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1vki

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

    Title Crystal structure of hypothetical protein (ATU3699) from Agrobacterium tumefaciens at 1.60 A resolution. To be published
    Site JCSG
    PDB Id 1vki Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1325,15159614, RER070207001267
    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 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.02 Rfactor 0.15201
    Waters
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    Solvent Content 38.78

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 1vki
    1. Protein function prediction using local 3D templates
    RA Laskowski, JD Watson, JM Thornton - Journal of Molecular Biology, 2005 - Elsevier
     
    2. On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination
    S Panjikar, V Parthasarathy, VS Lamzin - Section D: Biological , 2009 - scripts.iucr.org
     
    3. Structures of Two Bacterial Prolyl-tRNA Synthetases with and without a cis-Editing Domain
    T Crepin, A Yaremchuk, M Tukalo, S Cusack - Structure, 2006 - Elsevier
     
    4. Efficient protein tertiary structure retrievals and classifications using content based comparison algorithms
    PH Chi - 2007 - mospace.umsystem.edu
     
    5. Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution
    K Murayama, M Kato-Murayama, K Katsura - Section F: Structural , 2004 - scripts.iucr.org
     
    6. CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology
    A Paiardini, F Bossa, S Pascarella - Nucleic acids research, 2005 - Oxford Univ Press
     

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    Protein Summary

    The gene Atu3699 (or AGR_L_2275) from Agrobacterium tumefaciens encodes the NP_356919, a putative conserved domain of the PrdX deacylase.  The PrdX protein is a homolog of the YbaK and ProX proteins (PF04073), and the prolyl-tRNA synthetase-editing domain (ProRS-INS). PrdX deacylases specifically hydrolyze Ala-tRNA(Pro).

    The 1vki structure belongs to the class of alpha and beta (a+b) proteins and reveals  YbaK/ProRS associated domain fold type SCOP55825, inside the YbaK/ProRS (super)family. The structure of a close homologue of this protein from Caulobacter crescentus has been solved, 1VJF (Z=26). Other similar structures include the APE2540 protein 1wdv (Z=16), the cysteinyl-tRNA(Pro) deacylase 1dbu (Z=16), and the TTHA1699 protein 2z0x (Z=15).

    Ligand Summary



    References

    Reviews

    References

     

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