3gne: Difference between revisions

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<StructureSection load='3gne' size='340' side='right'caption='[[3gne]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
<StructureSection load='3gne' size='340' side='right'caption='[[3gne]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3gne]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlorella_virus_cv-k2 Chlorella virus cv-k2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GNE FirstGlance]. <br>
<table><tr><td colspan='2'>[[3gne]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paramecium_bursaria_Chlorella_virus_CVK2 Paramecium bursaria Chlorella virus CVK2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GNE FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.2&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a0n|3a0n]], [[3im0|3im0]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vAL-1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31555 Chlorella virus CV-K2])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Poly(beta-D-mannuronate)_lyase Poly(beta-D-mannuronate) lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.3 4.2.2.3] </span></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=3gne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gne OCA], [https://pdbe.org/3gne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gne RCSB], [https://www.ebi.ac.uk/pdbsum/3gne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gne ProSAT]</span></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=3gne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gne OCA], [https://pdbe.org/3gne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gne RCSB], [https://www.ebi.ac.uk/pdbsum/3gne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gne ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9DTZ2_9PHYC Q9DTZ2_9PHYC]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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/main_output.php?pdb_ID=3gne ConSurf].
</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=3gne ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Chlorella virus enzyme vAL-1 (38 kDa), a member of polysaccharide lyase family 14, degrades the Chlorella cell wall by cleaving the glycoside bond of the glucuronate residue (GlcA) through a beta-elimination reaction. The enzyme consists of an N-terminal cell wall-attaching domain (11 kDa) and a C-terminal catalytic module (27 kDa). Here, we show the enzyme characteristics of vAL-1, especially its pH-dependent modes of action, and determine the structure of the catalytic module. vAL-1 also exhibited alginate lyase activity at alkaline pH, and truncation of the N-terminal domain increased the lyase activity by 50-fold at pH 7.0. The truncated form vAL-1(S) released di- to hexasaccharides from alginate at pH 7.0, whereas disaccharides were preferentially generated at pH 10.0. This indicates that vAL-1(S) shows two pH-dependent modes of action: endo- and exotypes. The x-ray crystal structure of vAL-1(S) at 1.2 A resolution showed two antiparallel beta-sheets with a deep cleft showing a beta-jelly roll fold. The structure of GlcA-bound vAL-1(S) at pH 7.0 and 10.0 was determined: GlcA was found to be bound outside and inside the cleft at pH 7.0 and 10.0, respectively. This suggests that the electric charges at the active site greatly influence the binding mode of substrates and regulate endo/exo activity. Site-directed mutagenesis demonstrated that vAL-1(S) has a specific amino acid arrangement distinct from other alginate lyases crucial for catalysis. This is, to our knowledge, the first study in which the structure of a family 14 polysaccharide lyase with two different modes of action has been determined.
Crystal structure of family 14 polysaccharide lyase with pH-dependent modes of action.,Ogura K, Yamasaki M, Yamada T, Mikami B, Hashimoto W, Murata K J Biol Chem. 2009 Dec 18;284(51):35572-9. Epub . PMID:19846561<ref>PMID:19846561</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3gne" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Chlorella virus cv-k2]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Hashidume, T]]
[[Category: Paramecium bursaria Chlorella virus CVK2]]
[[Category: Hashimoto, W]]
[[Category: Hashidume T]]
[[Category: Mikami, B]]
[[Category: Hashimoto W]]
[[Category: Murata, K]]
[[Category: Mikami B]]
[[Category: Ogura, K]]
[[Category: Murata K]]
[[Category: Yamada, T]]
[[Category: Ogura K]]
[[Category: Yamasaki, M]]
[[Category: Yamada T]]
[[Category: Alginate lyase]]
[[Category: Yamasaki M]]
[[Category: Chlorella virus]]
[[Category: Lyase]]
[[Category: Polysaccharide lyase family 14]]
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