2vn4: Difference between revisions

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-{{Seed}}
-[[Image:2vn4.png|left|200px]]
-<!--
+==Glycoside Hydrolase Family 15 Glucoamylase from Hypocrea jecorina==
-The line below this paragraph, containing "STRUCTURE_2vn4", creates the "Structure Box" on the page.
+<StructureSection load='2vn4' size='340' side='right'caption='[[2vn4]], [[Resolution|resolution]] 1.85&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'>[[2vn4]] is a 1 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=2VN4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VN4 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]] 1.85&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_2vn4|  PDB=2vn4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vn4 OCA], [https://pdbe.org/2vn4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vn4 RCSB], [https://www.ebi.ac.uk/pdbsum/2vn4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vn4 ProSAT]</span></td></tr>
+</table>
+== 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/vn/2vn4_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=2vn4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The three-dimensional structure of a complete Hypocrea jecorina glucoamylase has been determined at 1.8 A resolution. The presented structure model includes the catalytic and starch binding domains and traces the course of the 37-residue linker segment. While the structures of other fungal and yeast glucoamylase catalytic and starch binding domains have been determined separately, this is the first intact structure that allows visualization of the juxtaposition of the starch binding domain relative to the catalytic domain. The detailed interactions we see between the catalytic and starch binding domains are confirmed in a second independent structure determination of the enzyme in a second crystal form. This second structure model exhibits an identical conformation compared to the first structure model, which suggests that the H. jecorina glucoamylase structure we report is independent of crystal lattice contact restraints and represents the three-dimensional structure found in solution. The proposed starch binding regions for the starch binding domain are aligned with the catalytic domain in the three-dimensional structure in a manner that supports the hypothesis that the starch binding domain serves to target the glucoamylase at sites where the starch granular matrix is disrupted and where the enzyme might most effectively function.
-===GLYCOSIDE HYDROLASE FAMILY 15 GLUCOAMYLASE FROM HYPOCREA JECORINA===
+Three-dimensional structure of an intact glycoside hydrolase family 15 glucoamylase from Hypocrea jecorina.,Bott R, Saldajeno M, Cuevas W, Ward D, Scheffers M, Aehle W, Karkehabadi S, Sandgren M, Hansson H Biochemistry. 2008 May 27;47(21):5746-54. Epub 2008 May 6. PMID:18457422<ref>PMID:18457422</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_18457422}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vn4" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18457422 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18457422}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-VN4 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=2VN4 OCA].
+[[Category: Trichoderma reesei]]
+[[Category: Bott R]]
-==Reference==
+[[Category: Hansson H]]
-Three-dimensional structure of an intact glycoside hydrolase family 15 glucoamylase from Hypocrea jecorina., Bott R, Saldajeno M, Cuevas W, Ward D, Scheffers M, Aehle W, Karkehabadi S, Sandgren M, Hansson H, Biochemistry. 2008 May 27;47(21):5746-54. Epub 2008 May 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18457422 18457422]
+[[Category: Sandgren M]]
-[[Category: Glucan 1,4-alpha-glucosidase]]
-[[Category: Hypocrea jecorina]]
-[[Category: Single protein]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
-[[Category: Amyloglucosidase]]
-[[Category: Carbohydrate binding]]
-[[Category: Glucoamylase]]
-[[Category: Glycoside hydrolase family 15]]
-[[Category: Hydrolase]]
-[[Category: Hypocrea jecorina]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 24 20:24:07 2008''