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

    Title Crystal structure of a M20A metallo peptidase (dapE, lpg0809) from Legionella pneumophila subsp. pneumophila str. philadelphia 1 at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3pfe Target Id 403140
    Molecular Characteristics
    Source Legionella pneumophila subsp. pneumophila str. philadelphia 1
    Alias Ids TPS30642,YP_094844.1, 3.40.630.10, 324423 Molecular Weight 52493.43 Da.
    Residues 471 Isoelectric Point 5.57
    Sequence mfkpqglydyicqqwqeeilpslcdyikipnksphfdakweehgymeqavnhianwckshapkgmtlei vrlknrtpllfmeipgqiddtvllyghldkqpemsgwsddlhpwkpvlkngllygrggaddgysayasl tairaleqqglpyprciliieaceesgsydlpfyiellkerigkpslvicldsgagnyeqlwmttslrg nlvgkltvelinegvhsgsasgivadsfrvarqlisriedentgeiklpqlycdipderikqakqcaei lgeqvysefpwidsakpviqdkqqlilnrtwrpaltvtgadgfpaiadagnvmrpvtslklsmrlpplv dpeaasvamekaltqnppynakvdfkiqnggskgwnapllsdwlakaaseasmtyydkpaaymgeggti pfmsmlgeqfpkaqfmitgvlgphsnahgpneflhldmvkkltscvsyvlysfsqkk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.50 Rfree 0.1630
    Matthews' coefficent 2.53 Rfactor 0.1376
    Waters 552 Solvent Content 51.32

    Ligand Information


    Google Scholar output for 3pfe
    1. Assessment of ligand_binding residue predictions in CASP9
    T Schmidt, J Haas, TG Cassarino - Structure, Function, and , 2011 - Wiley Online Library
    2. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
    3. Mutational and structural analysis of LN-carbamoylase: new insights into a peptidase M20/M25/M40 family member.
    S Martnez-Rodrguez, A Garca-Pino - Journal of , 2012 - Am Soc Microbiol
    4. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of succinyl-diaminopimelate desuccinylase (Rv1202, DapE) from
    L Reinhard, J Mueller-Dieckmann - Section F: Structural , 2012 - scripts.iucr.org

    Protein Summary

    Pfam Update:

    This proetin is part of peptidease_M20 family which has known structures so this is not a high priority for us.

    This protein is annotated as succinyl-diaminopimelate desuccinylase belonging to Pfam PF01546 (Zinc peptidase domain) and PF07687 (Peptidase dimerization domain).

    JCSG has been increasing the structural coverage for this Pfam clan. For furtther information on these structures solved by JCSG, see the TOPSAN Zinc_Peptidase page in the Tags button below.

    The protein is a monomer in the asymmetric unit of the crystal structure and Zn (grey spheres) has been modeled at the putative active site (red sticks) based on the anomalous difference Fourier map (ADP) and its presence in a fluorescence excitation scan. A glycerol molecule from the cryoprotectant has been modeled near this putative active site. Two other Zn ions (pink and red spheres) have also been modeled based on the ADF.


    Analytical size-exclusion chromatography suggests a dimer as the stable oligomeric form in solution.

    Ligand Summary




    No references found.

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