3iod: Difference between revisions

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-{{Seed}}
-[[Image:3iod.jpg|left|200px]]
-<!--
+==Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.75 Ang resolution in complex with 5'-deoxy-5'-((3-nitrobenzyl)disulfanyl)-adenosine==
-The line below this paragraph, containing "STRUCTURE_3iod", creates the "Structure Box" on the page.
+<StructureSection load='3iod' size='340' side='right'caption='[[3iod]], [[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'>[[3iod]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IOD 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=A6D:(2R,3R,4S,5S)-2-(6-AMINO-9H-PURIN-9-YL)-5-{[(3-NITROBENZYL)DISULFANYL]METHYL}TETRAHYDROFURAN-3,4-DIOL'>A6D</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3iod|  PDB=3iod  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3iod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iod OCA], [https://pdbe.org/3iod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iod RCSB], [https://www.ebi.ac.uk/pdbsum/3iod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iod ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PANC_MYCTU PANC_MYCTU] Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate.<ref>PMID:11669627</ref>
+== 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/io/3iod_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=3iod ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A new strategy that combines the concepts of fragment-based drug design and dynamic combinatorial chemistry (DCC) for targeting adenosine recognition sites on enzymes is reported. We demonstrate the use of 5'-deoxy-5'-thioadenosine as a noncovalent anchor fragment in dynamic combinatorial libraries templated by Mycobacterium tuberculosis pantothenate synthetase. A benzyl disulfide derivative was identified upon library analysis by HPLC. Structural and binding studies of protein-ligand complexes by X-ray crystallography and isothermal titration calorimetry informed the subsequent optimisation of the DCC hit into a disulfide containing the novel meta-nitrobenzyl fragment that targets the pantoate binding site of pantothenate synthetase. Given the prevalence of adenosine-recognition motifs in enzymes, our results provide a proof-of-concept for using this strategy to probe adjacent pockets for a range of adenosine binding enzymes, including other related adenylate-forming ligases, kinases, and ATPases, as well as NAD(P)(H), CoA and FAD(H2) binding proteins.
-===Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.75 Ang resolution in complex with 5'-deoxy-5'-((3-nitrobenzyl)disulfanyl)-adenosine===
+A fragment-based approach to probing adenosine recognition sites by using dynamic combinatorial chemistry.,Scott DE, Dawes GJ, Ando M, Abell C, Ciulli A Chembiochem. 2009 Nov 23;10(17):2772-9. PMID:19827080<ref>PMID:19827080</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3iod" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19827080}}, adds the Publication Abstract to the page
+*[[Pantothenate synthetase|Pantothenate synthetase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19827080 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19827080}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-IOD is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IOD OCA].
-==Reference==
-<ref group="xtra">PMID:19827080</ref><references group="xtra"/>
-[[Category: Mycobacterium tuberculosis]]
-[[Category: Pantoate--beta-alanine ligase]]
-[[Category: Abell, C.]]
-[[Category: Ciulli, A.]]
-[[Category: Scott, D E.]]
-[[Category: Atp-binding]]
-[[Category: Cytoplasm]]
-[[Category: Drug design]]
-[[Category: Dynamic combinatorial chemistry]]
-[[Category: Enzyme]]
-[[Category: Fragment-based]]
-[[Category: Inhibitor]]
-[[Category: Ligase]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
 [[Category: Mycobacterium tuberculosis]]
-[[Category: Nucleotide-binding]]
+[[Category: Abell C]]
-[[Category: Pantothenate biosynthesis]]
+[[Category: Ciulli A]]
+[[Category: Scott DE]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec  2 09:51:56 2009''