1od6: Difference between revisions

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-[[Image:1od6.jpg|left|200px]]<br /><applet load="1od6" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1od6, resolution 1.5&Aring;" />
-'''THE CRYSTAL STRUCTURE OF PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE FROM THERMUS THERMOPHILUS IN COMPLEX WITH 4'-PHOSPHOPANTETHEINE'''<br />
-==Overview==
+==The Crystal Structure of Phosphopantetheine adenylyltransferase from Thermus Thermophilus in complex with 4'-phosphopantetheine==
-Phosphopantetheine adenylyltransferase (PPAT) is an essential enzyme in, bacteria that catalyzes the rate-limiting step in coenzyme A (CoA), biosynthesis by transferring an adenylyl group from ATP to, 4'-phosphopantetheine (Ppant), yielding 3'-dephospho-CoA (dPCoA). The, crystal structure of PPAT from Thermus thermophilus HB8 (Tt PPAT), complexed with Ppant has been determined by the molecular-replacement, method at 1.5 A resolution. The overall fold of the enzyme is almost the, same as that of Escherichia coli PPAT, a hexamer having point group 32., The asymmetric unit of Tt PPAT contains a monomer and the crystallographic, triad and dyad coincide with the threefold and twofold axes of the, hexamer, respectively. Most of the important atoms surrounding the active, site in E. coli PPAT are conserved in Tt PPAT, indicating similarities in, their substrate binding and enzymatic reaction. The notable difference, between E. coli PPAT and Tt PPAT is the simultaneous substrate recognition, by all six subunits of Tt PPAT compared with substrate recognition by only, three subunits in E. coli PPAT. Comparative analysis also revealed that, the higher stability of Tt PPAT arises from stabilization of each subunit, by hydrophobic effects, hydrogen bonds and entropic effects.
+<StructureSection load='1od6' size='340' side='right'caption='[[1od6]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1od6]] is a 1 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=1OD6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OD6 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]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PNS:4-PHOSPHOPANTETHEINE'>PNS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1od6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1od6 OCA], [https://pdbe.org/1od6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1od6 RCSB], [https://www.ebi.ac.uk/pdbsum/1od6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1od6 ProSAT], [https://www.topsan.org/Proteins/RSGI/1od6 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/COAD_THET8 COAD_THET8] Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate.[HAMAP-Rule:MF_00151]
+== 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/od/1od6_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=1od6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Phosphopantetheine adenylyltransferase (PPAT) is an essential enzyme in bacteria that catalyzes the rate-limiting step in coenzyme A (CoA) biosynthesis by transferring an adenylyl group from ATP to 4'-phosphopantetheine (Ppant), yielding 3'-dephospho-CoA (dPCoA). The crystal structure of PPAT from Thermus thermophilus HB8 (Tt PPAT) complexed with Ppant has been determined by the molecular-replacement method at 1.5 A resolution. The overall fold of the enzyme is almost the same as that of Escherichia coli PPAT, a hexamer having point group 32. The asymmetric unit of Tt PPAT contains a monomer and the crystallographic triad and dyad coincide with the threefold and twofold axes of the hexamer, respectively. Most of the important atoms surrounding the active site in E. coli PPAT are conserved in Tt PPAT, indicating similarities in their substrate binding and enzymatic reaction. The notable difference between E. coli PPAT and Tt PPAT is the simultaneous substrate recognition by all six subunits of Tt PPAT compared with substrate recognition by only three subunits in E. coli PPAT. Comparative analysis also revealed that the higher stability of Tt PPAT arises from stabilization of each subunit by hydrophobic effects, hydrogen bonds and entropic effects.
-==About this Structure==
+Structure and implications for the thermal stability of phosphopantetheine adenylyltransferase from Thermus thermophilus.,Takahashi H, Inagaki E, Fujimoto Y, Kuroishi C, Nodake Y, Nakamura Y, Arisaka F, Yutani K, Kuramitsu S, Yokoyama S, Yamamoto M, Miyano M, Tahirov TH Acta Crystallogr D Biol Crystallogr. 2004 Jan;60(Pt 1):97-104. Epub 2003, Dec 18. PMID:14684898<ref>PMID:14684898</ref>
-OD6 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=SO4:'>SO4</scene> and <scene name='pdbligand=PNS:'>PNS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Pantetheine-phosphate_adenylyltransferase Pantetheine-phosphate adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.3 2.7.7.3] Known structural/functional Site: <scene name='pdbsite=AC1:So4+Binding+Site+For+Chain+A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OD6 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure and implications for the thermal stability of phosphopantetheine adenylyltransferase from Thermus thermophilus., Takahashi H, Inagaki E, Fujimoto Y, Kuroishi C, Nodake Y, Nakamura Y, Arisaka F, Yutani K, Kuramitsu S, Yokoyama S, Yamamoto M, Miyano M, Tahirov TH, Acta Crystallogr D Biol Crystallogr. 2004 Jan;60(Pt 1):97-104. Epub 2003, Dec 18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14684898 14684898]
+</div>
-[[Category: Pantetheine-phosphate adenylyltransferase]]
+<div class="pdbe-citations 1od6" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+== References ==
-[[Category: Thermus thermophilus]]
+<references/>
-[[Category: Inagaki, E.]]
+__TOC__
-[[Category: Miyano, M.]]
+</StructureSection>
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+[[Category: Large Structures]]
-[[Category: Tahirov, T.]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Takahashi, H.]]
+[[Category: Inagaki E]]
-[[Category: PNS]]
+[[Category: Miyano M]]
-[[Category: SO4]]
+[[Category: Tahirov TH]]
-[[Category: coenzyme a biosynthesis]]
+[[Category: Takahashi H]]
-[[Category: nucleotidyltransferase]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rsgi]]
-[[Category: structural genomics]]
-[[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 09:56:23 2008''