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2pok

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

    Title Crystal structure of a M20 family metallo peptidase from Streptococcus pneumoniae. TO BE PUBLISHED
    Site MCSG
    PDB Id 2pok Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS5587,AAK74332, 170187
    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 2.44 Rfactor 0.1781
    Waters
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    Solvent Content 49.52

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    Ligand Information
    Ligands BGC (BETA-D-GLUCOSE) x 4
    Metals MN (MANGANESE) x 2

    Jmol

     
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    Google Scholar output for 2pok
    1. 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
     

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    Protein Summary

    This protein has been classified as a non-peptidase homologue in subfamily M20A of the MEROPS database because one of the important active site residues is not conserved.  Subfamily M20A contains metal-dependent exopeptidases (carboxypeptidases, aminopeptidases, dipeptidases) as well as other enzymes such as aminoacylase and acetylornithine deacetylase.  All active enzymes in this subfamily bind two zinc ions and are described as co-catalytic metalloenzymes.  The zinc ions are bound by five ligands, with one of the ligands binding both zinc ions.  In the type example for the family, glutamate carboxypeptidase from a Pseudomonas species (Uniprot accesssion P06621), zinc 1 is bound by Asp141, Glu176 and His385 whereas zinc 2 is bound by His112, Asp141 and Glu200.  In this protein from Streptococcus pneumoniae the equivalent residues are His90, Asp123, Glu158, Gln185 and His431.  Glutamine is not known to be a zinc ligand for any member of family M20; and the only peptidase family where Gln is known as a metal ligand is family M11, in homologues from Volvox species in which copper rather than zinc is bound (Heitzer & Hallmann, 2002).  The structure shows that the Streptococcus pneumoniae protein binds manganese rather than zinc and only one ion rather than two.  This ion is bound by His90, Asp123 and Glu158, mixing ligands from both homologous metal-binding sites.  The replacement of the fourth metal ligand for glutamine is therefore irrelevant for the function of this protein.  Manganese is known to be the metal in X-Pro dipeptidase (MEROPS identifier M24.003), where two manganese ions are bound, but no peptidase is known with a mono-catalytic manganese ion.  It is therefore possible that the Streptococcus pneumoniae protein is not a peptidase. 
     

     

    The Streptococcus pneumoniae protein does have conserved two residues known to be important for catalysis (Asp92 and Glu157) which implies that it may be an enzyme.

    There are over eighty members of subfamily M20A that are classified as non-peptidase homologues because only either the fourth or fifth zinc ligand (or both) has been replaced.  Conceivably, all of these proteins may be manganese-dependent enzymes.

    Ligand Summary

    Reviews

    References

     

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