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

    Title Crystal structure of Putative 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NP_282733.1) from Campylobacter jejuni at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 2rij Target Id 377381
    Molecular Characteristics
    Source Campylobacter jejuni subsp. jejuni nctc 11168
    Alias Ids TPS1687,NP_282733.1, 104322 Molecular Weight 42358.53 Da.
    Residues 386 Isoelectric Point 5.77
    Sequence mintkedflllikqieqksgykkpkafgiarldrgqlnknkilqasfalinyeqnfgsaaimleafmqr gveidfnasefvqtlkledidfalscfkpfleedghqnidllkiikdkfkddefsfvclfedkeplsve siylklyllstkkvplrsinlngafgllsnvawsddkpieleylranemrlkmsnqypkidfvdkfprf lahiipedntrilesskvrmgaslaagttimpgasyvnfnagttgacmvegrisssaivgegsdvggga silgvlsgtsgnaisvgkacllgansvtgiplgdncivdagiavlegtkfllkdaeelaklnpyfnfdk eiykglelkglnglhfrqdsisgamivalnkkavklnealh
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.185
    Matthews' coefficent 4.38 Rfactor 0.156
    Waters 450 Solvent Content 71.89

    Ligand Information


    Google Scholar output for 2rij
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    2. Docking flexible ligands in proteins with a solvent exposure-and distance-dependent dielectric function
    DP Garden, BS Zhorov - Journal of computer-aided molecular design, 2010 - Springer
    3. The three-dimensional Structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism
    L Schuldt, S Weyand, G Kefala, MS Weiss - Journal of molecular biology, 2009 - Elsevier
    4. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of tetrahydrodipicolinate-N-succinyltransferase (Rv1201c) from
    L Schuldt, S Weyand, G Kefala - Section F: Structural , 2008 - scripts.iucr.org
    5. Direct methods and residue type specific isotope labeling in NMR structure determination and model-driven sequential assignment
    A Schedlbauer, R Auer, K Ledolter, M Tollinger - Journal of biomolecular , 2008 - Springer
    6. Tetrahydrodipicolinate N-Succinyltransferase and Dihydrodipicolinate Synthase from Pseudomonas aeruginosa: Structure Analysis and Gene Deletion
    R Schnell, W Oehlmann, T Sandalova, Y Braun - PloS one, 2012 - dx.plos.org
    7. Two-, Three-, and Four-State Events Occur in the Mechanical Unfolding of Small Protein L Using Molecular Dynamics Simulations
    AV Glyakina, NK Balabaev - Protein and Peptide , 2010 - benthamscience.com
    8. The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules
    JK Noel, JN Onuchic - Computational Modeling of Biological Systems, 2012 - Springer
    9. The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins
    Y Chebaro, S Pasquali - The Journal of Physical , 2012 - ACS Publications
    10. Computer simulation study of folding thermodynamics and kinetics of proteins in osmolytes and denaturants
    A Linhananta, G Amadei, T Miao - Journal of Physics: Conference , 2012 - iopscience.iop.org
    D Garden - 2011 - digitalcommons.mcmaster.ca
    12. A Quantitative Reconstruction of the Amide I Contour in the IR Spectra of Peptides and Proteins: From Structure to Spectrum
    JW Brauner, R Mendelsohn - Protein Folding and Misfolding, 2012 - Springer
    13. Modelling protein backbone loops using the Monte Carlo method
    J Fernandez-Carmona - 2009 - eprints.soton.ac.uk
    14. Development and experimental validation of a protein design software
    MT Stiebritz - 2008 - deposit.ddb.de

    Protein Summary

    The dapD gene from Campylobacter jejuni encodes a putative 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (PF, COG2171, EC that adopts a single-stranded left-handed beta-helix fold with an additional N-terminal 3-helical domain. For more information about the structure and function of this protein, see [Ref].


    To do: check oligomerization state of this protein - is it a trimer? check position of citrate - is it comparable to position of succinate in succinyl-CoA ligand?

    Ligand Summary





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