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| | ==High resolution structure of M23 peptidase LytM with substrate analogue== | | ==High resolution structure of M23 peptidase LytM with substrate analogue== |
| - | <StructureSection load='4zyb' size='340' side='right' caption='[[4zyb]], [[Resolution|resolution]] 1.50Å' scene=''> | + | <StructureSection load='4zyb' size='340' side='right'caption='[[4zyb]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4zyb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staa8 Staa8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZYB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZYB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4zyb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_NCTC_8325 Staphylococcus aureus subsp. aureus NCTC 8325]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZYB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4SQ:TETRAGLYCINE+PHOSPHINATE'>4SQ</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4SQ:TETRAGLYCINE+PHOSPHINATE'>4SQ</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qwy|1qwy]], [[2b0p|2b0p]], [[2b13|2b13]], [[2b44|2b44]], [[4lxc|4lxc]], [[4qp5|4qp5]], [[4qpb|4qpb]], [[4bh5|4bh5]], [[1r77|1r77]], [[3it5|3it5]], [[3it7|3it7]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4zyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zyb OCA], [https://pdbe.org/4zyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zyb RCSB], [https://www.ebi.ac.uk/pdbsum/4zyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zyb ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lytM, SAS0252 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93061 STAA8])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysostaphin Lysostaphin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.75 3.4.24.75] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4zyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zyb OCA], [http://pdbe.org/4zyb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zyb RCSB], [http://www.ebi.ac.uk/pdbsum/4zyb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zyb ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/LYTM_STAAS LYTM_STAAS]] Peptidoglycan hydrolase (autolysin) specifically acting on polyglycine interpeptide bridges of the cell wall peptidoglycan. | + | [https://www.uniprot.org/uniprot/LYTM_STAA8 LYTM_STAA8] Peptidoglycan hydrolase (autolysin) specifically acting on polyglycine interpeptide bridges of the cell wall peptidoglycan.<ref>PMID:10220159</ref> <ref>PMID:8095258</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Lysostaphin]] | + | [[Category: Large Structures]] |
| - | [[Category: Staa8]] | + | [[Category: Staphylococcus aureus subsp. aureus NCTC 8325]] |
| - | [[Category: Bochtler, M]] | + | [[Category: Bochtler M]] |
| - | [[Category: Czapinska, H]] | + | [[Category: Czapinska H]] |
| - | [[Category: Grabowska, M]] | + | [[Category: Grabowska M]] |
| - | [[Category: Jagielska, E]] | + | [[Category: Jagielska E]] |
| - | [[Category: Sabala, I]] | + | [[Category: Sabala I]] |
| - | [[Category: Complex]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Lytm]]
| + | |
| - | [[Category: Peptidase]]
| + | |
| - | [[Category: Peptidoglycan amidase]]
| + | |
| - | [[Category: Tetraglycine phosphinate]]
| + | |
| - | [[Category: Transition state analogue]]
| + | |
| Structural highlights
4zyb is a 4 chain structure with sequence from Staphylococcus aureus subsp. aureus NCTC 8325. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
LYTM_STAA8 Peptidoglycan hydrolase (autolysin) specifically acting on polyglycine interpeptide bridges of the cell wall peptidoglycan.[1] [2]
Publication Abstract from PubMed
LytM is a Staphylococcus aureus autolysin and a homologue of the S. simulans lysostaphin. Both enzymes are members of M23 metallopeptidase family (MEROPS) comprising primarily bacterial peptidoglycan hydrolases. LytM occurs naturally in a latent form, but can be activated by cleavage of an inhibitory N-terminal proregion. Here, we present a 1.45 A crystal structure of LytM catalytic domain with a transition state analogue, tetraglycine phosphinate, bound in the active site. In the electron density, the active site of the peptidase, the phosphinate and the "diglycine" fragment on the P1' side of the transition state analogue are very well defined. The density is much poorer or even absent for the P1 side of the ligand. The structure is consistent with the involvement of His260 and/or His291 in the activation of the water nucleophile and suggests a possible catalytic role for Tyr204, which we confirmed by mutagenesis. Possible mechanisms of catalysis and the structural basis of substrate specificity are discussed based on the structure analysis.
High resolution structure of an M23 peptidase with a substrate analogue.,Grabowska M, Jagielska E, Czapinska H, Bochtler M, Sabala I Sci Rep. 2015 Oct 6;5:14833. doi: 10.1038/srep14833. PMID:26437833[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ramadurai L, Lockwood KJ, Nadakavukaren MJ, Jayaswal RK. Characterization of a chromosomally encoded glycylglycine endopeptidase of Staphylococcus aureus. Microbiology. 1999 Apr;145 ( Pt 4):801-8. PMID:10220159
- ↑ Mani N, Tobin P, Jayaswal RK. Isolation and characterization of autolysis-defective mutants of Staphylococcus aureus created by Tn917-lacZ mutagenesis. J Bacteriol. 1993 Mar;175(5):1493-9. PMID:8095258
- ↑ Grabowska M, Jagielska E, Czapinska H, Bochtler M, Sabala I. High resolution structure of an M23 peptidase with a substrate analogue. Sci Rep. 2015 Oct 6;5:14833. doi: 10.1038/srep14833. PMID:26437833 doi:http://dx.doi.org/10.1038/srep14833
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