1gkl: Difference between revisions

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<StructureSection load='1gkl' size='340' side='right'caption='[[1gkl]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
<StructureSection load='1gkl' size='340' side='right'caption='[[1gkl]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1gkl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"ruminiclostridium_thermocellum"_(viljoen_et_al._1926)_yutin_and_galperin_2013 "ruminiclostridium thermocellum" (viljoen et al. 1926) yutin and galperin 2013]. 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>
<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='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>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dyo|1dyo]], [[1gkk|1gkk]], [[1h6x|1h6x]], [[1h6y|1h6y]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=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>
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/XYNY_ACETH XYNY_ACETH]
== 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=1gkl 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=1gkl ConSurf].
<div style="clear:both"></div>
<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.
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>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1gkl" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Endo-1,4-beta-xylanase]]
[[Category: Acetivibrio thermocellus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Charnock, S J]]
[[Category: Charnock SJ]]
[[Category: Davies, G J]]
[[Category: Davies GJ]]
[[Category: Ferreira, L M.A]]
[[Category: Ferreira LMA]]
[[Category: Fontes, C M.G A]]
[[Category: Fontes CMGA]]
[[Category: Prates, J A.M]]
[[Category: Prates JAM]]
[[Category: Tarbouriech, N]]
[[Category: Tarbouriech N]]
[[Category: Esterase family 1]]
[[Category: Hydrolase]]
[[Category: Inactive mutant]]

Revision as of 14:22, 27 March 2024

S954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with ferulic acidS954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with ferulic acid

Structural highlights

1gkl is a 2 chain structure with sequence from Acetivibrio thermocellus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.4Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XYNY_ACETH

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1gkl, resolution 1.40Å

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OCA
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