2iy6: Difference between revisions

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-[[Image:2iy6.gif|left|200px]]<br /><applet load="2iy6" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2iy6, resolution 1.80&Aring;" />
-'''1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND CITRATE'''<br />
-==Overview==
+==1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND CITRATE==
-Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDh) plays an important, role in the metabolic pathway from proline to glutamate. It irreversibly, catalyzes the oxidation of glutamate-gamma-semialdehyde, the product of, the non-enzymatic hydrolysis of Delta(1)-pyrroline-5-carboxylate, into, glutamate with the reduction of NAD(+) into NADH. We have confirmed the, P5CDh activity of the Thermus thermophilus protein TT0033 (TtP5CDh), and, determined the crystal structure of the enzyme in the ligand-free form at, 1.4 A resolution. To investigate the structural basis of TtP5CDh function, the TtP5CDh structures with NAD(+), with NADH, and with its product, glutamate were determined at 1.8 A, 1.9 A, and 1.4 A resolution, respectively. The solved structures suggest an overall view of the P5CDh, catalytic mechanism and provide insights into the P5CDh deficiencies in, the case of the human type II hyperprolinemia.
+<StructureSection load='2iy6' size='340' side='right'caption='[[2iy6]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2iy6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IY6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IY6 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]] 1.8&#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=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=2iy6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iy6 OCA], [https://pdbe.org/2iy6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iy6 RCSB], [https://www.ebi.ac.uk/pdbsum/2iy6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iy6 ProSAT], [https://www.topsan.org/Proteins/RSGI/2iy6 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5SI02_THET8 Q5SI02_THET8]
+== 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/iy/2iy6_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=2iy6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDh) plays an important role in the metabolic pathway from proline to glutamate. It irreversibly catalyzes the oxidation of glutamate-gamma-semialdehyde, the product of the non-enzymatic hydrolysis of Delta(1)-pyrroline-5-carboxylate, into glutamate with the reduction of NAD(+) into NADH. We have confirmed the P5CDh activity of the Thermus thermophilus protein TT0033 (TtP5CDh), and determined the crystal structure of the enzyme in the ligand-free form at 1.4 A resolution. To investigate the structural basis of TtP5CDh function, the TtP5CDh structures with NAD(+), with NADH, and with its product glutamate were determined at 1.8 A, 1.9 A, and 1.4 A resolution, respectively. The solved structures suggest an overall view of the P5CDh catalytic mechanism and provide insights into the P5CDh deficiencies in the case of the human type II hyperprolinemia.
-==About this Structure==
+Crystal structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase.,Inagaki E, Ohshima N, Takahashi H, Kuroishi C, Yokoyama S, Tahirov TH J Mol Biol. 2006 Sep 22;362(3):490-501. Epub 2006 Jul 29. PMID:16934832<ref>PMID:16934832</ref>
-IY6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=FLC:'>FLC</scene>, <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=MRD:'>MRD</scene> and <scene name='pdbligand=MPD:'>MPD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/1-pyrroline-5-carboxylate_dehydrogenase 1-pyrroline-5-carboxylate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.12 1.5.1.12] Known structural/functional Site: <scene name='pdbsite=AC1:Cl+Binding+Site+For+Chain+B'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IY6 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of Thermus thermophilus Delta1-pyrroline-5-carboxylate dehydrogenase., Inagaki E, Ohshima N, Takahashi H, Kuroishi C, Yokoyama S, Tahirov TH, J Mol Biol. 2006 Sep 22;362(3):490-501. Epub 2006 Jul 29. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16934832 16934832]
+</div>
-[[Category: 1-pyrroline-5-carboxylate dehydrogenase]]
+<div class="pdbe-citations 2iy6" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
-[[Category: Thermus thermophilus]]
-[[Category: Inagaki, E.]]
-[[Category: Nishio, M.]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
-[[Category: Sakamoto, K.]]
-[[Category: Yokoyama, S.]]
-[[Category: CL]]
-[[Category: FLC]]
-[[Category: MPD]]
-[[Category: MRD]]
-[[Category: NA]]
-[[Category: 1-pyrroline-5-carboxylate]]
-[[Category: citrate]]
-[[Category: dehyrogenase]]
-[[Category: oxidoreductase]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rsgi]]
-[[Category: structural genomics]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 10:39:36 2008''
+==See Also==
+*[[Pyrroline-5-carboxylate dehydrogenase|Pyrroline-5-carboxylate dehydrogenase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Thermus thermophilus HB8]]
+[[Category: Inagaki E]]
+[[Category: Nishio M]]
+[[Category: Sakamoto K]]
+[[Category: Yokoyama S]]