2ntb: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2ntb.png|left|200px]]
-<!--
+==Crystal structure of pectin methylesterase in complex with hexasaccharide V==
-The line below this paragraph, containing "STRUCTURE_2ntb", creates the "Structure Box" on the page.
+<StructureSection load='2ntb' size='340' side='right'caption='[[2ntb]], [[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'>[[2ntb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Dickeya_dadantii_3937 Dickeya dadantii 3937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NTB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NTB 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=ADA:ALPHA-D-GALACTOPYRANURONIC+ACID'>ADA</scene></td></tr>
-{{STRUCTURE_2ntb|  PDB=2ntb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ntb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ntb OCA], [https://pdbe.org/2ntb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ntb RCSB], [https://www.ebi.ac.uk/pdbsum/2ntb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ntb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PMEA_DICD3 PMEA_DICD3] Involved in maceration and soft-rotting of plant tissue.
+== 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/nt/2ntb_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2ntb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We provide a mechanism for the activity of pectin methylesterase (PME), the enzyme that catalyses the essential first step in bacterial invasion of plant tissues. The complexes formed in the crystal using specifically methylated pectins, together with kinetic measurements of directed mutants, provide clear insights at atomic resolution into the specificity and the processive action of the Erwinia chrysanthemi enzyme. Product complexes provide additional snapshots along the reaction coordinate. We previously revealed that PME is a novel aspartic-esterase possessing parallel beta-helix architecture and now show that the two conserved aspartates are the nucleophile and general acid-base in the mechanism, respectively. Other conserved residues at the catalytic centre are shown to be essential for substrate binding or transition state stabilisation. The preferential binding of methylated sugar residues upstream of the catalytic site, and demethylated residues downstream, drives the enzyme along the pectin molecule and accounts for the sequential pattern of demethylation produced by both bacterial and plant PMEs.
-===Crystal structure of pectin methylesterase in complex with hexasaccharide V===
+Molecular basis of the activity of the phytopathogen pectin methylesterase.,Fries M, Ihrig J, Brocklehurst K, Shevchik VE, Pickersgill RW EMBO J. 2007 Sep 5;26(17):3879-87. Epub 2007 Aug 23. PMID:17717531<ref>PMID:17717531</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ntb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17717531}}, adds the Publication Abstract to the page
+*[[Methylesterase 3D structures|Methylesterase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17717531 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17717531}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Dickeya dadantii 3937]]
-NTB is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Erwinia_chrysanthemi Erwinia chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NTB OCA].
+[[Category: Large Structures]]
+[[Category: Brocklehurst K]]
-==Reference==
+[[Category: Fries M]]
-<ref group="xtra">PMID:17717531</ref><references group="xtra"/>
+[[Category: Pickersgill RW]]
-[[Category: Erwinia chrysanthemi]]
+[[Category: Shevchik VE]]
-[[Category: Pectinesterase]]
-[[Category: Brocklehurst, K.]]
-[[Category: Fries, M.]]
-[[Category: Pickersgill, R W.]]
-[[Category: Shevchik, V E.]]
-[[Category: Hydrolase]]
-[[Category: Product complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:58:08 2009''