1ree: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1ree.gif|left|200px]]
- {{Structure
+==ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 3,4-EPOXYBUTYL-BETA-D-XYLOSIDE==
-|PDB= 1ree |SIZE=350|CAPTION= <scene name='initialview01'>1ree</scene>, resolution 1.6&Aring;
+<StructureSection load='1ree' size='340' side='right'caption='[[1ree]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=C4X:3,4-EPOXYBUTYL-BETA-D-XYLOSIDE'>C4X</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>
+<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>
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+</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>
-|GENE=
+<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>
-|DOMAIN=
+<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>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ree FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ree OCA], [http://www.ebi.ac.uk/pdbsum/1ree PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ree RCSB]</span>
+== Function ==
-}}
+[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>
+== Evolutionary Conservation ==
-'''ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 3,4-EPOXYBUTYL-BETA-D-XYLOSIDE'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/re/1ree_consurf.spt"</scriptWhenChecked>
-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.
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==About this Structure==
+  </jmolCheckbox>
-REE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1REE OCA].
+</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>
-==Reference==
+== References ==
-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://www.ncbi.nlm.nih.gov/pubmed/8755744 8755744]
+<references/>
-[[Category: Endo-1,4-beta-xylanase]]
+__TOC__
-[[Category: Hypocrea jecorina]]
+</StructureSection>
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Havukainen, R.]]
+[[Category: Trichoderma reesei]]
-[[Category: Rouvinen, J.]]
+[[Category: Havukainen R]]
-[[Category: Torronen, A.]]
+[[Category: Rouvinen J]]
-[[Category: hydrolase]]
+[[Category: Torronen A]]
-[[Category: xylan degradation]]
-[[Category: xylanase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:26:58 2008''