1ree: Difference between revisions

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New page: left|200px<br /><applet load="1ree" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ree, resolution 1.6Å" /> '''ENDO-1,4-BETA-XYLANAS...
 
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'''ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 3,4-EPOXYBUTYL-BETA-D-XYLOSIDE'''<br />


==Overview==
==ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 3,4-EPOXYBUTYL-BETA-D-XYLOSIDE==
The three-dimensional structures of endo-1,4-xylanase II (XYNII) from, Trichoderma reesei complexed with 4,5-epoxypentyl beta-D-xyloside, (X-O-C5),3,4-epoxybutyl beta-D-xyloside (X-O-C4), and 2,3-epoxypropyl, beta-D-xyloside (X-O-C3) were determined by X-ray crystallography., High-resolution measurement revealed clear electron densities for each, ligand. Both X-O-C5 and X-O-C3 were found to form a covalent bond with the, putative nucleophile Glu86. Unexpectedly, X-O-C4 was found to bind to the, putative acid/base catalyst Glu177. In all three complexes, clear, conformational changes were found in XYNII compared to the native, structure. These changes were largest in the X-O-C3 complex structure.
<StructureSection load='1ree' size='340' side='right'caption='[[1ree]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1ree]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_reesei Trichoderma reesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1REE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1REE FirstGlance]. <br>
1REE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina] with C4X and BEZ 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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1REE OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=07E:(3S)-3-hydroxybutyl+beta-D-xylopyranoside'>07E</scene>, <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ree FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ree OCA], [https://pdbe.org/1ree PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ree RCSB], [https://www.ebi.ac.uk/pdbsum/1ree PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ree ProSAT]</span></td></tr>
Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei., Havukainen R, Torronen A, Laitinen T, Rouvinen J, Biochemistry. 1996 Jul 23;35(29):9617-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8755744 8755744]
</table>
[[Category: Endo-1,4-beta-xylanase]]
== Function ==
[[Category: Hypocrea jecorina]]
[https://www.uniprot.org/uniprot/XYN2_HYPJR XYN2_HYPJR] Glycoside hydrolase involved in the hydrolysis of xylan, a major plant cell wall hemicellulose made up of 1,4-beta-linked D-xylopyranose residues. Catalyzes the endohydrolysis of the main-chain 1,4-beta-glycosidic bonds connecting the xylose subunits yielding various xylooligosaccharides and xylose (PubMed:1369024, Ref.5). The catalysis proceeds by a double-displacement reaction mechanism with a putative covalent glycosyl-enzyme intermediate, with retention of the anomeric configuration (PubMed:7988708). Produces xylobiose and xylose as the main degradation products (PubMed:19556747).<ref>PMID:1369024</ref> <ref>PMID:19556747</ref> <ref>PMID:7988708</ref> <ref>PMID:1369024</ref>
[[Category: Single protein]]
== Evolutionary Conservation ==
[[Category: Havukainen, R.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Rouvinen, J.]]
Check<jmol>
[[Category: Torronen, A.]]
  <jmolCheckbox>
[[Category: BEZ]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/re/1ree_consurf.spt"</scriptWhenChecked>
[[Category: C4X]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: hydrolase]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: xylan degradation]]
  </jmolCheckbox>
[[Category: xylanase]]
</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=1ree ConSurf].
 
<div style="clear:both"></div>
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:31:23 2007''
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Trichoderma reesei]]
[[Category: Havukainen R]]
[[Category: Rouvinen J]]
[[Category: Torronen A]]

Latest revision as of 11:22, 1 May 2024

ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 3,4-EPOXYBUTYL-BETA-D-XYLOSIDEENDO-1,4-BETA-XYLANASE II COMPLEX WITH 3,4-EPOXYBUTYL-BETA-D-XYLOSIDE

Structural highlights

1ree is a 2 chain structure with sequence from Trichoderma reesei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XYN2_HYPJR Glycoside hydrolase involved in the hydrolysis of xylan, a major plant cell wall hemicellulose made up of 1,4-beta-linked D-xylopyranose residues. Catalyzes the endohydrolysis of the main-chain 1,4-beta-glycosidic bonds connecting the xylose subunits yielding various xylooligosaccharides and xylose (PubMed:1369024, Ref.5). The catalysis proceeds by a double-displacement reaction mechanism with a putative covalent glycosyl-enzyme intermediate, with retention of the anomeric configuration (PubMed:7988708). Produces xylobiose and xylose as the main degradation products (PubMed:19556747).[1] [2] [3] [4]

Evolutionary Conservation

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

References

  1. ↑ Torronen A, Mach RL, Messner R, Gonzalez R, Kalkkinen N, Harkki A, Kubicek CP. The two major xylanases from Trichoderma reesei: characterization of both enzymes and genes. Biotechnology (N Y). 1992 Nov;10(11):1461-5. PMID:1369024
  2. ↑ Jun H, Bing Y, Keying Z, Xuemei D, Daiwen C. Sequencing and expression of the xylanase gene 2 from Trichoderma reesei Rut C-30 and characterization of the recombinant enzyme and its activity on xylan. J Mol Microbiol Biotechnol. 2009;17(3):101-9. doi: 10.1159/000226590. Epub 2009, Jun 26. PMID:19556747 doi:http://dx.doi.org/10.1159/000226590
  3. ↑ Biely P, Kremnicky L, Alfoldi J, Tenkanen M. Stereochemistry of the hydrolysis of glycosidic linkage by endo-beta-1,4-xylanases of Trichoderma reesei. FEBS Lett. 1994 Dec 12;356(1):137-40. PMID:7988708
  4. ↑ Torronen A, Mach RL, Messner R, Gonzalez R, Kalkkinen N, Harkki A, Kubicek CP. The two major xylanases from Trichoderma reesei: characterization of both enzymes and genes. Biotechnology (N Y). 1992 Nov;10(11):1461-5. PMID:1369024

1ree, resolution 1.60Å

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