2jig: Difference between revisions

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-[[Image:2jig.gif|left|200px]]<br /><applet load="2jig" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2jig, resolution 1.85&Aring;" />
-'''CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII PROLYL-4 HYDROXYLASE TYPE I COMPLEXED WITH ZINC AND PYRIDINE-2,4-DICARBOXYLATE'''<br />
-==Overview==
+==Crystal structure of Chlamydomonas reinhardtii prolyl-4 hydroxylase type I complexed with zinc and pyridine-2,4-dicarboxylate==
-Prolyl 4-hydroxylases (P4Hs) are 2-oxoglutarate dioxygenases that catalyze, the hydroxylation of peptidyl prolines. They play an important role in, collagen synthesis, oxygen homeostasis, and plant cell wall formation. We, describe four structures of a P4H from the green alga Chlamydomonas, reinhardtii, two of the apoenzyme at 1.93 and 2.90A resolution, one, complexed with the competitive inhibitor Zn(2+), and one with Zn(2+) and, pyridine 2,4-dicarboxylate (which is an analogue of 2-oxoglutarate) at, 1.85A resolution. The structures reveal the double-stranded beta-helix, core fold (jellyroll motif), typical for 2-oxoglutarate dioxygenases. The, catalytic site is at the center of an extended shallow groove lined by two, flexible loops. Mutagenesis studies together with the crystallographic, data indicate that this groove participates in the binding of the, proline-rich peptide-substrates. It is discussed that the algal P4H and, the catalytic domain of collagen P4Hs have notable structural, similarities, suggesting that these enzymes form a separate structural, subgroup of P4Hs different from the hypoxia-inducible factor P4Hs. Key, structural differences between these two subgroups are described. These, studies provide first insight into the structure-function relationships of, the collagen P4Hs, which unlike the hypoxia-inducible factor P4Hs use, proline-rich peptides as their substrates.
+<StructureSection load='2jig' size='340' side='right'caption='[[2jig]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2jig]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JIG FirstGlance]. <br>
+</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PD2:PYRIDINE-2,4-DICARBOXYLIC+ACID'>PD2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jig OCA], [https://pdbe.org/2jig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jig RCSB], [https://www.ebi.ac.uk/pdbsum/2jig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jig 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/ji/2jig_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=2jig ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Prolyl 4-hydroxylases (P4Hs) are 2-oxoglutarate dioxygenases that catalyze the hydroxylation of peptidyl prolines. They play an important role in collagen synthesis, oxygen homeostasis, and plant cell wall formation. We describe four structures of a P4H from the green alga Chlamydomonas reinhardtii, two of the apoenzyme at 1.93 and 2.90 A resolution, one complexed with the competitive inhibitor Zn2+, and one with Zn2+ and pyridine 2,4-dicarboxylate (which is an analogue of 2-oxoglutarate) at 1.85 A resolution. The structures reveal the double-stranded beta-helix core fold (jellyroll motif), typical for 2-oxoglutarate dioxygenases. The catalytic site is at the center of an extended shallow groove lined by two flexible loops. Mutagenesis studies together with the crystallographic data indicate that this groove participates in the binding of the proline-rich peptide-substrates. It is discussed that the algal P4H and the catalytic domain of collagen P4Hs have notable structural similarities, suggesting that these enzymes form a separate structural subgroup of P4Hs different from the hypoxia-inducible factor P4Hs. Key structural differences between these two subgroups are described. These studies provide first insight into the structure-function relationships of the collagen P4Hs, which unlike the hypoxia-inducible factor P4Hs use proline-rich peptides as their substrates.
-==About this Structure==
+The active site of an algal prolyl 4-hydroxylase has a large structural plasticity.,Koski MK, Hieta R, Bollner C, Kivirikko KI, Myllyharju J, Wierenga RK J Biol Chem. 2007 Dec 21;282(51):37112-23. Epub 2007 Oct 16. PMID:17940281<ref>PMID:17940281</ref>
-JIG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=PD2:'>PD2</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Zn+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Zn+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Pd2+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:Zn+Binding+Site+For+Chain+B'>AC4</scene>, <scene name='pdbsite=AC5:Zn+Binding+Site+For+Chain+B'>AC5</scene>, <scene name='pdbsite=AC6:Gol+Binding+Site+For+Chain+A'>AC6</scene> and <scene name='pdbsite=AC7:So4+Binding+Site+For+Chain+A'>AC7</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JIG OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-The active site of an algal prolyl 4-hydroxylase has a large structural plasticity., Koski MK, Hieta R, Bollner C, Kivirikko KI, Myllyharju J, Wierenga RK, J Biol Chem. 2007 Dec 21;282(51):37112-23. Epub 2007 Oct 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17940281 17940281]
+</div>
+<div class="pdbe-citations 2jig" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Hydroxylases 3D structures|Hydroxylases 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Chlamydomonas reinhardtii]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bollner, C.]]
+[[Category: Bollner C]]
-[[Category: Hieta, R.]]
+[[Category: Hieta R]]
-[[Category: Kivirikko, K.I.]]
+[[Category: Kivirikko KI]]
-[[Category: Koski, K.M.]]
+[[Category: Koski MK]]
-[[Category: Myllyharju, J.]]
+[[Category: Myllyharju J]]
-[[Category: Wierenga, R.K.]]
+[[Category: Wierenga RK]]
-[[Category: GOL]]
-[[Category: PD2]]
-[[Category: SO4]]
-[[Category: ZN]]
-[[Category: hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 10:46:15 2008''