1uzh: Difference between revisions

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-{{Seed}}
-[[Image:1uzh.png|left|200px]]
-<!--
+==A CHIMERIC CHLAMYDOMONAS, SYNECHOCOCCUS RUBISCO ENZYME==
-The line below this paragraph, containing "STRUCTURE_1uzh", creates the "Structure Box" on the page.
+<StructureSection load='1uzh' size='340' side='right'caption='[[1uzh]], [[Resolution|resolution]] 2.20&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'>[[1uzh]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii] and [https://en.wikipedia.org/wiki/Synechococcus_sp. Synechococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UZH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UZH 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]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SMC:S-METHYLCYSTEINE'>SMC</scene></td></tr>
-{{STRUCTURE_1uzh|  PDB=1uzh  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1uzh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uzh OCA], [https://pdbe.org/1uzh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uzh RCSB], [https://www.ebi.ac.uk/pdbsum/1uzh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uzh ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RBL_CHLRE RBL_CHLRE] 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/uz/1uzh_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=1uzh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Comparison of subunit sequences and X-ray crystal structures of ribulose-1,5-bisphosphate carboxylase/oxygenase indicates that the loop between beta-strands A and B of the small subunit is one of the most variable regions of the holoenzyme. In prokaryotes and nongreen algae, the loop contains 10 residues. In land plants and green algae, the loop is comprised of approximately 22 and 28 residues, respectively. Previous studies indicated that the longer betaA-betaB loop was required for the assembly of cyanobacterial small subunits with plant large subunits in isolated chloroplasts. In the present study, chimeric small subunits were constructed by replacing the loop of the green alga Chlamydomonas reinhardtii with the sequences of Synechococcus or spinach. When these engineered genes were transformed into a Chlamydomonas mutant that lacks small-subunit genes, photosynthesis-competent colonies were recovered, indicating that loop size is not essential for holoenzyme assembly. Whereas the Synechococcus loop causes decreases in carboxylation V(max), K(m)(O(2)), and CO(2)/O(2) specificity, the spinach loop causes complementary decreases in carboxylation V(max), K(m)(O(2)), and K(m)(CO(2)) without a change in specificity. X-ray crystal structures of the engineered proteins reveal remarkable similarity between the introduced betaA-betaB loops and the respective loops in the Synechococcus and spinach enzymes. The side chains of several large-subunit residues are altered in regions previously shown by directed mutagenesis to influence CO(2)/O(2) specificity. Differences in the catalytic properties of divergent Rubisco enzymes may arise from differences in the small-subunit betaA-betaB loop. This loop may be a worthwhile target for genetic engineering aimed at improving photosynthetic CO(2) fixation.
-===A CHIMERIC CHLAMYDOMONAS, SYNECHOCOCCUS RUBISCO ENZYME===
+Chimeric small subunits influence catalysis without causing global conformational changes in the crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase.,Karkehabadi S, Peddi SR, Anwaruzzaman M, Taylor TC, Cederlund A, Genkov T, Andersson I, Spreitzer RJ Biochemistry. 2005 Jul 26;44(29):9851-61. PMID:16026157<ref>PMID:16026157</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1uzh" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16026157}}, adds the Publication Abstract to the page
+*[[RuBisCO 3D structures|RuBisCO 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16026157 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16026157}}
+__TOC__
+</StructureSection>
-==About this Structure==
-UZH is a 16 chains structure of sequences from [http://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii,_synechococcus_sp Chlamydomonas reinhardtii, synechococcus sp] and [http://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UZH OCA]. Relevant biological numbers for this protein at [http://bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&org=%25&trm=%22rubisco%22 B10NUMB3R5]
-==Reference==
-<ref group="xtra">PMID:16026157</ref><references group="xtra"/>
 [[Category: Chlamydomonas reinhardtii]]
-[[Category: Chlamydomonas reinhardtii, synechococcus sp]]
+[[Category: Large Structures]]
-[[Category: Ribulose-bisphosphate carboxylase]]
+[[Category: Synechococcus sp]]
-[[Category: Andersson, I.]]
+[[Category: Andersson I]]
-[[Category: Karkehabadi, S.]]
+[[Category: Karkehabadi S]]
-[[Category: Spreitzer, R J.]]
+[[Category: Spreitzer RJ]]
-[[Category: Carbon dioxide fixation]]
-[[Category: Chloroplast]]
-[[Category: Lyase]]
-[[Category: Monooxygenase]]
-[[Category: Multigene family]]
-[[Category: Oxidoreductase]]
-[[Category: Photorespiration]]
-[[Category: Photosynthesis]]
-[[Category: Rubisco]]
-[[Category: Transit peptide]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 23 11:32:33 2009''