This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1zrs

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:06, 14 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1zrs.gif|left|200px]]
 
-
{{Structure
+
==wild-type LD-carboxypeptidase==
-
|PDB= 1zrs |SIZE=350|CAPTION= <scene name='initialview01'>1zrs</scene>, resolution 1.50&Aring;
+
<StructureSection load='1zrs' size='340' side='right'caption='[[1zrs]], [[Resolution|resolution]] 1.50&Aring;' 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]] 1.5&#8491;</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''
+

Current revision

wild-type LD-carboxypeptidase

PDB ID 1zrs

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1zrs"
Personal tools