2vo9

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[[Image:2vo9.png|left|200px]]
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==CRYSTAL STRUCTURE OF THE ENZYMATICALLY ACTIVE DOMAIN OF THE LISTERIA MONOCYTOGENES BACTERIOPHAGE 500 ENDOLYSIN PLY500==
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<StructureSection load='2vo9' size='340' side='right' caption='[[2vo9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[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]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vo9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vo9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vo9 RCSB], [http://www.ebi.ac.uk/pdbsum/2vo9 PDBsum]</span></td></tr>
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<table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vo/2vo9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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/chain_selection.php?pdb_ID=2ata ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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The line below this paragraph, containing "STRUCTURE_2vo9", creates the "Structure Box" on the page.
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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or leave the SCENE parameter empty for the default display.
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-->
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{{STRUCTURE_2vo9| PDB=2vo9 | SCENE= }}
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===CRYSTAL STRUCTURE OF THE ENZYMATICALLY ACTIVE DOMAIN OF THE LISTERIA MONOCYTOGENES BACTERIOPHAGE 500 ENDOLYSIN PLY500===
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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The line below this paragraph, {{ABSTRACT_PUBMED_18560152}}, adds the Publication Abstract to the page
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__TOC__
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(as it appears on PubMed at http://www.pubmed.gov), where 18560152 is the PubMed ID number.
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</StructureSection>
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{{ABSTRACT_PUBMED_18560152}}
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==About this Structure==
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[[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].
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==Reference==
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<ref group="xtra">PMID:018560152</ref><references group="xtra"/>
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[[Category: Listeria phage a500]]
[[Category: Listeria phage a500]]
[[Category: Kanitz, A.]]
[[Category: Kanitz, A.]]

Revision as of 08:41, 7 May 2014

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

2vo9, resolution 1.80Å

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