3rub: Difference between revisions

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-{{Seed}}
-[[Image:3rub.png|left|200px]]
-<!--
+==CRYSTAL STRUCTURE OF THE UNACTIVATED FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM TOBACCO REFINED AT 2.0-ANGSTROMS RESOLUTION==
-The line below this paragraph, containing "STRUCTURE_3rub", creates the "Structure Box" on the page.
+<StructureSection load='3rub' size='340' side='right'caption='[[3rub]], [[Resolution|resolution]] 2.00&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'>[[3rub]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nicotiana_tabacum Nicotiana tabacum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RUB 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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASN:ASPARAGINE'>ASN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3rub|  PDB=3rub  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rub OCA], [https://pdbe.org/3rub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rub RCSB], [https://www.ebi.ac.uk/pdbsum/3rub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rub ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RBL_TOBAC RBL_TOBAC] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01338]
+== 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/ru/3rub_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3rub ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase was refined at a resolution of 2.0 A to an R-factor of 17.1%. The previous model (Chapman et al., 1988) was extensively rebuilt, and the small subunit was retraced. The refined model consists of residues 22-63 and 69-467 of the large subunit and the complete small subunit. A striking feature of the model is that several loops have very high B-factors, probably representing mobile regions of the molecule. An examination of the intersubunit contacts shows that the L8S8 hexadecamer is composed of four L2 dimers. The dominant contacts between these L2 dimers are formed by the small subunits. This suggests that the small subunits may be essential for maintaining the integrity of the L8S8 structure. The active site shows differences between the unactivated form and the quaternary complex. In particular, Lys334 has moved out of the active site by about 10A. This residue lies on loop 6 of the alpha beta barrel, which is a particularly mobile loop. The site of ribulose-1,5-bisphosphate carboxylase/oxygenase activation is well ordered in the absence of the carbamylation of Lys201 and Mg2+ binding. The residues are held poised by a network of hydrogen bonds. In the unactivated state, the active site is accessible to substrate binding.
-===CRYSTAL STRUCTURE OF THE UNACTIVATED FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM TOBACCO REFINED AT 2.0-ANGSTROMS RESOLUTION===
+Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution.,Curmi PM, Cascio D, Sweet RM, Eisenberg D, Schreuder H J Biol Chem. 1992 Aug 25;267(24):16980-9. PMID:1512238<ref>PMID:1512238</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3rub" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_1512238}}, adds the Publication Abstract to the page
+*[[RuBisCO 3D structures|RuBisCO 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 1512238 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_1512238}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-RUB is a 2 chains structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RUB OCA].
+[[Category: Nicotiana tabacum]]
+[[Category: Cascio D]]
-==Reference==
+[[Category: Chapman MS]]
-<ref group="xtra">PMID:1512238</ref><references group="xtra"/>
+[[Category: Curmi PMG]]
-[[Category: Ribulose-bisphosphate carboxylase]]
+[[Category: Eisenberg DS]]
-[[Category: Cascio, D.]]
+[[Category: Schreuder H]]
-[[Category: Chapman, M S.]]
+[[Category: Suh SW]]
-[[Category: Curmi, P M.G.]]
-[[Category: Eisenberg, D S.]]
-[[Category: Schreuder, H.]]
-[[Category: Suh, S W.]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:41:08 2009''