2ab8: Difference between revisions

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-{{Seed}}
-[[Image:2ab8.png|left|200px]]
-<!--
+==Crystal structure of T. gondii adenosine kinase complexed with 6-methylmercaptopurine riboside and AMP-PCP==
-The line below this paragraph, containing "STRUCTURE_2ab8", creates the "Structure Box" on the page.
+<StructureSection load='2ab8' size='340' side='right'caption='[[2ab8]], [[Resolution|resolution]] 1.75&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'>[[2ab8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Toxoplasma_gondii Toxoplasma gondii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AB8 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]] 1.75&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MTP:2-HYDROXYMETHYL-5-(6-METHYLSULFANYL-PURIN-9-YL)-TETRAHYDRO-FURAN-3,4-DIOL'>MTP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_2ab8|  PDB=2ab8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ab8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ab8 OCA], [https://pdbe.org/2ab8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ab8 RCSB], [https://www.ebi.ac.uk/pdbsum/2ab8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ab8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ADK_TOXGO ADK_TOXGO] ATP-dependent phosphorylation of adenosine and other related nucleoside analogs to monophosphate derivatives. It is a key purine metabolic enzyme in the opportunistic parasitic protozoan toxoplasma gondii as it cannot synthesize purines de novo.
+== 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/ab/2ab8_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=2ab8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Adenosine kinase (AK) is a key enzyme in purine metabolism in the ubiquitous intracellular parasite Toxoplasma gondii and is a potential chemotherapeutic target for the treatment of T. gondii infections. To better understand the structure-activity relationship of 6-substituted purine ribosides, the structures of the T. gondii AK-N6,N6-dimethyladenosine (DMA) complex, the AK-DMA-AMP-PCP complex, the AK-6-methyl mercaptopurine riboside (MMPR) complex and the AK-MMPR-AMP-PCP complex were determined to 1.35, 1.35, 1.75 and 1.75 A resolution, respectively. These structures reveal a conformation intermediate between open and closed, with a small lid-domain rotation of 12 degrees . Residues Gly143-X-X-Gly146 undergo torsional changes upon substrate binding, which together with a Gly68-Gly69 switch induces a hinge bending of the lid domain. The intermediate conformation suggests that ATP binding is independent of adenosine binding. Orienting the gamma-phosphate group of ATP into the optimal catalytic position may be the last step before the onset of chemical catalysis and may require the translocation of Arg136 following the complete closure of the lid domain. 6-Substituted purine-nucleoside analogs are accommodated in a hydrophobic cavity. Modification at the N6 or C6 position of the nucleoside would affect the interactions with the surrounding residues and the binding affinity.
-===Crystal structure of T. gondii adenosine kinase complexed with 6-methylmercaptopurine riboside and AMP-PCP===
+Substrate analogs induce an intermediate conformational change in Toxoplasma gondii adenosine kinase.,Zhang Y, El Kouni MH, Ealick SE Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):126-34. Epub 2007, Jan 16. PMID:17242506<ref>PMID:17242506</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ab8" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17242506}}, adds the Publication Abstract to the page
+*[[Adenosine kinase 3D structures|Adenosine kinase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17242506 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17242506}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-AB8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Toxoplasma_gondii Toxoplasma gondii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AB8 OCA].
-==Reference==
-Substrate analogs induce an intermediate conformational change in Toxoplasma gondii adenosine kinase., Zhang Y, El Kouni MH, Ealick SE, Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):126-34. Epub 2007, Jan 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17242506 17242506]
-[[Category: Adenosine kinase]]
-[[Category: Single protein]]
 [[Category: Toxoplasma gondii]]
-[[Category: Ealick, S E.]]
+[[Category: Ealick SE]]
-[[Category: Kouni, M H.el.]]
+[[Category: Zhang Y]]
-[[Category: Zhang, Y.]]
+[[Category: El Kouni MH]]
-[[Category: Alpha/beta]]
-[[Category: Intermediate conformation]]
-[[Category: Ribokinase fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 16:28:19 2008''