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1vp4

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

    Title Crystal structure of Aminotransferase, putative (TM1131) from Thermotoga maritima at 1.82 A resolution. To be published
    Site JCSG
    PDB Id 1vp4 Target Id 282997
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1264,TM1131, 3.40.640.10, 84760 Molecular Weight 47133.13 Da.
    Residues 413 Isoelectric Point 5.60
    Sequence mvvnlegkiskigqnmkssiireilkfaadkdaisfgggvpdpetfprkelaeiakeiiekeyhytlqy sttegdpvlkqqilkllermygitgldednliftvgsqqaldligklflddesycvlddpaylgainaf rqylanfvvvpleddgmdlnvlerklsefdkngkikqvkfiyvvsnfhnpagvttslekrkalveiaek ydlfiveddpygalryegetvdpifkiggpervvllntfskvlapglrigmvagskefirkivqakqsa dlcspaithrlaarylerydlleqlkptielyrrkrtvmlnaleeyfsdipgvkwvksegglfiwltlp egfdtwemfeyakrkkvfyvpgrvfkvydepspsmrlsfclppdekivegikrlrevvleygkekhll
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.82 Rfree 0.20341
    Matthews' coefficent 2.73 Rfactor 0.17902
    Waters 353 Solvent Content 54.59

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    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vp4
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    2. Crystal structure of human kynurenine aminotransferase II, a drug target for the treatment of schizophrenia
    F Rossi, S Garavaglia, V Montalbano, MA Walsh - Journal of Biological , 2008 - ASBMB
     
    3. Crystal structure of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3 at 2.20 resolution
    H Chon, H Matsumura, Y Koga - Proteins: Structure, , 2005 - Wiley Online Library
     
    4. Comparative modelling of the human UDP-glucuronosyltransferases: insights into structure and mechanism
    CW Locuson, TS Tracy - Xenobiotica, 2007 - informahealthcare.com
     
    5. The Three-dimensional Structure of N-Succinyldiaminopimelate Aminotransferase from Mycobacterium tuberculosis
    S Weyand, G Kefala, MS Weiss - Journal of molecular biology, 2007 - Elsevier
     
    6. Mechanism for multiple_substrates recognition of __aminoadipate aminotransferase from Thermus thermophilus
    T Tomita, T Miyagawa, T Miyazaki - Proteins: Structure, , 2009 - Wiley Online Library
     
    7. Two groups of thermophilic amino acid aminotransferases exhibiting broad substrate specificities for the synthesis of phenylglycine derivatives
    D Koma, T Sawai, R Hara, S Harayama - Applied microbiology and , 2008 - Springer
     
    8. Structure of an archaeal alanine: glyoxylate aminotransferase
    H Sakuraba, K Yoneda, K Takeuchi - Section D: Biological , 2008 - scripts.iucr.org
     
    9. The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway
    AK Gauger, DD Axe - BIO-Complexity, 2011 - bio-complexity.org
     
    10. Microbial drug target identification using different computational approaches: Specific application to Pseudomonas aeruginosa
    D Perumal, CS Lim - Innovations in Information , 2008 - ieeexplore.ieee.org
     

    Protein Summary

    The gene TM1131 from Thermotoga maritima encodes a PLP-dependent aspartate aminotransferase E.C.2.6.1.1  (fold I) COG0075, and member of the aminotransferase class I and II superfamily PF00155.  

    The 1vp4 structure belongs to the SCOP PLP-dependent transferases superfamily,  AAT-like family. According to DALI, 1vp4 is structuraly similar to the multiple substrate aminotransferase from Thermococcus profundus PDB:1wst (Z=55), and other aminotransferases like PDB:2egy (Z=52), PDB:2zp7 (Z=51), PDB:2zc0 (Z=50).  

    The enzyme catalyzes the amino group transfer from L-aspartate to 2-oxoglutarate to form oxaloacetate and L-glutamate.  PLP plays an active role in the reaction combining with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups, given enzyme), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. PLP-dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed.

    Ligand Summary



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