1od6: Difference between revisions

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-{{Seed}}
-[[Image:1od6.png|left|200px]]
-<!--
+==The Crystal Structure of Phosphopantetheine adenylyltransferase from Thermus Thermophilus in complex with 4'-phosphopantetheine==
-The line below this paragraph, containing "STRUCTURE_1od6", creates the "Structure Box" on the page.
+<StructureSection load='1od6' size='340' side='right'caption='[[1od6]], [[Resolution|resolution]] 1.50&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'>[[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>
-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]] 1.5&#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>
-{{STRUCTURE_1od6|  PDB=1od6  |  SCENE=  }}
+<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.
-===THE CRYSTAL STRUCTURE OF PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE FROM THERMUS THERMOPHILUS IN COMPLEX WITH 4'-PHOSPHOPANTETHEINE===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_14684898}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1od6" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 14684898 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14684898}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-OD6 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OD6 OCA].
+[[Category: Thermus thermophilus HB8]]
+[[Category: Inagaki E]]
-==Reference==
+[[Category: Miyano M]]
-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://www.ncbi.nlm.nih.gov/pubmed/14684898 14684898]
+[[Category: Tahirov TH]]
-[[Category: Pantetheine-phosphate adenylyltransferase]]
+[[Category: Takahashi H]]
-[[Category: Thermus thermophilus]]
-[[Category: Inagaki, E.]]
-[[Category: Miyano, M.]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
-[[Category: Tahirov, T.]]
-[[Category: Takahashi, H.]]
-[[Category: Coenzyme a biosynthesis]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 18:29:49 2008''