4w5h: Difference between revisions
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==New structural conformations of adenylate kinase from Streptococcus pneumoniae D39== | ==New structural conformations of adenylate kinase from Streptococcus pneumoniae D39== | ||
<StructureSection load='4w5h' size='340' side='right' caption='[[4w5h]], [[Resolution|resolution]] 1.96Å' scene=''> | <StructureSection load='4w5h' size='340' side='right'caption='[[4w5h]], [[Resolution|resolution]] 1.96Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4w5h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W5H OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4w5h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_D39 Streptococcus pneumoniae D39]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W5H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W5H FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=4w5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w5h OCA], [https://pdbe.org/4w5h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w5h RCSB], [https://www.ebi.ac.uk/pdbsum/4w5h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w5h ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/KAD_STRP2 KAD_STRP2] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism (By similarity). | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4w5h" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Streptococcus pneumoniae D39]] | ||
[[Category: | [[Category: Lee SH]] | ||
[[Category: | [[Category: Thach TT]] | ||
Latest revision as of 18:21, 8 November 2023
New structural conformations of adenylate kinase from Streptococcus pneumoniae D39New structural conformations of adenylate kinase from Streptococcus pneumoniae D39
Structural highlights
FunctionKAD_STRP2 Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism (By similarity). Publication Abstract from PubMedAdenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase from Streptococcus pneumoniae D39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groups P21 and P1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 A resolution, respectively, are reported. The new ligand-free crystal belonged to space group C2, with unit-cell parameters a = 73.5, b = 54.3, c = 62.7 A, beta = 118.8 degrees . The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on C(alpha) atoms of 1.4 A. The new crystal of the complex with the two-substrate-mimicking inhibitor P(1),P(5)-bis(adenosine-5'-)pentaphosphate (Ap5A) belonged to space group P1, with unit-cell parameters a = 53.9, b = 62.3, c = 63.0 A, alpha = 101.9, beta = 112.6, gamma = 89.9 degrees . Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation. New crystal structures of adenylate kinase from Streptococcus pneumoniae D39 in two conformations.,Thach TT, Lee S Acta Crystallogr F Struct Biol Commun. 2014 Nov;70(Pt 11):1468-71. doi:, 10.1107/S2053230X14020718. Epub 2014 Oct 25. PMID:25372811[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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