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

    Title Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake. Plos One 6 e21875-e21875 2011
    Site JCSG
    PDB Id 3oyv Target Id 416712
    Related PDB Ids 3n8u 
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS33815,ZP_02066800.1, PF04302, 327428 Molecular Weight 39687.36 Da.
    Residues 360 Isoelectric Point 4.40
    Sequence sdddnptvdpanidytpenasswhnymrnvaallktdatnlynawnssykggesyaslfkahsgspyas alscveeivdkcaeianevgtakigdpynlykagnteealyaveswyswhsrddytnniysirnayygs ldgninanslstviaganssldtkiknaiqkaakaiqdipqpfrnhipsnetvaamdacaelesilknd lksyiannsnnintdavlnpvvtqyvdavvvptykslkekndalynavivladnpsnsafetacdawit arepwekseaflfgpvdemgldpnmdswpldqnaivqilnsqswsdlewsegddeaavesaqnvrgfht lefllykngeprkvq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.25 Rfree 0.1630
    Matthews' coefficent 2.16 Rfactor 0.1318
    Waters 553 Solvent Content 43.10

    Ligand Information


    Google Scholar output for 3oyv
    1. Structural and Sequence Analysis of Imelysin-Like Proteins Implicated in Bacterial Iron Uptake
    Q Xu, ND Rawlings, CL Farr, HJ Chiu, JC Grant - PloS one, 2011 - dx.plos.org

    Protein Summary


    The following is contributed by Neil Rawlings from MEROPS:


    PDB entry 3N8U is the first structure solved for a member of peptidase family M75. The only known peptidase in this family is the partially characterized imelysin (also known as insulin-cleaving membrane protease) from Pseudomonas aeruginosa. The peptidase was detected in the outer membrane and shown to contain one zinc ion per molecule. The active site is extracellular (Fricke et al., 1999). Nothing experimental is known about active site residues or metal ligands; however there is well conserved HXXE motif in the family, which is also found in carboxypeptidases from family M14 where the His and Glu are known to be two of the three zinc ligands. Because Pseudomonas aeruginosa is a pathogen affecting patients with a compromised immune system, such as cystic fibrosis and burns patients, its peptidases are of potential pharmacological interest.


    Family M75 contains a number of homologues, all from bacteria. Sequences fall into two groups: those that are very similar to imelysin and probably represent orthologues from different species, and those that are more distantly related. Most of the homologues from Bacteroides species fall into the latter group, including the solved structure from Bacteroides ovatus. There are significant structural differences between the two groups; the Bacteroides-like homologues have a large 200-residue insert at the N-terminus, and are missing a 250-residue region at the C-terminus. This difference might possibly be explained by subdomain shuffling during the course of evolution.


    The structure shows a homodimer with each monomer being predominantly helical, consisting of a cluster of seven long, almost parallel, helices. Each monomer shows two subdomains, with four long helices in the N-terminal subdomain and three in the C-terminal subdomain. The insert relative to imelysin consists of all the helices comprising one half of the molecule and one helix from the other half. The structure is not related to that of any known peptidase (results from a DALI comparison).


    Instead of zinc, three magnesium ions per molecule are bound, one within each monomer (between the subdomains) and one between the monomers. There are no known metallopeptidases where the catalytic metal is magnesium; if the presence of magnesium in the B. ovatus homologue is not a cystallization artefact, then this is either the first metallopeptidase containing magnesium discovered, or it is not a peptidase. On the assumption that the Bacteroides ovatus homologue is an active enzyme and that Mg 1 replaces the zinc ion of imelysin, then possible ligands are Glu111, Lys116, Glu309, Asp322 and Asp326. However, Glu111 and Lys116 are present on the insert relative to imelysin. In all the imelysin sequences, Asp322 is replaced by Glu and Asp326 by Asn. Replacement of metal ligands is unusual but not unprecedented, especially if the metal is different. The only known example concerns a homologue of gametolysin (peptidase family M11) from Volvox where the zinc is replaced by copper and the histidine ligands are replaced by glutamine (Heitzer & Hallmann, 2002). The residues of the HXXE motif (His368 and Glu371) appear to be too distant to be metal ligands, but His368 could be an active site residue with the imidazolium ring orientated by Glu371. This would place all the metal ligands and active site residues within the same subdomain; it is more usual for two of the three metal ligands to be from one subdomain and the third from another subdomain.


    In the dimer, the monomers are arranged to that one is inverted relative to the other, but the potential active sites face in the same direction, so one active site is facing the junction of the monomers. If the molecule is arranged in the membrane so that the helices are at right angles, then the potential active sites would be within the membrane and not on the outer surface as predicted.


    In conclusion, the difference in domain organization, replacement of zinc for magnesium, the absence of an extracellular domain, and the probable location of the active site within the membrane spanning region, make it likely that the Bacteroides ovatus homologue is either a very different peptidase from imelysin, or not a peptidase at all (but possibly still an enzyme). Biochemical characterization of the protein would be useful.


    Fricke,B., Parchmann,O., Kruse,K., Rucknagel,P., Schierhorn,A. & Menge,S. Characterization and purification of an outer membrane metalloproteinase from Pseudomonas aeruginosa with fibrinogenolytic activity.
    Biochim Biophys Acta (1999) 1454, 236-250.

    Heitzer,M. & Hallmann,A. An extracellular matrix-localized metalloproteinase with an exceptional QEXXH metal binding site prefers copper for catalytic activity. J Biol Chem (2002) 277, 28280-28286.

    Ligand Summary




    No references found.

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