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The Open Protein Structure Annotation Network
PDB Keyword
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3h50

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

    Title Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris. Acta Crystallogr.,Sect.F 66 1347-1353 2010
    Site JCSG
    PDB Id 3h50 Target Id 367064
    Molecular Characteristics
    Source Xanthomonas campestris pv. campestris str. atcc 33913
    Alias Ids TPS1498,NP_636471.1, 2.60.120.10, 104365, 90798 Molecular Weight 12165.88 Da.
    Residues 113 Isoelectric Point 4.85
    Sequence mqyatlelnnafkvlfslrqvqaaemviapgdreggpdnrhrgadqwlfvvdgageaivdghtqalqag sliaiergqaheirntgdtplktvnfyhppaydaqgeplpageg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.60 Rfree 0.220
    Matthews' coefficent 2.19 Rfactor 0.182
    Waters 154 Solvent Content 43.79

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3h50
    1. Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris
    HL Axelrod, P Kozbial, D McMullan - Section F: Structural , 2009 - scripts.iucr.org
     
    2. Experimental phasing using zinc anomalous scattering
    SS Cha, YJ An, CS Jeong, MK Kim, SG Lee - Section D: Biological , 2012 - scripts.iucr.org
     
    3. Mcanismes de rgulation de l'ATP synthase mitochondriale de S. cerevisiae par son peptide endogne IF1 et tude de l'oligomrisation d'IF1 de S. cerevisiae.
    T Andrianaivomananjaona - 2011 - hal.archives-ouvertes.fr
     

    Protein Summary

    The TcmJ gene of Xanthomonas campestris pv. campestris str. ATCC 33913 encodes a zinc-binding protein from cupin superfamily with a molecular weight of 12,166 Da (residues 1 - 113) and a calculated isoelectric point of 4.85.

    Xanthomonas campestris pv. Campestris (Xcc) is a Gram-negative pathogenic bacterium causing black rot, one of the major worldwide diseases of cruciferous crops. It also synthesizes a variety of polyketide metabolites that lead to important antibiotics.

    TcmJ belongs to cupin superfamily (PF07883), where proteins of this superfamily have conserved beta-barrel fold and are classified into at least 18 functional classes performing many different biochemical reactions, including several involved in plant growth and development {Dunwell, 2004 #6}. In enzymatic cupins the metal cofactor determines reaction type {Dunwell, 2004 #6}, and zinc-binding cupins with known structure are either phosphomannose isomerases (i.e. PDB structure 1PMI; Z=8), glucose-6-phosphate isomerase (PDB structure 2GC3; Z=10), 5-keto-4-deoxyuronate isomerase (PDB structure 1XRU; Z=8), hydroxypropylphosphonic acid epoxidase (PDB structure 2BNM; Z=9), or plant auxin binding proteins (i.e. PDB structure 1LRH, Z=11, that also binds alpha-D-mannose and N-acetyl glucosamine).

    No metal ion was found in the crystal structure of identical protein (XC5357, PDB structure 2GU9) and Chin et al. proposed alternative to our conclusion that XC5357 is likely a tetracenomycin polyketide synthesis enzyme with a novel substrate binding cavity requiring no metal ion for activity {Chin, 2006 #9}.

    Sequence database search found only four (YP_362950, NP_641528, YP_411980, YP_136688; Figure 2B) highly similar homologs of TcmJ (NP_636471), and over a thousand less similar proteins from different protein families: Pfam01050 (mannose-6-phosphate isomerase type II), Pfam02041 (auxin binding protein), Pfam07883 (cupin domain), Pfam03079 (ARD/ARD` family), Pfam02311 (AraC-like ligand binding domain), Pfam05523 (WxcM-like, C-terminal), Pfam05995 (Cysteine dioxygenase type I), Pfam02678 (pirin), Pfam07847 (DUF1637), Pfam06845 (myo-inositol catabolism protein IolB), Pfam07385 (DUF1498), Pfam04074 (DUF386), Pfam04962 (5-keto 4-deoxyuronate isomerase). By sequence similarity it was not possible to assign function to TcmJ.

    Dali provides hits with the BH2720 protein 2oa2 (Z=15), TTHA0104 protein 2dct (Z=14), and the oxalate oxidase 2ete (Z=13).

     


    This protein has many acidic residues and it might be interesting to see if it can interact with its genomic neighbor a protein that is rich in basic amino acids.

    Ligand Summary



    References

    Reviews

    References

     

    No references found.

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