.
The Open Protein Structure Annotation Network
PDB Keyword
.

3ez1

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

    Title Crystal structure of putative aminotransferase (MocR family) (YP_604413.1) from DEINOCOCCUS GEOTHERMALIS DSM 11300 at 2.60 A resolution. To be published
    Site JCSG
    PDB Id 3ez1 Target Id 390749
    Molecular Characteristics
    Source Deinococcus geothermalis dsm 11300
    Alias Ids TPS14616,YP_604413.1, 3.40.640.10, 332027 Molecular Weight 45543.12 Da.
    Residues 422 Isoelectric Point 5.32
    Sequence mtkeasrpaldlarqayeafkarglnlnmqrgqpadadfdlsnglltvlgaedvrmdgldlrnypggva glpsaralfagyldvkaenvlvwnnsslelqglvltfallhgvrgstgpwlsqtpkmivtvpgydrhfl llqtlgfelltvdmqsdgpdvdaverlagtdpsvkgilfvptysnpggetislekarrlaglqaaapdf tifaddayrvhhlveedraepvnfvvlardagypdrafvfastskitfagaglgfvassednirwlsky lgaqsigpnkveqarhvkflteypggleglmrdhaaiiapkfravdevlraelgeggeyatwtlpkggy fisldtaepvadrvvklaeaagvsltpagatypagqdphnrnlrlaptrppveevrtamqvvaacirla teeyragh
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.60 Rfree 0.264
    Matthews' coefficent 2.42 Rfactor 0.224
    Waters 131 Solvent Content 49.08

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ez1

    Protein Summary

    This target is annonated as a hypothetical protein. However, it could be an Amino-transferase based on the homology with a number of structures. Some of these are shown below with this structure in green and 1vp4 (cyan), 1wst (magenta), 1x0m (yellow), 2dtv (pink), 2egy (grey), 2zc0 (blue), 2zg5 (orange).

    all.png

    Most of these homologs have PLP bound to them. But, this protein does not show clear density to model PLP in it. However, there is some residual density corresponding to the phosphate moity of the PLP. A phosphate molecule has been modeled in this density (not shown). A closer look between this target and 1vp4 highlights the conservation of residues in the PLP binding site, in the figure below with this target depicted in green and 1vp4 in cyan.

    MG14492C_1vp4.png

     

    The protein assembles as a dimer in the crystal structure and could represent its natural oligomeric state.

    MG14492C_dimer.png

     

     

    A search of PFAM also provides support for the protein to be annotated as an Amino-transferase:     

     Pfam-A  Description  Entry type  Sequence Start  End  HMM Start End  Bits score  E-value
     DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)  Family  3  20  255  272  7.0  0.12
     Aminotran_1_2   Aminotransferase class I and II  Domain  36  407  1  413  -85.9  0.0063
     UPF0175  Uncharacterised protein family (UPF0175)  Family  158  227  1  75  -12.2  0.71
     MOSC_N   MOSC N-terminal beta barrel domain  Domain  271  280  132  142  4.5  0.87

     

    References:

    •  Chon, H.,  Matsumura, H.,  Koga, Y.,  Takano, K.,  Kanaya, S.   (2005) Crystal structure of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3 at 2.20 A resolution  Proteins   61: 685-688
    • Sakuraba, H.,  Yoneda, K.,  Takeuchi, K.,  Tsuge, H.,  Katunuma, N.,  Ohshima, T.   (2008) Structure of an archaeal alanine:glyoxylate aminotransferase  Acta Crystallogr.,Sect.D   64: 696-699

     

    Note from PFAM:

    ID Aminotran_MocR

    AC PF12897

    DE Alanine-glyoxylate amino-transferase

    AU Coggill P

    SE JCSG_target_390749_3ez1

    GA 20.30 20.30;

    TC 20.30 20.30;

    NC 20.20 20.20;

    BM hmmbuild --amino -o /dev/null HMM SEED

    SM hmmsearch -Z 9421015 -E 1000 --cpu 4 HMM pfamseq

    TP Family

    CL CL0061

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    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