2v4a: Difference between revisions

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-{{Seed}}
-[[Image:2v4a.png|left|200px]]
-<!--
+==Crystal structure of the SeMet-labeled prolyl-4 hydroxylase (P4H) type I from green algae Chlamydomonas reinhardtii.==
-The line below this paragraph, containing "STRUCTURE_2v4a", creates the "Structure Box" on the page.
+<StructureSection load='2v4a' size='340' side='right'caption='[[2v4a]], [[Resolution|resolution]] 1.93&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'>[[2v4a]] is a 4 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=2V4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V4A 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]] 1.93&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2v4a|  PDB=2v4a  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2v4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v4a OCA], [https://pdbe.org/2v4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v4a RCSB], [https://www.ebi.ac.uk/pdbsum/2v4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v4a 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/v4/2v4a_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=2v4a 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.
-===CRYSTAL STRUCTURE OF THE SEMET-LABELED PROLYL-4 HYDROXYLASE (P4H) TYPE I FROM GREEN ALGAE CHLAMYDOMONAS REINHARDTII.===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2v4a" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17940281}}, adds the Publication Abstract to the page
+*[[Hydroxylases 3D structures|Hydroxylases 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17940281 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17940281}}
+__TOC__
+</StructureSection>
-==About this Structure==
-V4A is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V4A OCA].
-==Reference==
-<ref group="xtra">PMID:17940281</ref><references group="xtra"/>
 [[Category: Chlamydomonas reinhardtii]]
-[[Category: Bollner, C.]]
+[[Category: Large Structures]]
-[[Category: Hieta, R.]]
+[[Category: Bollner C]]
-[[Category: Kivirikko, K I.]]
+[[Category: Hieta R]]
-[[Category: Koski, M K.]]
+[[Category: Kivirikko KI]]
-[[Category: Myllyharju, J.]]
+[[Category: Koski MK]]
-[[Category: Wierenga, R K.]]
+[[Category: Myllyharju J]]
-[[Category: Hydrolase]]
+[[Category: Wierenga RK]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:22:18 2009''