2ntp

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[[Image:2ntp.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of pectin methylesterase in complex with hexasaccharide VI==
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|PDB= 2ntp |SIZE=350|CAPTION= <scene name='initialview01'>2ntp</scene>, resolution 1.70&Aring;
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<StructureSection load='2ntp' size='340' side='right'caption='[[2ntp]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ADA:ALPHA-D-GALACTOPYRANURONIC+ACID'>ADA</scene>, <scene name='pdbligand=M8C:METHYL+ALPHA-D-GALACTOPYRANURONATE'>M8C</scene>
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<table><tr><td colspan='2'>[[2ntp]] 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=2NTP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NTP FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectinesterase Pectinesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.11 3.1.1.11] </span>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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|GENE= pemA, pem ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=556 Erwinia chrysanthemi])
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<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>, <scene name='pdbligand=M8C:METHYL+ALPHA-D-GALACTOPYRANURONATE'>M8C</scene>, <scene name='pdbligand=SHB:METHYL+BETA-D-GALACTOPYRANURONATE'>SHB</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ntp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ntp OCA], [https://pdbe.org/2ntp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ntp RCSB], [https://www.ebi.ac.uk/pdbsum/2ntp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ntp ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1qjv|1QJV]], [[2nsp|2NSP]], [[2nst|2NST]], [[2nt6|2NT6]], [[2nt9|2NT9]], [[2ntb|2NTB]], [[2ntq|2NTQ]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ntp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ntp OCA], [http://www.ebi.ac.uk/pdbsum/2ntp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ntp RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/PMEA_DICD3 PMEA_DICD3] Involved in maceration and soft-rotting of plant tissue.
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== Evolutionary Conservation ==
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'''Crystal structure of pectin methylesterase in complex with hexasaccharide VI'''
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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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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nt/2ntp_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=2ntp 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 ==
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.
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.
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==About this Structure==
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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>
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2NTP is a [[Single protein]] structure of sequence 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=2NTP OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17717531 17717531]
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</div>
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[[Category: Erwinia chrysanthemi]]
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<div class="pdbe-citations 2ntp" style="background-color:#fffaf0;"></div>
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[[Category: Pectinesterase]]
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[[Category: Single protein]]
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[[Category: Brocklehurst, K.]]
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[[Category: Fries, M.]]
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[[Category: Pickersgill, R W.]]
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[[Category: Shevchik, V E.]]
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[[Category: hydrolase]]
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[[Category: pme hexasaccharide complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:08:22 2008''
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==See Also==
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*[[Methylesterase 3D structures|Methylesterase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Dickeya dadantii 3937]]
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[[Category: Large Structures]]
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[[Category: Brocklehurst K]]
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[[Category: Fries M]]
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[[Category: Pickersgill RW]]
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[[Category: Shevchik VE]]

Current revision

Crystal structure of pectin methylesterase in complex with hexasaccharide VI

PDB ID 2ntp

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