3x2s: Difference between revisions
New page: '''Unreleased structure''' The entry 3x2s is ON HOLD Authors: Fujii, A., Sekiguchi, Y., Matsumura, H., Inoue, T., Chung, W-S., Hirota, S., Matsuo, T. Description: Crystal structure of ... |
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The | ==Crystal structure of pyrene-conjugated adenylate kinase== | ||
<StructureSection load='3x2s' size='340' side='right'caption='[[3x2s]], [[Resolution|resolution]] 2.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3x2s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MDS42 Escherichia coli str. K-12 substr. MDS42]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X2S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X2S 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]] 2.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=JPY:N-(PYREN-1-YLMETHYL)ACETAMIDE'>JPY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3x2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x2s OCA], [https://pdbe.org/3x2s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x2s RCSB], [https://www.ebi.ac.uk/pdbsum/3x2s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x2s ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A0J9X1X4_ECOLI A0A0J9X1X4_ECOLI] 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.[HAMAP-Rule:MF_00235] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The excimer emission of pyrene is popularly employed for investigating the association between pyrene-labeled biomolecules or between pyrene-labeled places in a biomolecule. The property of pyrene excimer emission is affected by the fluctuation in ring stacking modes, which originates from the structural flexibilities of pyrene probes and/or of labeled places. Investigations of the excimer emission in terms of dynamics of pyrene stacking modes provide the detailed spatial information between pyrene-labeled places. In order to evaluate the effects of probe structures and fluctuation in pyrene-pyrene association modes on their emission properties on protein surface, three types of pyrene probe with different linker lengths were synthesized and conjugated to two cysteine residues in the A55C/C77S/V169C mutant of adenylate kinase (Adk), an enzyme that shows a structural transition between OPEN and CLOSED forms. In the CLOSED form of Adk labeled by a pyrene probe with a short linker, excimer emission was found to be predominated by the ground-state association of pyrenes. The pyrene stacking structure on the protein surface was successfully determined by an X-ray crystallographic analysis. However, the emission decay in the protein suggested the existence of several stacking orientations in solution. With the increase in the linker length, the effect of fluctuation in pyrene association modes on the spectral properties distinctly emerged at both ground and excited states. The combination of steady-state and time-resolved spectroscopic analyses is useful for differentiation in the origin of the excimer emission, which is essential for precisely understanding the interaction fashions between pyrene-labeled biomolecules. | |||
Excimer Emission Properties on Pyrene-Labeled Protein Surface: Correlation between Emission Spectra, Ring Stacking Modes, and Flexibilities of Pyrene Probes.,Fujii A, Sekiguchi Y, Matsumura H, Inoue T, Chung WS, Hirota S, Matsuo T Bioconjug Chem. 2015 Mar 18;26(3):537-48. doi: 10.1021/acs.bioconjchem.5b00026., Epub 2015 Feb 18. PMID:25646669<ref>PMID:25646669</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[ | </div> | ||
[[Category: | <div class="pdbe-citations 3x2s" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: Chung | ==See Also== | ||
[[Category: | *[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]] | ||
[[Category: Hirota | == References == | ||
[[Category: | <references/> | ||
[[Category: Matsumura | __TOC__ | ||
</StructureSection> | |||
[[Category: Escherichia coli str. K-12 substr. MDS42]] | |||
[[Category: Large Structures]] | |||
[[Category: Chung W-S]] | |||
[[Category: Fujii A]] | |||
[[Category: Hirota S]] | |||
[[Category: Inoue T]] | |||
[[Category: Matsumura H]] | |||
[[Category: Matsuo T]] | |||
[[Category: Sekiguchi Y]] | |||