1gkl: Difference between revisions

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-[[Image:1gkl.gif|left|200px]]<br />
-<applet load="1gkl" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1gkl, resolution 1.40&Aring;" />
-'''S954A MUTANT OF THE FERULOYL ESTERASE MODULE FROM CLOSTRIDIUM THERMOCELLUM COMPLEXED WITH FERULIC ACID'''<br />
-==Overview==
+==S954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with ferulic acid==
-BACKGROUND: Degradation of the plant cell wall requires the synergistic, action of a consortium of predominantly modular enzymes. In Clostridiae, these biocatalysts are organized into a supramolecular assembly termed a, "cellulosome." This multienzyme complex possesses, in addition to its, well-described cellulolytic activity, an apparatus specific for xylan, degradation. Cinnamic acid esterases hydrolyze the ferulate groups, involved in the crosslinking of arabinoxylans to lignin and thus play a, key role in the degradation of the plant cell wall in addition to having, promising industrial and medical applications. RESULTS: We have cloned and, overexpressed the feruloyl esterase module from a 5 domain xylanase, Xyn10B from Clostridium thermocellum. The native structure at 1.6 A, resolution has been solved with selenomethionine multiple wavelength, anomalous dispersion and refined to a final R(free) of 17.8%. The, structure of a hydrolytically inactive mutant, S954A, in complex with the, reaction product ferulic acid has been refined at a resolution of 1.4 A, with an R(free) of 16.0%. CONCLUSIONS: The C. thermocellum Xyn10B ferulic, acid esterase displays the alpha/beta-hydrolase fold and possesses a, classical Ser-His-Asp catalytic triad. Ferulate esterases are, characterized by their specificity, and the active center reveals the, binding site for ferulic acid and related compounds. Ferulate binds in a, small surface depression that possesses specificity determinants for both, the methoxy and hydroxyl ring substituents of the substrate. There appears, to be a lack of specificity for the xylan backbone, which may reflect the, intrinsic chemical heterogeneity of the natural substrate.
+<StructureSection load='1gkl' size='340' side='right'caption='[[1gkl]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1gkl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus Acetivibrio thermocellus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GKL FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=FER:3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC+ACID'>FER</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=1gkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gkl OCA], [https://pdbe.org/1gkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gkl RCSB], [https://www.ebi.ac.uk/pdbsum/1gkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gkl ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/XYNY_ACETH XYNY_ACETH]
+== 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/gk/1gkl_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1gkl ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: Degradation of the plant cell wall requires the synergistic action of a consortium of predominantly modular enzymes. In Clostridiae, these biocatalysts are organized into a supramolecular assembly termed a "cellulosome." This multienzyme complex possesses, in addition to its well-described cellulolytic activity, an apparatus specific for xylan degradation. Cinnamic acid esterases hydrolyze the ferulate groups involved in the crosslinking of arabinoxylans to lignin and thus play a key role in the degradation of the plant cell wall in addition to having promising industrial and medical applications. RESULTS: We have cloned and overexpressed the feruloyl esterase module from a 5 domain xylanase, Xyn10B from Clostridium thermocellum. The native structure at 1.6 A resolution has been solved with selenomethionine multiple wavelength anomalous dispersion and refined to a final R(free) of 17.8%. The structure of a hydrolytically inactive mutant, S954A, in complex with the reaction product ferulic acid has been refined at a resolution of 1.4 A with an R(free) of 16.0%. CONCLUSIONS: The C. thermocellum Xyn10B ferulic acid esterase displays the alpha/beta-hydrolase fold and possesses a classical Ser-His-Asp catalytic triad. Ferulate esterases are characterized by their specificity, and the active center reveals the binding site for ferulic acid and related compounds. Ferulate binds in a small surface depression that possesses specificity determinants for both the methoxy and hydroxyl ring substituents of the substrate. There appears to be a lack of specificity for the xylan backbone, which may reflect the intrinsic chemical heterogeneity of the natural substrate.
-==About this Structure==
+The structure of the feruloyl esterase module of xylanase 10B from Clostridium thermocellum provides insights into substrate recognition.,Prates JA, Tarbouriech N, Charnock SJ, Fontes CM, Ferreira LM, Davies GJ Structure. 2001 Dec;9(12):1183-90. PMID:11738044<ref>PMID:11738044</ref>
-GKL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum] with CD, FER, GOL and ACY as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] Structure known Active Site: FEA. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1GKL OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-The structure of the feruloyl esterase module of xylanase 10B from Clostridium thermocellum provides insights into substrate recognition., Prates JA, Tarbouriech N, Charnock SJ, Fontes CM, Ferreira LM, Davies GJ, Structure. 2001 Dec;9(12):1183-90. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11738044 11738044]
+</div>
-[[Category: Clostridium thermocellum]]
+<div class="pdbe-citations 1gkl" style="background-color:#fffaf0;"></div>
-[[Category: Endo-1,4-beta-xylanase]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Charnock, S.J.]]
+__TOC__
-[[Category: Davies, G.J.]]
+</StructureSection>
-[[Category: Ferreira, L.M.A.]]
+[[Category: Acetivibrio thermocellus]]
-[[Category: Fontes, C.M.G.A.]]
+[[Category: Large Structures]]
-[[Category: Prates, J.A.M.]]
+[[Category: Charnock SJ]]
-[[Category: Tarbouriech, N.]]
+[[Category: Davies GJ]]
-[[Category: ACY]]
+[[Category: Ferreira LMA]]
-[[Category: CD]]
+[[Category: Fontes CMGA]]
-[[Category: FER]]
+[[Category: Prates JAM]]
-[[Category: GOL]]
+[[Category: Tarbouriech N]]
-[[Category: esterase family 1]]
-[[Category: ferulic acid]]
-[[Category: inactive mutant]]
-[[Category: x-ray crystallography]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov  5 12:30:44 2007''