2vo9

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:02, 9 May 2024) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2vo9.png|left|200px]]
 
-
<!--
+
==CRYSTAL STRUCTURE OF THE ENZYMATICALLY ACTIVE DOMAIN OF THE LISTERIA MONOCYTOGENES BACTERIOPHAGE 500 ENDOLYSIN PLY500==
-
The line below this paragraph, containing "STRUCTURE_2vo9", creates the "Structure Box" on the page.
+
<StructureSection load='2vo9' size='340' side='right'caption='[[2vo9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2vo9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_phage_A500 Listeria phage A500]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1xp2 1xp2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VO9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VO9 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
{{STRUCTURE_2vo9| PDB=2vo9 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vo9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vo9 OCA], [https://pdbe.org/2vo9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vo9 RCSB], [https://www.ebi.ac.uk/pdbsum/2vo9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vo9 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/AEPE_BPA50 AEPE_BPA50] Cell wall lytic enzyme. Hydrolyzes the link between L-alanine and D-glutamate residues in certain bacterial cell-wall glycopeptides.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vo/2vo9_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=2vo9 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Similar to many other bacterial cell-wall-hydrolyzing enzymes, the Listeria bacteriophage A500 endopeptidase Ply500 has a modular architecture consisting of an enzymatically active domain (EAD) linked to a cell-wall-binding domain (CBD) in a single polypeptide chain. The crystal structure of the EAD of Ply500 has been solved at 1.8 A resolution. The shape of the enzyme resembles a sofa chair: one alpha-helix and three antiparallel beta-strands form the seat, which is supported by two more alpha-helices, while another alpha-helix together with the following loop give rise to the backrest. A sulfate anion bound to the active site, which harbours a catalytic Zn2+ ion, indicates mechanistic details of the peptidase reaction, which involves a tetrahedral transition state. Despite very low sequence similarity, a clear structural relationship was detected to the peptidases VanX, DDC, MSH and MepA, which belong to the so-called 'LAS' family. Their gross functional similarity is supported by a common bound Zn2+ ion and a highly conserved set of coordinating residues (His80, Asp87 and His133) as well as other side chains (Arg50, Gln55, Ser78 and Asp130) in the active site. Considering the high sequence similarity to the EAD of the Listeria phage endopeptidase Ply118, both enzymes can thus be assigned to the LAS family. The same is the case for the L,D-endopeptidase CwlK from Bacillus subtilis, which shows both functional and amino-acid sequence similarity. The fact that the CBD of Ply500 is closely homologous to the CBD of the Listeria phage N-acetylmuramoyl-L-alanine amidase PlyPSA, which exhibits a totally different EAD, illustrates the modular composition and functional variability of this class of enzymes and opens interesting possibilities for protein engineering.
-
===CRYSTAL STRUCTURE OF THE ENZYMATICALLY ACTIVE DOMAIN OF THE LISTERIA MONOCYTOGENES BACTERIOPHAGE 500 ENDOLYSIN PLY500===
+
Structural analysis of the L-alanoyl-D-glutamate endopeptidase domain of Listeria bacteriophage endolysin Ply500 reveals a new member of the LAS peptidase family.,Korndorfer IP, Kanitz A, Danzer J, Zimmer M, Loessner MJ, Skerra A Acta Crystallogr D Biol Crystallogr. 2008 Jun;64(Pt 6):644-50. Epub 2008, May 14. PMID:18560152<ref>PMID:18560152</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_18560152}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2vo9" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 18560152 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18560152}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
[[2vo9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Listeria_phage_a500 Listeria phage a500]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1xp2 1xp2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VO9 OCA].
+
[[Category: Listeria phage A500]]
-
 
+
[[Category: Kanitz A]]
-
==Reference==
+
[[Category: Korndoerfer IP]]
-
<ref group="xtra">PMID:018560152</ref><references group="xtra"/>
+
[[Category: Skerra A]]
-
[[Category: Listeria phage a500]]
+
-
[[Category: Kanitz, A.]]
+
-
[[Category: Korndoerfer, I P.]]
+
-
[[Category: Skerra, A.]]
+
-
[[Category: Cell wall]]
+
-
[[Category: Cell wall biogenesis/degradation]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Secreted]]
+

Current revision

CRYSTAL STRUCTURE OF THE ENZYMATICALLY ACTIVE DOMAIN OF THE LISTERIA MONOCYTOGENES BACTERIOPHAGE 500 ENDOLYSIN PLY500

PDB ID 2vo9

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/2vo9"
Personal tools