1jhd: Difference between revisions

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 ==Crystal Structure of Bacterial ATP Sulfurylase from the Riftia pachyptila Symbiont==
-<StructureSection load='1jhd' size='340' side='right' caption='[[1jhd]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='1jhd' size='340' side='right'caption='[[1jhd]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1jhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rifps Rifps]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JHD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1jhd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfur-oxidizing_endosymbiont_of_Riftia_pachyptila Sulfur-oxidizing endosymbiont of Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JHD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sulfate_adenylyltransferase Sulfate adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.4 2.7.7.4] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jhd OCA], [http://pdbe.org/1jhd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jhd RCSB], [http://www.ebi.ac.uk/pdbsum/1jhd PDBsum]</span></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=1jhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jhd OCA], [https://pdbe.org/1jhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jhd RCSB], [https://www.ebi.ac.uk/pdbsum/1jhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jhd ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SAT_RIFPS SAT_RIFPS]
 == 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/jh/1jhd_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jh/1jhd_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1jhd ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-In sulfur chemolithotrophic bacteria, the enzyme ATP sulfurylase functions to produce ATP and inorganic sulfate from APS and inorganic pyrophosphate, which is the final step in the biological oxidation of hydrogen sulfide to sulfate. The giant tubeworm, Riftia pachyptila, which lives near hydrothermal vents on the ocean floor, harbors a sulfur chemolithotroph as an endosymbiont in its trophosome tissue. This yet-to-be-named bacterium was found to contain high levels of ATP sulfurylase that may provide a substantial fraction of the organisms ATP. We present here, the crystal structure of ATP sulfurylase from this bacterium at 1.7 A resolution. As predicted from sequence homology, the enzyme folds into distinct N-terminal and catalytic domains, but lacks the APS kinase-like C-terminal domain that is present in fungal ATP sulfurylase. The enzyme crystallizes as a dimer with one subunit in the crystallographic asymmetric unit. Many buried solvent molecules mediate subunit contacts at the interface. Despite the high concentration of sulfate needed for crystallization, no ordered sulfate was observed in the sulfate-binding pocket. The structure reveals a mobile loop positioned over the active site. This loop is in a "closed" or "down" position in the reported crystal structures of fungal ATP sulfurylases, which contained bound substrates, but it is in an "open" or "up" position in the ligand-free Riftia symbiont enzyme. Thus, closure of the loop correlates with occupancy of the active site, although the loop itself does not interact directly with bound ligands. Rather, it appears to assist in the orientation of residues that do interact with active-site ligands. Amino acid differences between the mobile loops of the enzymes from sulfate assimilators and sulfur chemolithotrophs may account for the significant kinetic differences between the two classes of ATP sulfurylase.
-Crystal structure of ATP sulfurylase from the bacterial symbiont of the hydrothermal vent tubeworm Riftia pachyptila.,Beynon JD, MacRae IJ, Huston SL, Nelson DC, Segel IH, Fisher AJ Biochemistry. 2001 Dec 4;40(48):14509-17. PMID:11724564<ref>PMID:11724564</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1jhd" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Rifps]]
+[[Category: Large Structures]]
-[[Category: Sulfate adenylyltransferase]]
+[[Category: Sulfur-oxidizing endosymbiont of Riftia pachyptila]]
-[[Category: Beynon, J D]]
+[[Category: Beynon JD]]
-[[Category: Fisher, A J]]
+[[Category: Fisher AJ]]
-[[Category: Huston, S L]]
+[[Category: Huston SL]]
-[[Category: MacRae, I J]]
+[[Category: MacRae IJ]]
-[[Category: Nelson, D C]]
+[[Category: Nelson DC]]
-[[Category: Segel, I H]]
+[[Category: Segel IH]]
-[[Category: Adenylyl transferase]]
-[[Category: Ap]]
-[[Category: Bromide]]
-[[Category: Chemoautotroph]]
-[[Category: Sulfurylase]]
-[[Category: Transferase]]