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The Open Protein Structure Annotation Network
PDB Keyword
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3clm

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

    Title Crystal structure of transaldolase (YP_208650.1) from Neisseria gonorrhoeae FA 1090 at 1.14 A resolution. To be published
    Site JCSG
    PDB Id 3clm Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1746,YP_208650.1, 86650
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.08 Rfactor 0.130
    Waters
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    Solvent Content 40.82

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3clm
    1. Structure and cleavage specificity of the chymotrypsin-like serine protease (3CLSP/nsp4) of porcine reproductive and respiratory syndrome virus (PRRSV)
    X Tian, G Lu, F Gao, H Peng, Y Feng, G Ma - Journal of molecular , 2009 - Elsevier
     
    2. ACORN2: New developments of the ACORN concept
    EJ Dodson, MM Woolfson - Acta Crystallographica Section D: , 2009 - scripts.iucr.org
     
    3. Conservation of structure and mechanism within the transaldolase enzyme family
    AK Samland, S Baier, M Schrmann, T Inoue - FEBS , 2012 - Wiley Online Library
     

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    Protein Summary

    This protein (YP_208650.1) is monomeric, alpha-helical in structure with a beta-sheet in the core, like a TIM barrel fold. It belongs to Pfam PF00923. Members of this family are transaldolases which can catalyze the reversible transfer of a three-carbon ketol unit from sedoheptulose 7-phosphate to glyceraldehyde 3-phosphate to form erythrose 4-phosphate and fructose 6-phosphate. Along with transketolase, this enzyme links the glycolytic and pentose-phosphate pathways. Transaldolases have well conserved sequences. The catalytic mechanism is believed to me mediated by a lysine residue which acts as a nucleophilic group to attack the carbonyl group of fructose-6-phosphate.

    PSI-BLAST (1 round) returns hits with transaldolases with sequence identities ranging from 95% (exp=3e-166) to 28% id (exp=7e-05). There are several PDB structures of proteins in this range: 1VPX, 1ONR, 1I2R, 1I2P, 1I2N, 1I2Q, 1UCW, 1I2O.

    The picture below depicts the superimposition of this protein structure (purple) with the top DALI hit, 1ONR (Transaldolase B from Escherichia coli=top FFAS hit 1UCW, orange) and 1JCJ (lime, DALI hit no. 6, Ref. 1):


    The comparison reveals that the proteins are similar in structure. Active site is quite conserved between YP_208650.1 (spatial location shown below in red) and 1ONR (K138=K132 resp., N160, S199, D17, N43= N154, S176, D17, D35 resp.).


    It's possible that the solvent ligands EDO (green), SO4 (yellow) and HOH (blue) and Cl (grey) near the active site K138 (red) in this protein are mimicing reaction pathway and intermediates as shown below (See Ref1 for further details):


    Superposition of YP_208650.1 (magenta) with 1JCJ (Ref. 1) with bound reactions intermediates in cyan and active site lysine in black:


    Ligand Summary

    SO4, EDO and Cl-

    References

    Reviews

    References

     

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