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==Crystal structure of Adenylosuccinate lyase from Thermus thermophilus HB8, TtPurB== | |||
<StructureSection load='8jbd' size='340' side='right'caption='[[8jbd]], [[Resolution|resolution]] 2.38Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8jbd]] is a 2 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=8JBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8JBD FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.38Å</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=8jbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8jbd OCA], [https://pdbe.org/8jbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8jbd RCSB], [https://www.ebi.ac.uk/pdbsum/8jbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8jbd ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q5SI61_THET8 Q5SI61_THET8] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Adenylosuccinate lyase (PurB) catalyzes two distinct reactions in the purine nucleotide biosynthetic pathway using the same active site. The ability to recognize two different sets of substrates is of structural and evolutionary interest. In the present study, the crystal structure of PurB from the thermophilic bacterium Thermus thermophilus HB8 (TtPurB) was determined at a resolution of 2.38 A by molecular replacement using a structure predicted by AlphaFold2 as a template. The asymmetric unit of the TtPurB crystal contained two TtPurB molecules, and some regions were disordered in the crystal structure. The disordered regions were the substrate-binding site and domain 3. TtPurB forms a homotetramer and the monomer is composed of three domains (domains 1, 2 and 3), which is a typical structure for the aspartase/fumarase superfamily. Molecular dynamics simulations with and without substrate/product were performed using a full-length model of TtPurB which was obtained before deletion of the disordered regions. The substrates and products were bound to the model structures during the MD simulations. The fluctuations of amino-acid residues were greater in the disordered regions and became smaller upon the binding of substrate or product. These results demonstrate that the full-length model obtained using AlphaFold2 can be used to generate the coordinates of disordered regions within the crystal structure. | |||
Crystal structure of adenylosuccinate lyase from the thermophilic bacterium Thermus thermophilus HB8.,Nemoto N, Kawai G, Sampei GI Acta Crystallogr F Struct Biol Commun. 2023 Nov 1;79(Pt 11):278-284. doi: , 10.1107/S2053230X23009020. Epub 2023 Oct 24. PMID:37873935<ref>PMID:37873935</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 8jbd" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Thermus thermophilus HB8]] | |||
[[Category: Kawai G]] | |||
[[Category: Nemoto N]] | |||
[[Category: Sampei G]] | |||
Revision as of 10:36, 15 November 2023
Crystal structure of Adenylosuccinate lyase from Thermus thermophilus HB8, TtPurBCrystal structure of Adenylosuccinate lyase from Thermus thermophilus HB8, TtPurB
Structural highlights
FunctionPublication Abstract from PubMedAdenylosuccinate lyase (PurB) catalyzes two distinct reactions in the purine nucleotide biosynthetic pathway using the same active site. The ability to recognize two different sets of substrates is of structural and evolutionary interest. In the present study, the crystal structure of PurB from the thermophilic bacterium Thermus thermophilus HB8 (TtPurB) was determined at a resolution of 2.38 A by molecular replacement using a structure predicted by AlphaFold2 as a template. The asymmetric unit of the TtPurB crystal contained two TtPurB molecules, and some regions were disordered in the crystal structure. The disordered regions were the substrate-binding site and domain 3. TtPurB forms a homotetramer and the monomer is composed of three domains (domains 1, 2 and 3), which is a typical structure for the aspartase/fumarase superfamily. Molecular dynamics simulations with and without substrate/product were performed using a full-length model of TtPurB which was obtained before deletion of the disordered regions. The substrates and products were bound to the model structures during the MD simulations. The fluctuations of amino-acid residues were greater in the disordered regions and became smaller upon the binding of substrate or product. These results demonstrate that the full-length model obtained using AlphaFold2 can be used to generate the coordinates of disordered regions within the crystal structure. Crystal structure of adenylosuccinate lyase from the thermophilic bacterium Thermus thermophilus HB8.,Nemoto N, Kawai G, Sampei GI Acta Crystallogr F Struct Biol Commun. 2023 Nov 1;79(Pt 11):278-284. doi: , 10.1107/S2053230X23009020. Epub 2023 Oct 24. PMID:37873935[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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