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The Open Protein Structure Annotation Network
PDB Keyword
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3na6

    Table of contents
        1. 1.1.1. Protein Summary
    1. 2. DALI Summary
        1. 2.1.1. Ligand Summary

    Title Crystal structure of a succinylglutamate desuccinylase (TM1040_2694) from SILICIBACTER SP. TM1040 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3na6 Target Id 375176
    Molecular Characteristics
    Source Silicibacter sp. tm1040
    Alias Ids TPS6835,YP_614688.1, 93044 Molecular Weight 35653.48 Da.
    Residues 330 Isoelectric Point 4.80
    Sequence mkdnpisptipldqdgvhhgflklpysrddsawgsvmipitviqngagktalltganhgdeyegpvalq elaattraedvtgrliivpyfnypafrasartspidrgnlnrafpgrpdgtvtqkiadyfqrtllpmad vavdfhsggktldfvpfaaahiledkvlqdacfaamqafnapysvqlleidsegmydtaveemgkvlvt telggggmstarsnaiakkglrnvlihfgilqgemqidpsvtldmpdgdcylfsehdglfeimidlgep vqegdlvarvwspdrtgeapveyrarrsgvlisrhfpgmiksgdcaavigvveg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.195
    Matthews' coefficent 2.72 Rfactor 0.161
    Waters 314 Solvent Content 54.74

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    YP_614688.1 from Silicibacter sp. tm1040 encodes a protein that belongs to the AstE_AspA (Succinylglutamate desuccinylase / Aspartoacylase family) group PF04952 . The protein structure is quite complex and a single chain could be broken into two domains, one alpha/beta/alpha sandwich and the other a pure beta structure.

    The crystal structure contains a monomer in asu. However, PISA suggests a hexamer is a biological unit.

     monomer.png

    Figure 1. Monomer of YP_614688.1

     

     hexamer.png

    Figure 2. Biological hexamer of YP_614688.1.

     

    Similar structures determined by JCSG are 2qj8 and 3fmc. DALI results are shown below:

    DALI Summary

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 3cdx-A 41.6 1.7 320 329 38 PDB MOLECULE: SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE; 2: 3cdx-E 41.5 1.6 319 326 38 PDB MOLECULE: SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE; 3: 3cdx-B 41.5 1.6 319 328 38 PDB MOLECULE: SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE; 4: 3cdx-C 41.4 1.6 318 325 38 PDB MOLECULE: SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE; 5: 3cdx-F 41.2 1.6 317 328 38 PDB MOLECULE: SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE; 6: 3cdx-D 40.6 1.6 315 322 38 PDB MOLECULE: SUCCINYLGLUTAMATEDESUCCINYLASE/ASPARTOACYLASE; 7: 2qj8-A 34.8 2.1 306 314 31 PDB MOLECULE: MLR6093 PROTEIN; 8: 2qj8-B 28.9 2.2 276 289 30 PDB MOLECULE: MLR6093 PROTEIN; 9: 3fmc-D 26.8 2.7 292 365 19 PDB MOLECULE: PUTATIVE SUCCINYLGLUTAMATE DESUCCINYLASE / 10: 3fmc-C 26.7 2.8 293 366 19 PDB MOLECULE: PUTATIVE SUCCINYLGLUTAMATE DESUCCINYLASE / 11: 3fmc-A 26.6 2.8 293 365 19 PDB MOLECULE: PUTATIVE SUCCINYLGLUTAMATE DESUCCINYLASE / 12: 3fmc-B 26.6 2.8 292 365 20 PDB MOLECULE: PUTATIVE SUCCINYLGLUTAMATE DESUCCINYLASE / 13: 2g9d-A 18.7 4.5 267 340 15 PDB MOLECULE: SUCCINYLGLUTAMATE DESUCCINYLASE; 14: 2bco-A 18.6 4.6 265 338 14 PDB MOLECULE: SUCCINYLGLUTAMATE DESUCCINYLASE; 15: 2gu2-B 18.4 3.0 239 307 13 PDB MOLECULE: ASPA PROTEIN; 16: 2gu2-A 18.3 3.1 239 307 13 PDB MOLECULE: ASPA PROTEIN; 17: 2q4z-A 18.2 3.0 239 307 13 PDB MOLECULE: ASPARTOACYLASE; 18: 2nsm-A 17.9 2.6 200 390 13 PDB MOLECULE: CARBOXYPEPTIDASE N CATALYTIC CHAIN; 19: 1h8l-A 17.9 2.6 196 380 16 PDB MOLECULE: CARBOXYPEPTIDASE GP180 RESIDUES 503-882; 20: 2q4z-B 17.9 3.0 239 307 13 PDB MOLECULE: ASPARTOACYLASE; 21: 2i3c-B 17.9 3.1 239 302 12 PDB MOLECULE: ASPARTOACYLASE; 22: 2o53-B 17.9 3.2 241 302 12 PDB MOLECULE: ASPARTOACYLASE; 23: 1yw4-A 17.8 4.0 224 319 13 PDB MOLECULE: SUCCINYLGLUTAMATE DESUCCINYLASE; 24: 2o53-A 17.8 3.1 239 302 12 PDB MOLECULE: ASPARTOACYLASE; 25: 1qmu-A 17.8 2.7 199 380 15 PDB MOLECULE: CARBOXYPEPTIDASE GP180 RESIDUES 503-882; 26: 2i3c-A 17.8 3.1 239 302 12 PDB MOLECULE: ASPARTOACYLASE; 27: 2o4h-B 17.7 3.2 239 302 12 PDB MOLECULE: ASPARTOACYLASE; 28: 3l2n-B 17.7 2.8 203 376 14 PDB MOLECULE: PEPTIDASE M14, CARBOXYPEPTIDASE A; 29: 3l2n-A 17.6 2.8 202 376 14 PDB MOLECULE: PEPTIDASE M14, CARBOXYPEPTIDASE A; 30: 3k2k-A 17.5 2.6 201 387 15 PDB MOLECULE: PUTATIVE CARBOXYPEPTIDASE;

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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    477.68 kB05:28, 25 Mar 2010gyewonActions
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    200.1 kB05:26, 25 Mar 2010gyewonActions
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