1h6x: 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:1h6x.png|left|200px]]
-<!--
+==The role of conserved amino acids in the cleft of the C-terminal family 22 carbohydrate binding module of Clostridium thermocellum Xyn10B in ligand binding==
-The line below this paragraph, containing "STRUCTURE_1h6x", creates the "Structure Box" on the page.
+<StructureSection load='1h6x' size='340' side='right'caption='[[1h6x]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1h6x]] is a 1 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=1H6X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H6X FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-{{STRUCTURE_1h6x|  PDB=1h6x  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1h6x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h6x OCA], [https://pdbe.org/1h6x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h6x RCSB], [https://www.ebi.ac.uk/pdbsum/1h6x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h6x 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/h6/1h6x_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=1h6x ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The majority of plant cell wall hydrolases are modular enzymes which, in addition to a catalytic module, possess one or more carbohydrate-binding modules (CBMs). These carbohydrate-active enzymes and their constituent modules have been classified into a number of families based upon amino acid sequence similarity. The Clostridium thermocellum xylanase, Xyn10B, contains two CBMs that belong to family 22 (CBM22). The crystal structure of the C-terminal CBM22 (CBM22-2) was determined in a previous study [Charnock, S. J., et al. (2000) Biochemistry 39, 5013--5021] and revealed a surface cleft which presents several conserved residues that are implicated in ligand binding. These amino acids have been substituted and the structure and biochemical properties of the mutants analyzed. The data show that R25A, W53A, Y103A, Y136A, and E138A exhibit greatly reduced affinity for xylotetraose relative to that of the wild-type protein. Conversely, mutations Y103F and Y136F have little effect on ligand binding. Using thermodynamic, X-ray, and NMR measurements on the mutants, we show that the cleft of CBM22-2 does indeed form the ligand-binding site. Trp 53 and Tyr 103 most likely participate in hydrophobic stacking interactions with the ligand, while Glu 138 makes one or more important hydrogen bonds with the tetrasaccharide. Although Arg 25 and Tyr 136 are likely to form hydrogen bonds with the ligand, they are also shown to play a critical role in maintaining the structural integrity of the binding cleft.
-===THE ROLE OF CONSERVED AMONI ACIDS IN THE CLEFT OF THE C-TERMINAL FAMILY 22 CARBOHYDRATE BINDING MODULE OF CLOSTRIDIUM THERMOCELLUM XYN10B IN LIGAND BINDING===
+Clostridium thermocellum Xyn10B carbohydrate-binding module 22-2: the role of conserved amino acids in ligand binding.,Xie H, Gilbert HJ, Charnock SJ, Davies GJ, Williamson MP, Simpson PJ, Raghothama S, Fontes CM, Dias FM, Ferreira LM, Bolam DN Biochemistry. 2001 Aug 7;40(31):9167-76. PMID:11478884<ref>PMID:11478884</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_11478884}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1h6x" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11478884 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11478884}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Acetivibrio thermocellus]]
-[[1h6x]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum Clostridium thermocellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H6X OCA].
+[[Category: Large Structures]]
+[[Category: Bolam DN]]
-==Reference==
+[[Category: Charnock SJ]]
-<ref group="xtra">PMID:11478884</ref><ref group="xtra">PMID:10819965</ref><references group="xtra"/>
+[[Category: Davies GJ]]
-[[Category: Clostridium thermocellum]]
+[[Category: Ferreira LMA]]
-[[Category: Bolam, D N.]]
+[[Category: Fontes CMGA]]
-[[Category: Charnock, S J.]]
+[[Category: Gilbert HJ]]
-[[Category: Davies, G J.]]
+[[Category: Simpson PJ]]
-[[Category: Ferreira, L M.A.]]
+[[Category: Williamson MP]]
-[[Category: Fontes, C M.G A.]]
+[[Category: Xie H]]
-[[Category: Gilbert, H J.]]
-[[Category: Simpson, P J.]]
-[[Category: Williamson, M P.]]
-[[Category: Xie, H.]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Xylan degradation]]