1ge6

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[[Image:1ge6.gif|left|200px]]
 
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{{Structure
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==ZINC PEPTIDASE FROM GRIFOLA FRONDOSA==
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|PDB= 1ge6 |SIZE=350|CAPTION= <scene name='initialview01'>1ge6</scene>, resolution 2.2&Aring;
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<StructureSection load='1ge6' size='340' side='right'caption='[[1ge6]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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<table><tr><td colspan='2'>[[1ge6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Grifola_frondosa Grifola frondosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GE6 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidyl-Lys_metalloendopeptidase Peptidyl-Lys metalloendopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.20 3.4.24.20] </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]] 2.2&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1ge6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ge6 OCA], [https://pdbe.org/1ge6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ge6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ge6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ge6 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1g12|1G12]], [[1ge5|1GE5]], [[1ge7|1GE7]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ge6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ge6 OCA], [http://www.ebi.ac.uk/pdbsum/1ge6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ge6 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/PLMP_GRIFR PLMP_GRIFR]
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== Evolutionary Conservation ==
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'''ZINC PEPTIDASE FROM GRIFOLA FRONDOSA'''
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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/ge/1ge6_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=1ge6 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 ==
Crystal structures of a peptidyl-Lys metalloendopeptidase (MEP) from the edible mushroom Grifola frondosa (GfMEP) were solved in four crystal forms. This represents the first structure of the new family 'aspzincins' with a novel active-site architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs conserved among aspzincins. His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner. A Tyr133 side chain located on the S1' pocket had different configurations in two crystal forms and was not observed in the other crystal forms. The flexible Tyr133 plays two roles in the enzymatic function of GfMEP. The first is to provide a hydrophobic environment with Phe83 in order to accommodate the alkyl part of the Lys side chain of a substrate and the second is as a 'proton donor' to the oxyanion of the tetrahedral transition state to stabilize the reaction transition state.
Crystal structures of a peptidyl-Lys metalloendopeptidase (MEP) from the edible mushroom Grifola frondosa (GfMEP) were solved in four crystal forms. This represents the first structure of the new family 'aspzincins' with a novel active-site architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs conserved among aspzincins. His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner. A Tyr133 side chain located on the S1' pocket had different configurations in two crystal forms and was not observed in the other crystal forms. The flexible Tyr133 plays two roles in the enzymatic function of GfMEP. The first is to provide a hydrophobic environment with Phe83 in order to accommodate the alkyl part of the Lys side chain of a substrate and the second is as a 'proton donor' to the oxyanion of the tetrahedral transition state to stabilize the reaction transition state.
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==About this Structure==
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Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms.,Hori T, Kumasaka T, Yamamoto M, Nonaka N, Tanaka N, Hashimoto Y, Ueki U, Takio K Acta Crystallogr D Biol Crystallogr. 2001 Mar;57(Pt 3):361-8. PMID:11223512<ref>PMID:11223512</ref>
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1GE6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Grifola_frondosa Grifola frondosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GE6 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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Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms., Hori T, Kumasaka T, Yamamoto M, Nonaka N, Tanaka N, Hashimoto Y, Ueki U, Takio K, Acta Crystallogr D Biol Crystallogr. 2001 Mar;57(Pt 3):361-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11223512 11223512]
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</div>
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<div class="pdbe-citations 1ge6" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Grifola frondosa]]
[[Category: Grifola frondosa]]
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[[Category: Peptidyl-Lys metalloendopeptidase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Hashimoto Y]]
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[[Category: Hashimoto, Y.]]
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[[Category: Hori T]]
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[[Category: Hori, T.]]
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[[Category: Kumasaka T]]
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[[Category: Kumasaka, T.]]
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[[Category: Nonaka T]]
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[[Category: Nonaka, T.]]
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[[Category: Takio K]]
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[[Category: Takio, K.]]
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[[Category: Tanaka N]]
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[[Category: Tanaka, N.]]
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[[Category: Ueki T]]
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[[Category: Ueki, T.]]
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[[Category: Yamamoto M]]
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[[Category: Yamamoto, M.]]
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[[Category: zinc coordinate,metalloprotease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:42:10 2008''
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Current revision

ZINC PEPTIDASE FROM GRIFOLA FRONDOSA

PDB ID 1ge6

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