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The Open Protein Structure Annotation Network
PDB Keyword
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3qqm

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

    Title Crystal structure of a Putative amino-acid aminotransferase (NP_104211.1) from Mesorhizobium loti at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 3qqm Target Id 394461
    Molecular Characteristics
    Source Mesorhizobium loti maff303099
    Alias Ids TPS25802,NP_104211.1, _0052.000773_, 326778 Molecular Weight 24291.11 Da.
    Residues 220 Isoelectric Point 5.49
    Sequence mpaqsplrdgdtadfelietmrwqpgtsflrfdrhlarlygsaaelgfacdpqriaevlsdaldgarta mrtrlalarngdatasaqpyeplaadkvwilrlartrldsqntllrhktsrrqlytharseylvtqade vllanergeicegtitnvfadfgdgvlatprldcgllpgvlraelldegraeeaiysyddlksakalfv gnslrglipaklv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 8
    Resolution (Å) 2.30 Rfree 0.2407
    Matthews' coefficent 2.59 Rfactor 0.1932
    Waters 773 Solvent Content 52.49

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam Summary: This protein is now in family PF01063.12 Aminotran_4 along with other structures.

     

    Target ID 394461 has been determined to a resolution of 2.3 Angstroms using Se-SAD phasing. Several molecules of iodide from the crystallization solution were modeled into the structure. The modeling of these iodides were supported by anomalous difference maps.The amino acid sequence of target ID 394461 shows significant similarity to those sequences belonging to the Aminotran_4 (PF01063) Pfam group. This group includes those proteins that are involved in the pyridoxal-5'-phosphate dependent formation of D-alanine and D-glutamic acids. These modified amino acids are essential for bacterial cell wall formation. Crystal packing suggests that the monomer is a significant oligoimerization state of the protein in solution.Shown below is a ribbon representation of the structure of a monomer of target ID 394461 color coded so that the N-terminal and C-terminal ends of the protein are in blue and red respectively. 

     

     

     

    monomer_ribbons.png

     

     A DALI search using the refined coordinates of target ID 396441 has structural similarity with related entries in the PDB

     

     

     

    PDB ID Z-Score rmsd (Ang) Lalign %Seq ID Description
    2zgi 22.6 2.1 198 26 PUTATIVE 4-AMINO-4-DEOXYCHORISMATE LYASE
    1i2l 22.5 2.2 208 20 4-AMINO-4-DEOXYCHORISMATE LYASE
    3csw 21.7 2.1 204 23 PUTATIVE BRANCHED-CHAIN-AMINO-ACID
    1iye 21.2 2.4 210 20 BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE
    1et0 21.1 2.2 199   4-AMINO-4-DEOXYCHORISMATE LYASE

     

     

     Shown below is 2fo-fc electron density contoured at 2 sigma. The electron density maps show that pyridoxal-5'-Phosphate is covalently bound to the protein by the formation of an aldimine linkage via the sidechain of Lys 117.

     plp_DENSITY.PNG

     

     

    Shown below is a ribbon representation that shows the pyridoxal-5'-phosphate bound to Lys 117 at the active site.

     

    monomer_llp.png

     

     

    References

    Nakai T, Mizutani H, Miyahara I, Hirotsu K, Takeda S, Jhee KH, Yoshimura T, Esaki
    N. " Three-dimensional structure of 4-amino-4-deoxychorismate lyase from Escherichia
    coli." J Biochem. 2000 Jul;128(1):29-38.
    Pubmed ID 10876155

     

     


     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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