3x2s

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of pyrene-conjugated adenylate kinase

Structural highlights

3x2s is a 2 chain structure with sequence from Escherichia coli str. K-12 substr. MDS42. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Fujii A, Sekiguchi Y, Matsumura H, Inoue T, Chung WS, Hirota S, Matsuo T. Excimer Emission Properties on Pyrene-Labeled Protein Surface: Correlation between Emission Spectra, Ring Stacking Modes, and Flexibilities of Pyrene Probes. Bioconjug Chem. 2015 Mar 18;26(3):537-48. doi: 10.1021/acs.bioconjchem.5b00026., Epub 2015 Feb 18. PMID:25646669 doi:http://dx.doi.org/10.1021/acs.bioconjchem.5b00026

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3x2s"

@@ Line 1: / Line 1: @@
 ==Crystal structure of pyrene-conjugated adenylate kinase==
-<StructureSection load='3x2s' size='340' side='right' caption='[[3x2s]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='3x2s' size='340' side='right'caption='[[3x2s]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3x2s]] is a 2 chain structure. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3X2S FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3x2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x2s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3x2s RCSB], [http://www.ebi.ac.uk/pdbsum/3x2s 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=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 ==
-[[http://www.uniprot.org/uniprot/H0QBG3_ECOLI H0QBG3_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]
+[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 ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3x2s" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Adenylate kinase]]
+[[Category: Escherichia coli str. K-12 substr. MDS42]]
-[[Category: Chung, W S]]
+[[Category: Large Structures]]
-[[Category: Fujii, A]]
+[[Category: Chung W-S]]
-[[Category: Hirota, S]]
+[[Category: Fujii A]]
-[[Category: Inoue, T]]
+[[Category: Hirota S]]
-[[Category: Matsumura, H]]
+[[Category: Inoue T]]
-[[Category: Matsuo, T]]
+[[Category: Matsumura H]]
-[[Category: Sekiguchi, Y]]
+[[Category: Matsuo T]]
-[[Category: Kinase]]
+[[Category: Sekiguchi Y]]
-[[Category: Nmp and lid domain]]
-[[Category: Transferase]]

3x2s

From Proteopedia

Current revision

Crystal structure of pyrene-conjugated adenylate kinase

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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