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3ezs

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

    Title Crystal structure of aminotransferase AspB (NP_207418.1) from HELICOBACTER PYLORI 26695 at 2.19 A resolution. To be published
    Site JCSG
    PDB Id 3ezs Target Id 390859
    Molecular Characteristics
    Source Helicobacter pylori 26695
    Alias Ids TPS18295,NP_207418.1, 3.40.640.10, 85538 Molecular Weight 43122.13 Da.
    Residues 375 Isoelectric Point 8.24
    Sequence mtfepypferlrallkeitpkkrgldlgigepqfetpkfiqdalknhthslniypksafeeslraaqrg ffkrrfkielkenelistlgsrevlfnfpsfvlfdyqnptiaypnpfyqiyegaakfikaksllmpltk endftpslnekelqevdlvilnspnnptgrtlsleeliswvklalkhdfilindecyseiyentpppsl leacmlagneafknvlvihslskrssapglrsgfiagdsrllekykafraylgytsanaiqkaseaawl ddrhaeffrniyannlklarkifkntliypysfyvylpvqngenfaktlyqnegiitlpalylgrnrig adyvrlalvydtpllekpleiietyrenha
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.19 Rfree 0.215
    Matthews' coefficent 2.28 Rfactor 0.159
    Waters 407 Solvent Content 45.94

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ezs
    1. STRUCTURAL AND FUNCTIONAL STUDIES ON THE HELICOBACTER PYLORI PROTEOME: THE STATE OF THE ART
    G Zanotti, L Cendron - Functional Proteomics & Nanotechnology- , 2010 - books.google.com
     

    Protein Summary

    NP_207418.1 belongs to the Aminotran_1_2(PF00155) Pfam A group. Currently, 275 structures in the PDB represent this particular Pfam group. This class of aminotransferases is believed to be functionally similar to other share certain pyridoxal-phosphate dependent enzymes, and shares similar mechanistic features including the formation of a Schiff base between the  pyridoxal-phosphate cofactor and an active site lysine sidechain. In the structure described here, pyridoxal phosphate could not be realiably modeled into density at the putative active site indicating low occupancy of the site and or loss of the pyridoxal phosphate cofactor during the purification and crystallization. A search of the SEED functional annotation tool suggests that this protein is succinyldiaminopimelate transaminase, EC 2.6.1.17,a pyridoxal phosphate dependent enzyme that plays a role in the lysine biosynthetic pathway.

    secondary_structure_seq_overlay.bmp The secondary structure of NP_207418.1 superimposed on the amino acid sequence. This diagram was generated with the PDBsum server. The 375 amino acid long protein monomer contains 2 beta sheets (one 7 stranded sheet and one 3 stranded sheet), 3 beta-alpha-beta motifs, 2 beta hairpins, 18 helices, 23 beta turns, and 6 gamma turns.

      

      

      

      

      

      

      

      

      

    topology_diagram.bmp\

      

      

      

    Secondary structure topologydiagram for NP_207418.1

      

      

      

      

      

      

      

      

      

      

    monomer.png The structure of NP_207418.1 belongs to the PLP-dependent transferases fold of enzymes found in the SCOP database. This fold can be described as consisting of a main domain: 3 layers: a/b/a, mixed beta-sheet of 7 strands, order 3245671; strand 7 is antiparallel to the rest. The figure to the left shows a ribbon representation of the structure of NP_207418.1. The direction of the polypeptide chain is colored with the N-terminal region in blue and the C-terminal region in red.

      

      

      

      

      

      

      

    dimer.pngThe biologically relevant oligimerization state of NP_207418.1 is the dimer. A ribbon representation of the dimer is shown on the right. In the crystal structure, the two monomers comprising the dimer are related by a two-fold non-crystallographic axis of symmetry. A large number of monomer-monomer hydrogen bons, 24, stabilize the dimer. In addition there, are three salt bridges between the two monomers. In the dimer, approximately 2400 Angstrom**2 of surface area is buried within the dimer. The monomer-monmer interaction domains are comprised of non-contiguous regions of the amino acid sequence.

      

      

      


      

    Hit   Select   Q-score   Z-score   No. 
     SSE 
     RMSD 
     (Å) 
     Seq. 
     id 
     PDB 
     entry 
    Name
     1  0.629 12.9 21 1.74  24.9%  2o1bA Structure of aminotransferase from staphylococcus aureus
     2  0.584 12.5 21 1.77  26.6%  2douA Probable n-succinyldiaminopimelate aminotransferase (ttha0342) from thermus thermophilus hb8
     3  0.580 11.6 20 2.02  25.1%  1o4sA Crystal structure of aspartate aminotransferase (tm1255) from thermotoga maritima at 1.90 a resolution
     4  0.544 11.1 20 2.08  27.9%  5bj4A Thermus thermophilus aspartate aminotransferase tetra mutant 2
     5  0.542 10.7 21 2.10  27.5%  2gb3A Crystal structure of aspartate aminotransferase (tm1698) from thermotoga maritima at 2.50 a resolution
     6  0.541 11.1 20 2.12  27.3%  5bj3A Thermus thermophilus aspartate aminotransferase tetra mutant 1
     7  0.537 9.8 21 2.07  27.1%  1v2dA Crystal structure of t.Th hb8 glutamine aminotransferase
     8  0.537 10.1 20 2.10  19.8%  1u08A Crystal structure and reactivity of ybdl from escherichia coli identify a methionine aminotransferase function.
     9  0.534 11.1 20 2.11  26.2%  1b5oA Thermus thermophilus aspartate aminotransferase single mutant 1
     10  0.533 11.0 20 2.09  27.3%  1b5pA Thermus thermophilus aspartate aminotransferase double mutant 1

      

     Shown above is a fold match table for the structure of NP_207418.1 from the Profunc server. Not suprisingly, the known structures that show fold similarity to NP_207418 are aminotransferases.  Among these structures is found the structure of PDB ID 1o4s(1) a JCSG targets and an aspartate amino transferase from Thermotoga maritima.

    TM1255_overlap.png

      

     Superposition of the structures of NP_207418.1 (green) and PDB ID 1o4s (blue). The red spheres represent the structures of pyridoxal phosphate from the coordinates of the aspartate aminotransferase from Thermotoga maritima (PDB ID 1o4s).

      

      

      

      

      

      

     

    Shown on the right is a structure based amino acid sequnence alignment for NP_207418.1 and the top scoring structures from the Secondary Structure Matcging search. The alignment was performed using the FASTA-Protein Similarity Search,  EXPRESSO and ESPRIPT. Based on this search, the following amino acids (NP_207408.1 numbering are stricly conserved:

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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