3e0w: Difference between revisions

(5 intermediate revisions by the same user not shown)

Line 1:

~~[[Image:3e0w.png|left|200px]]~~

<!--

==Crystal structure of pyruvate kinase from Leishmania mexicana==

~~The line below this paragraph, containing~~ "~~STRUCTURE_3e0w~~", ~~creates the~~ "~~Structure Box~~" on the ~~page~~.

You may ~~change~~ the ~~PDB parameter~~ (~~which sets~~ the ~~PDB file loaded into~~ the ~~applet~~)

== Structural highlights ==

or the ~~SCENE parameter (which sets~~ the ~~initial scene displayed when~~ the ~~page is loaded~~),

<table><tr><td colspan='2'>[[3e0w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_mexicana Leishmania mexicana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E0W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E0W FirstGlance]. <br>

~~or leave~~ the ~~SCENE parameter empty for~~ the ~~default display~~.

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</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=3e0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e0w OCA], [https://pdbe.org/3e0w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e0w RCSB], [https://www.ebi.ac.uk/pdbsum/3e0w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e0w ProSAT]</span></td></tr>

~~{{STRUCTURE_3e0w| PDB=3e0w | SCENE= }}~~

</table>

== Function ==

[https://www.uniprot.org/uniprot/KPYK_LEIME KPYK_LEIME]

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e0/3e0w_consurf.spt"</scriptWhenChecked>

<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>

<text>to colour the structure by Evolutionary Conservation</text>

</jmolCheckbox>

</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3e0w ConSurf].

== Publication Abstract from PubMed ==

We report X-ray structures of pyruvate kinase from Leishmania mexicana (LmPYK) that are trapped in different conformations. These, together with the previously reported structure of LmPYK in its inactive (T-state) conformation, allow comparisons of three different conformers of the same species of pyruvate kinase (PYK). Four new site point mutants showing the effects of side-chain alteration at subunit interfaces are also enzymatically characterised. The LmPYK tetramer crystals grown with ammonium sulphate as precipitant adopt an active-like conformation, with sulphate ions at the active and effector sites. The sulphates occupy positions similar to those of the phosphates of ligands bound to active (R-state) and constitutively active (nonallosteric) PYKs from several species, and provide insight into the structural roles of the phosphates of the substrates and effectors. Crystal soaking in sulphate-free buffers was found to induce major conformational changes in the tetramer. In particular, the unwinding of the Aalpha6' helix and the inward hinge movement of the B domain are coupled with a significant widening (4 A) of the tetramer caused by lateral movement of the C domains. The two new LmPYK structures and the activity studies of site point mutations described in this article are consistent with a developing picture of allosteric activity in which localised changes in protein flexibility govern the distribution of conformer families adopted by the tetramer in its active and inactive states.

~~===Crystal structure of~~ pyruvate kinase ~~from Leishmania mexicana===~~

Sulphate removal induces a major conformational change in Leishmania mexicana pyruvate kinase in the crystalline state.,Tulloch LB, Morgan HP, Hannaert V, Michels PA, Fothergill-Gilmore LA, Walkinshaw MD J Mol Biol. 2008 Nov 14;383(3):615-26. Epub 2008 Aug 23. PMID:18775437<ref>PMID:18775437</ref>

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

~~<!--~~

</div>

~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_18775437}}, adds the Publication Abstract to~~ the ~~page~~

~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 18775437 is the PubMed ID number~~.

-->

~~{{ABSTRACT_PUBMED_18775437}}~~

==~~About this Structure==~~

~~[[3e0w]] is a 1 chain structure with sequence from [http~~:/~~/en.wikipedia.org/wiki/Leishmania_mexicana Leishmania mexicana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E0W OCA].~~

==See Also==

*[[Pyruvate ~~Kinase~~|Pyruvate ~~Kinase~~]]

*[[Pyruvate kinase 3D structures|Pyruvate kinase 3D structures]]

== References ==

==~~Reference~~==

<~~ref group="xtra">PMID:018775437<~~/~~ref~~><~~references group="xtra"~~/>

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Leishmania mexicana]]

~~[[Category: Pyruvate kinase]]~~

[[Category: Gillmore LA]]

[[Category: Gillmore~~, L A.~~]]

[[Category: Tulloch LB]]

[[Category: Tulloch~~, L B.~~]]

[[Category: Walkinshaw MD]]

[[Category: Walkinshaw~~, M D.]]~~

~~[[Category: Adp]]~~

~~[[Category: Allosteric enzyme]]~~

~~[[Category: Glycolysis]]~~

~~[[Category: Kinase]]~~

~~[[Category: Leishmania]]~~

~~[[Category: Magnesium]]~~

~~[[Category: Metal-binding]]~~

~~[[Category: Mexicana]]~~

~~[[Category: Nad+ nadh]]~~

~~[[Category: Pep]]~~

~~[[Category: Phosphoenolpyruvate]]~~

~~[[Category: Pyruvate]]~~

~~[[Category: Transferase]]~~

~~[[Category: Trypanosomatid~~]]

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-[[Image:3e0w.png|left|200px]]
-<!--
+==Crystal structure of pyruvate kinase from Leishmania mexicana==
-The line below this paragraph, containing "STRUCTURE_3e0w", creates the "Structure Box" on the page.
+<StructureSection load='3e0w' size='340' side='right'caption='[[3e0w]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3e0w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_mexicana Leishmania mexicana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E0W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E0W FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</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=3e0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e0w OCA], [https://pdbe.org/3e0w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e0w RCSB], [https://www.ebi.ac.uk/pdbsum/3e0w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e0w ProSAT]</span></td></tr>
-{{STRUCTURE_3e0w|  PDB=3e0w  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KPYK_LEIME KPYK_LEIME]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e0/3e0w_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3e0w ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report X-ray structures of pyruvate kinase from Leishmania mexicana (LmPYK) that are trapped in different conformations. These, together with the previously reported structure of LmPYK in its inactive (T-state) conformation, allow comparisons of three different conformers of the same species of pyruvate kinase (PYK). Four new site point mutants showing the effects of side-chain alteration at subunit interfaces are also enzymatically characterised. The LmPYK tetramer crystals grown with ammonium sulphate as precipitant adopt an active-like conformation, with sulphate ions at the active and effector sites. The sulphates occupy positions similar to those of the phosphates of ligands bound to active (R-state) and constitutively active (nonallosteric) PYKs from several species, and provide insight into the structural roles of the phosphates of the substrates and effectors. Crystal soaking in sulphate-free buffers was found to induce major conformational changes in the tetramer. In particular, the unwinding of the Aalpha6' helix and the inward hinge movement of the B domain are coupled with a significant widening (4 A) of the tetramer caused by lateral movement of the C domains. The two new LmPYK structures and the activity studies of site point mutations described in this article are consistent with a developing picture of allosteric activity in which localised changes in protein flexibility govern the distribution of conformer families adopted by the tetramer in its active and inactive states.
-===Crystal structure of pyruvate kinase from Leishmania mexicana===
+Sulphate removal induces a major conformational change in Leishmania mexicana pyruvate kinase in the crystalline state.,Tulloch LB, Morgan HP, Hannaert V, Michels PA, Fothergill-Gilmore LA, Walkinshaw MD J Mol Biol. 2008 Nov 14;383(3):615-26. Epub 2008 Aug 23. PMID:18775437<ref>PMID:18775437</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18775437}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3e0w" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18775437 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_18775437}}
-==About this Structure==
-[[3e0w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Leishmania_mexicana Leishmania mexicana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E0W OCA].
 ==See Also==
-*[[Pyruvate Kinase|Pyruvate Kinase]]
+*[[Pyruvate kinase 3D structures|Pyruvate kinase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018775437</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Leishmania mexicana]]
-[[Category: Pyruvate kinase]]
+[[Category: Gillmore LA]]
-[[Category: Gillmore, L A.]]
+[[Category: Tulloch LB]]
-[[Category: Tulloch, L B.]]
+[[Category: Walkinshaw MD]]
-[[Category: Walkinshaw, M D.]]
-[[Category: Adp]]
-[[Category: Allosteric enzyme]]
-[[Category: Glycolysis]]
-[[Category: Kinase]]
-[[Category: Leishmania]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Mexicana]]
-[[Category: Nad+ nadh]]
-[[Category: Pep]]
-[[Category: Phosphoenolpyruvate]]
-[[Category: Pyruvate]]
-[[Category: Transferase]]
-[[Category: Trypanosomatid]]