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| | ==Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition== | | ==Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition== |
| - | <StructureSection load='4oxd' size='340' side='right' caption='[[4oxd]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='4oxd' size='340' side='right'caption='[[4oxd]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4oxd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Lactobacillus_acidophilus Lactobacillus acidophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OXD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OXD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4oxd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactobacillus_acidophilus Lactobacillus acidophilus] and [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OXD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSG:D-ASPARAGINE'>DSG</scene>, <scene name='pdbligand=MUB:N-ACETYLMURAMIC+ACID'>MUB</scene>, <scene name='pdbligand=ZGL:D-ALPHA-GLUTAMINE'>ZGL</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DSG:D-ASPARAGINE'>DSG</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MUB:N-ACETYLMURAMIC+ACID'>MUB</scene>, <scene name='pdbligand=ZGL:D-ALPHA-GLUTAMINE'>ZGL</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">[[4ox5|4ox5]], [[4ox3|4ox3]]</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=4oxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oxd OCA], [https://pdbe.org/4oxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oxd RCSB], [https://www.ebi.ac.uk/pdbsum/4oxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oxd ProSAT]</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=4oxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oxd OCA], [http://pdbe.org/4oxd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oxd RCSB], [http://www.ebi.ac.uk/pdbsum/4oxd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oxd ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8DQQ1_STRR6 Q8DQQ1_STRR6] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Carboxypeptidase|Carboxypeptidase]] | + | *[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Lactobacillus acidophilus]] | | [[Category: Lactobacillus acidophilus]] |
| - | [[Category: Aldridge, C]] | + | [[Category: Large Structures]] |
| - | [[Category: Cleverley, R M]] | + | [[Category: Streptococcus pneumoniae R6]] |
| - | [[Category: Daniel, R A]] | + | [[Category: Aldridge C]] |
| - | [[Category: Duchene, M C]]
| + | [[Category: Cleverley RM]] |
| - | [[Category: Hoyland, C N]] | + | [[Category: Daniel RA]] |
| - | [[Category: Lewis, R J]] | + | [[Category: Duchene MC]] |
| - | [[Category: Sidiq, K]] | + | [[Category: Hoyland CN]] |
| - | [[Category: Vollmer, W]] | + | [[Category: Lewis RJ]] |
| - | [[Category: Cell wall modifying enzyme]] | + | [[Category: Sidiq K]] |
| - | [[Category: Las family]] | + | [[Category: Vollmer W]] |
| - | [[Category: Ld-carboxypeptidase]] | + | |
| Structural highlights
4oxd is a 6 chain structure with sequence from Lactobacillus acidophilus and Streptococcus pneumoniae R6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.8Å |
| Ligands: | , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
Q8DQQ1_STRR6
Publication Abstract from PubMed
Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like beta-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.
Structure of the LdcB LD-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition.,Hoyland CN, Aldridge C, Cleverley RM, Duchene MC, Minasov G, Onopriyenko O, Sidiq K, Stogios PJ, Anderson WF, Daniel RA, Savchenko A, Vollmer W, Lewis RJ Structure. 2014 Jun 4. pii: S0969-2126(14)00139-7. doi:, 10.1016/j.str.2014.04.015. PMID:24909784[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hoyland CN, Aldridge C, Cleverley RM, Duchene MC, Minasov G, Onopriyenko O, Sidiq K, Stogios PJ, Anderson WF, Daniel RA, Savchenko A, Vollmer W, Lewis RJ. Structure of the LdcB LD-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition. Structure. 2014 Jun 4. pii: S0969-2126(14)00139-7. doi:, 10.1016/j.str.2014.04.015. PMID:24909784 doi:http://dx.doi.org/10.1016/j.str.2014.04.015
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