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5t3o

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Current revision (15:35, 6 March 2024) (edit) (undo)
 
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<StructureSection load='5t3o' size='340' side='right'caption='[[5t3o]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='5t3o' size='340' side='right'caption='[[5t3o]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5t3o]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T3O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5T3O FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5t3o]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T3O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T3O FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose-phosphate_diphosphokinase Ribose-phosphate diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.1 2.7.6.1] </span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5t3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t3o OCA], [http://pdbe.org/5t3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t3o RCSB], [http://www.ebi.ac.uk/pdbsum/5t3o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t3o ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5t3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t3o OCA], [https://pdbe.org/5t3o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t3o RCSB], [https://www.ebi.ac.uk/pdbsum/5t3o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t3o ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/Q5SHU3_THET8 Q5SHU3_THET8]] Involved in the biosynthesis of ribose 1,5-bisphosphate. Catalyzes the transfer of pyrophosphoryl group from ATP to ribose-5-phosphate to yield phosphoribosyl diphosphate (PRPP) and AMP.[HAMAP-Rule:MF_00583]
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[https://www.uniprot.org/uniprot/Q5SHU3_THET8 Q5SHU3_THET8] Involved in the biosynthesis of ribose 1,5-bisphosphate. Catalyzes the transfer of pyrophosphoryl group from ATP to ribose-5-phosphate to yield phosphoribosyl diphosphate (PRPP) and AMP.[HAMAP-Rule:MF_00583]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Phosphoribosylpyrophosphate synthetase (PRPPS) from the thermophilic bacterial strain Thermus thermophilus HB27 catalyzes the synthesis of phosphoribosylpyrophosphate from ribose 5-phosphate and ATP, and belongs to the class I PRPPSs. The three-dimensional structure of the recombinant enzyme was solved at 2.2 A resolution using crystals grown in microgravity from protein solution containing ATP, magnesium and sulfate ions. An ADP molecule was located in the active site of each subunit of the hexameric enzyme molecule and sulfate ions were located in both the active and allosteric sites. It was found that the catalytic loop that restricts the active-site area and is usually missing from the electron-density map of class I PRPPSs adopts different conformations in three independent subunits in T. thermophilus PRPPS. A closed conformation of the active site was found in one of subunits where the highly ordered catalytic beta-hairpin delivers the Lys and Arg residues that are essential for activity directly to the ADP molecule, which occupies the ATP-binding site. A comparison of the conformations of the catalytic loop in the three independent subunits reveals a possible mode of transition from the open to the closed state of the active site during the course of the catalyzed reaction.
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Crystal structure of recombinant phosphoribosylpyrophosphate synthetase 2 from Thermus thermophilus HB27 complexed with ADP and sulfate ions.,Timofeev VI, Sinitsyna EV, Kostromina MA, Muravieva TI, Makarov DA, Mikheeva OO, Kuranova IP, Esipov RS Acta Crystallogr F Struct Biol Commun. 2017 Jun 1;73(Pt 6):369-375. doi:, 10.1107/S2053230X17007488. Epub 2017 May 31. PMID:28580926<ref>PMID:28580926</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5t3o" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Ribose-phosphate diphosphokinase]]
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[[Category: Thermus thermophilus]]
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[[Category: Abramchik, Y A]]
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[[Category: Abramchik YA]]
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[[Category: Esipov, R S]]
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[[Category: Esipov RS]]
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[[Category: Kostromina, M A]]
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[[Category: Kostromina MA]]
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[[Category: Kuranova, I P]]
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[[Category: Kuranova IP]]
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[[Category: Sinitsyna, E V]]
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[[Category: Sinitsyna EV]]
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[[Category: Timofeev, V I]]
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[[Category: Timofeev VI]]
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[[Category: Modpipe model of up q5shu3]]
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[[Category: Transferase]]
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Current revision

Crystal structure of the Phosphorybosylpyrophosphate synthetase II from Thermus thermophilus

PDB ID 5t3o

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