkiatlydtplgfrhgpksi iddetliviffsndtyareyeydllkevysqngnhkvlaiseyedkliednsdyfiainkeeqeyedds flsldyllnaqmyafinsmelgigpdnpcptgevnrvvkgviihdyr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.35 Rfree 0.2640
    Matthews' coefficent 3.11 Rfactor 0.2278
    Waters 23 Solvent Content 60.42

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3odp

    Protein Summary

     The protein YP_878790.1 is annotated as predicted phosphosugar isomerase. YP_878790.1 belongs to PFAM PF01380 SIS which consists of  SIS (Sugar ISomerase) domains 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.

     

    The monomer structure of YP_878790.1 is structurally identical to another JCSG protein 3i0z (used as a Molecular Replacement search model to solve this structure; sequence identity 42%,  rmsd of 1.069 A over 359 residues).

    MG14470H.png

    Figure 1: YP_878790.1 color coded by secondary structure.

     

    Top 10 DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID Description (JCSG structures highlighted in red)
    1 3i0z 58.3 1.4 382 388 43 PUTATIVE TAGATOSE-6-PHOSPHATE KETOSE/ALDOSE
    2 3c3j 51.1 1.7 362 369 41 PUTATIVE TAGATOSE-6-PHOSPHATE KETOSE/ALDOSE
    3 2zj3 41.2 2.3 344 365 16 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE
    4 2zj4 40.9 2.4 346 365 16 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE
    5 2j6h 39.9 2.4 345 609 19 GLUCOSAMINE-FRUCTOSE-6-PHOSPHATE
    6 2bpj 39.9 2.5 345 609 19 GLUCOSAMINE-FRUCTOSE-6-PHOSPHATE
    7 2bpl 39.6 2.5 345 608 19 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE
    8 1moq 39.2 2.4 343 366 18 GLUCOSAMINE 6-PHOSPHATE SYNTHASE
    9 1jxa 39.2 2.5 345 608 19 GLUCOSAMINE 6-PHOSPHATE SYNTHASE
    10 2df8 39.1 2.1 322 325 25 325AA LONG HYPOTHETICAL PROTEIN

     

    MG14470H_3i0z.png

    Figure 2. YP_878790.1 (green) superimposed on 3i0z (magenta). The two proteins share a sequence identity of 42% and superimpose with an rmsd of 1.069 A over 359 residues.

    Both proteins assemeble as dimer, as shown below for YP_878790.1.

    MG14470H_dimer.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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