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3iuu

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

    Title Crystal structure of Putative metallopeptidase (YP_676511.1) from MESORHIZOBIUM SP. BNC1 at 2.13 A resolution. To be published
    Site JCSG
    PDB Id 3iuu Target Id 378347
    Molecular Characteristics
    Source Mesorhizobium sp. bnc1
    Alias Ids TPS7079,YP_676511.1, PF07364, PF07171, 91559 Molecular Weight 53908.20 Da.
    Residues 494 Isoelectric Point 5.13
    Sequence maqrsilvgqiwheghsfnpiltrekdflflrgeavleearasstalsgivktaealgyrcvpsisara rpggaieqkvfdnivdefvqaarmqdfdaicldlhgatlaehtldtegyllsrlrevvgndimislald lhayltpqmveqatiitsfrttphadieetgvramtlldslsnetrppraiyslipfltrgndetwsgp laeigaaadrwrarsdvvdlsifnvhpfldvpgygqvvlaydngsgaaidacrdlsdmlwkardefqeq lmsvdkaleiartsrqllalgdqgdrvmgagpgdspeiarvalehfpglkvavpvydpqavrtareage natvrmavggafthsvaplerdwtvrklcrarftnigpymagteadfgdaavltcdavtvivttmapnv hdpafyeavgvplasqqavvaraanhyklsfadiartitvdtpgltafkphqfpftqarpfypldivqw sfaplecnkvg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.13 Rfree 0.228
    Matthews' coefficent 2.78 Rfactor 0.184
    Waters 314 Solvent Content 55.75

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    378347 from Mesorhizobium sp. bnc1 likely encodes a novel zinc peptidase (Fig 1). The protein is a homolog to MlrC protein Sphingomonas sp. ACM-3962 (24% seq id, Fig 2). MlrC is a member of a gene cluster that is involved in degradation of cyanobacterial toxin mycrocystin LR (see ref). This structure is first member of this gene cluster and pfam (MlrC_C). Additional structural analysis will be added later.

     

    This protein is now in families PF07364.5 DUF1485, and PF07171.5 MlrC_C.

     

    The following is contributed by Dr. Neil Rawlings of MEROPS:

    PDB entry 3IUU contains the solved tertiary structure of a homologue of the microcystin-degrading peptidase MlrC from Mesorhizobium sp. BNC1.  The structure consists of two domains, each consisting of a beta-sheet surrounded by helices.  A single zinc ion sits between the domains. 

    The cyanobacterial cyclic peptide toxin microcystin LR is degraded in Sphingomonas by three peptidases.  Microcystinase (MlrA; peptidase family M79) linearizes the peptide; the MlrB peptidase (peptidase family S12) releases a C-terminal tripeptide; and the MlrC peptidase degrades the remaining peptide further, though cleavage positions and products are not known (Bourne et al., 1996).  The MlrC peptidase is only partially characterized.  It is assumed to be a metallopeptidase, because degradation of the microcystin fragment is inhibited by EDTA and 1,10-phenanthroline (Bourne et al., 2001).  There are over 260 known homologues, all of them uncharacterized.

    Inhibition by metal chelators is not in itself sufficient evidence to prove that a peptidase has a catalytic metal.  Structural metals could also be chelated, disrupting the structure and leading to inactivity.  In most metallopeptidases the catalytic metal is zinc (though peptidases with catalytic manganese or cobalt ions are known).  A single zinc ion is usually co-ordinated by two histidines and a third residue, either another histidine, a glutamate or an aspartate.  Peptidases with two co-catalytic zinc ions exist, and these usually have five ligands.  Other residues are important for catalysis, but these vary depending on the family, but are frequently aspartates, glutamates, histidines and tyrosines.

    The single zinc in the Mesorhizobium protein may be co-ordinated by Asp138, His140 and His162.  Catalytic residues may be Glu14 and His104.  All five of these residues are very well conserved in the family.   The nature of these five residues add weight to the hypothesis that this is a family of metallopeptidases.

    However, the structure shows no resemblance to any known metallopeptidase structure.  A DALI search reveals several significant structural matches, of which the highest scoring are structures of ribose ABC transporters and maltose operon transcriptional repressors.  It is not unusual for peptidases to share structures with other enzymes (for example members of peptidase family S9 have the alpha/beta hydrolase fold).  And many peptidase families contain proteins that are not peptidases because the active site residues have been replaced (for example haptoglobin is a homologue of trypsin).  The fact that the structure more closely resembles proteins that are not peptidases does not imply that the MlrC homologues are not themselves peptidases.

     

    References

     

    Bourne,D.G., Jones,G.J., Blakeley,R.L., Jones,A., Negri,A.P. & Riddles,P.  Enzymatic pathway for the bacterial degradation of the cyanobacterial cyclic peptide toxin microcystin LR.  Appl Environ Microbiol (1996) 62, 4086-4094.

    Bourne,D.G., Riddles,P., Jones,G.J., Smith,W. & Blakeley,R.L.   Characterisation of a gene cluster involved in bacterial degradation of the cyanobacterial toxin microcystin LR.  Environ Toxicol (2001) 16, 523-534.

     

     

    Figure 1. Monomer of 378347 with SO4 and IMD in the putative active site

    pt07364a.png

    Figure 2. alignment of 378347 and MlrC (Uniprot Q93CA9)

    YP_676511.1                 MAQRSILVG-------------------------QIWHEGHSFNPILTRE
    tr|Q93CA6|Q93CA6_9SPHN      MLDRRTLMGGILSMAGSKATGAALPGRRLRVFVATLGTETNSFSPLPTGL
                                * :*  *:*                          :  * :**.*: * 

    YP_676511.1                 KDF---LFLRGEAVLEEARASSTALSGIVKTAEALGYRCVPSISARARPG
    tr|Q93CA6|Q93CA6_9SPHN      DAFRATMLWRPGEHPDFATEATGPLWAARERAREGRYEVIEGTCAFAMPG
                                . *   :: *     : *  :: .* .  : *.   *. : . .* * **

    YP_676511.1                 GAIEQKVFDNIVDEFVQAAR-MQDFDAICLDLHGATLAEHTLDTEGYLLS
    tr|Q93CA6|Q93CA6_9SPHN      GPVSAQAYQLLRDEILDQLRRAMPVDIVAFGLHGAMLAFGEDECEADLLE
                                *.:. :.:: : **:::  *    .* :.:.**** **    : *. **.

    YP_676511.1                 RLREVVGNDIMISLALDLHAYLTPQMVEQATIITSFRTTPHADIEETGVR
    tr|Q93CA6|Q93CA6_9SPHN      RARAIVGPDVALGAELDLHAHLSQRLVRAADVLVAFKYYPHIDYVERARD
                                * * :** *: :.  *****:*: ::*. * ::.:*:  ** *  * . 

    YP_676511.1                 AMTLLDSLSNETRPPRAIYSLIPFLTRGNDETWSGPLAEIGAAADRWRAR
    tr|Q93CA6|Q93CA6_9SPHN      LLDLLERIRAGEIMP--TSSLFNCQMVAGLATQSSPMKELVADLFEFERR
                                 : **: :      *    **:     ..  * *.*: *: *   .:. *

    YP_676511.1                 SDVVDLSIFNVHPFLDVPGYGQVVLAYDN-----GSGAAIDACRDLSDML
    tr|Q93CA6|Q93CA6_9SPHN      GEVLSGSLIQGFRAGDVARMGSKVLIYTNNDQPAAASIAQDFGRRYQAMA
                                .:*:. *::: .   **.  *. ** * *     .:. * *  *  . *

    YP_676511.1                 WKARDEFQEQLMSVDKALEIARTSRQLLALGDQGDRVMGAGPGDSPEIAR
    tr|Q93CA6|Q93CA6_9SPHN      SIMKGNGPERSFAADIELAKAATAYPVILVDS-SDNPGGGASGDNMALAR
                                   :.:  *: ::.*  *  * *:  :: :.. .*.  *...**.  :**

    YP_676511.1                 VALEHFPGLKVAVPVYDPQAVRTAREAGENATVRMAVGGAFTHSVAPLER
    tr|Q93CA6|Q93CA6_9SPHN      AMLDNDLVPSCIGPIWDPLAVQLGFEAGLGADFSLRVGGKVGEASG---L
                                . *::    .   *::** **: . *** .* . : *** . .: . : 

    YP_676511.1                 DWTVRKLCRARFTNIGPYMAGTEADFGDAAVLTCDAVTVIVTTMAPNVHD
    tr|Q93CA6|Q93CA6_9SPHN      PLDVRGKITGLAENVTQNLQGSRPPLGRVVCISTAGLDIIVSEIRDQCYG
                                   **    .   *:   : *:.. :* .. ::  .: :**: :  : :.

    YP_676511.1                 PAFYEAVGVPLASQQAVVARAANHYKLSFADIARTITVDTPGLTAFKPHQ
    tr|Q93CA6|Q93CA6_9SPHN      PDMFRALGVEPANKRYVAVKSSEQWRIGFGDMGRSVIYVAS--SQQSSIR
                                * ::.*:**  *.:: *..::::::::.*.*:.*::   :. ::  .. :

    YP_676511.1                 FPFTQARPFYPLDIVQWSFAPLECNKVG
    tr|Q93CA6|Q93CA6_9SPHN      HYHKRSRPMWPFEPV-------------
                                . ..::**::*:: *   :  :    :

    Reference:

    Characterisation of a gene cluster involved in bacterial degradation of the cyanobacterial toxin microcystin LR.

    Bourne DG, Riddles P, Jones GJ, Smith W, Blakeley RL. Environ Toxicol. 2001;16(6):523-34. PMID: 11769251 [PubMed - indexed for MEDLINE]

    Ligand Summary

    Zinc, Imidazole and SO4 are tentatively assigned in the active site.

    Reviews

    References

     

    No references found.

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    Files (1)

    FileSizeDateAttached by 
     pt07364a.png
    PT07364A monomer
    177.14 kB17:49, 29 Jul 2009qxuActions
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