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| - | [[Image:1zrs.gif|left|200px]] | |
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| - | {{Structure
| + | ==wild-type LD-carboxypeptidase== |
| - | |PDB= 1zrs |SIZE=350|CAPTION= <scene name='initialview01'>1zrs</scene>, resolution 1.50Å
| + | <StructureSection load='1zrs' size='340' side='right'caption='[[1zrs]], [[Resolution|resolution]] 1.50Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND=
| + | <table><tr><td colspan='2'>[[1zrs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZRS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZRS FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Muramoyltetrapeptide_carboxypeptidase Muramoyltetrapeptide carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.13 3.4.17.13] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</td></tr> |
| - | |GENE=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zrs OCA], [https://pdbe.org/1zrs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zrs RCSB], [https://www.ebi.ac.uk/pdbsum/1zrs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zrs ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY= | + | == Function == |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zrs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zrs OCA], [http://www.ebi.ac.uk/pdbsum/1zrs PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zrs RCSB]</span> | + | [https://www.uniprot.org/uniprot/LDC_PSEAE LDC_PSEAE] Releases the terminal D-alanine residue from the cytoplasmic disaccharide-tetrapeptide GlcNAc-MurNAc-L-Ala-gamma-D-Glu-meso-Dap-D-Ala, which is a murein turnover product. Probably also act on free tetrapetide. May be involved in murein recycling. |
| - | }}
| + | == Evolutionary Conservation == |
| - | | + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | '''wild-type LD-carboxypeptidase'''
| + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zr/1zrs_consurf.spt"</scriptWhenChecked> |
| - | ==Overview== | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | LD-Carboxypeptidases (EC 3.4.17.13) are named for their ability to cleave amide bonds between l- and d-amino acids, which occur naturally in bacterial peptidoglycan. They are specific for the link between meso-diaminopimelic acid and d-alanine and therefore degrade GlcNAc-MurNAc tetrapeptides to the corresponding tripeptides. As only the tripeptides can be reused as peptidoglycan building blocks, ld-carboxypeptidases are thought to play a role in peptidoglycan recycling. Despite the pharmaceutical interest in peptidoglycan biosynthesis, the fold and catalytic type of ld-carboxypeptidases are unknown. Here, we show that a previously uncharacterized open reading frame in Pseudomonas aeruginosa has ld-carboxypeptidase activity and present the crystal structure of this enzyme. The structure shows that the enzyme consists of an N-terminal beta-sheet and a C-terminal beta-barrel domain. At the interface of the two domains, Ser(115) adopts a highly strained conformation in the context of a strand-turn-helix motif that is similar to the "nucleophilic elbow" in alphabeta-hydrolases. Ser(115) is hydrogen-bonded to a histidine residue, which is oriented by a glutamate residue. All three residues, which occur in the order Ser-Glu-His in the amino acid sequence, are strictly conserved in naturally occurring ld-carboxypeptidases and cannot be mutated to alanines without loss of activity. We conclude that ld-carboxypeptidases are serine peptidases with Ser-His-Glu catalytic triads.
| + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | | + | </jmolCheckbox> |
| - | ==About this Structure== | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1zrs ConSurf]. |
| - | 1ZRS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZRS OCA].
| + | <div style="clear:both"></div> |
| - | | + | __TOC__ |
| - | ==Reference== | + | </StructureSection> |
| - | Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow., Korza HJ, Bochtler M, J Biol Chem. 2005 Dec 9;280(49):40802-12. Epub 2005 Sep 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16162494 16162494]
| + | [[Category: Large Structures]] |
| - | [[Category: Muramoyltetrapeptide carboxypeptidase]] | + | |
| | [[Category: Pseudomonas aeruginosa]] | | [[Category: Pseudomonas aeruginosa]] |
| - | [[Category: Single protein]]
| + | [[Category: Bochtler M]] |
| - | [[Category: Bochtler, M.]] | + | [[Category: Korza HJ]] |
| - | [[Category: Korza, H J.]] | + | |
| - | [[Category: ld-carboxypeptidase]]
| + | |
| - | [[Category: nucleophilic elbow]]
| + | |
| - | [[Category: peptidoglycan hydrolase]]
| + | |
| - | [[Category: serine peptidase]]
| + | |
| - | [[Category: serine-histidine-glutamate triad]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:40:45 2008''
| + | |
