2x2e: Difference between revisions

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[[Image:2x2e.png|left|200px]]


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==Dynamin GTPase dimer, long axis form==
The line below this paragraph, containing "STRUCTURE_2x2e", creates the "Structure Box" on the page.
<StructureSection load='2x2e' size='340' side='right'caption='[[2x2e]], [[Resolution|resolution]] 2.00&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'>[[2x2e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X2E FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
{{STRUCTURE_2x2e|  PDB=2x2e  |  SCENE=  }}
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2x2f|2x2f]], [[2dyn|2dyn]], [[1dyn|1dyn]]</div></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Dynamin_GTPase Dynamin GTPase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.5.5 3.6.5.5] </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=2x2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x2e OCA], [https://pdbe.org/2x2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x2e RCSB], [https://www.ebi.ac.uk/pdbsum/2x2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x2e ProSAT]</span></td></tr>
</table>
== Function ==
[[https://www.uniprot.org/uniprot/DYN1_HUMAN DYN1_HUMAN]] Microtubule-associated force-producing protein involved in producing microtubule bundles and able to bind and hydrolyze GTP. Most probably involved in vesicular trafficking processes. Involved in receptor-mediated endocytosis.
== 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/x2/2x2e_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=2x2e ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Dynamin is an atypical GTPase that catalyses membrane fission during clathrin-mediated endocytosis. The mechanisms of dynamin's basal and assembly-stimulated GTP hydrolysis are unknown, though both are indirectly influenced by the GTPase effector domain (GED). Here we present the 2.0 A resolution crystal structure of a human dynamin 1-derived minimal GTPase-GED fusion protein, which was dimeric in the presence of the transition state mimic GDP.AlF(4)(-).The structure reveals dynamin's catalytic machinery and explains how assembly-stimulated GTP hydrolysis is achieved through G domain dimerization. A sodium ion present in the active site suggests that dynamin uses a cation to compensate for the developing negative charge in the transition state in the absence of an arginine finger. Structural comparison to the rat dynamin G domain reveals key conformational changes that promote G domain dimerization and stimulated hydrolysis. The structure of the GTPase-GED fusion protein dimer provides insight into the mechanisms underlying dynamin-catalysed membrane fission.


===DYNAMIN GTPASE DIMER, LONG AXIS FORM===
G domain dimerization controls dynamin's assembly-stimulated GTPase activity.,Chappie JS, Acharya S, Leonard M, Schmid SL, Dyda F Nature. 2010 May 27;465(7297):435-40. Epub 2010 Apr 28. PMID:20428113<ref>PMID:20428113</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2x2e" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 20428113 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_20428113}}
__TOC__
 
</StructureSection>
==About this Structure==
[[2x2e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X2E OCA].
 
==Reference==
<ref group="xtra">PMID:020428113</ref><references group="xtra"/>
[[Category: Dynamin GTPase]]
[[Category: Dynamin GTPase]]
[[Category: Homo sapiens]]
[[Category: Human]]
[[Category: Acharya, S.]]
[[Category: Large Structures]]
[[Category: Chappie, J S.]]
[[Category: Acharya, S]]
[[Category: Dyda, F.]]
[[Category: Chappie, J S]]
[[Category: Leonard, M.]]
[[Category: Dyda, F]]
[[Category: Schmid, S L.]]
[[Category: Leonard, M]]
[[Category: Schmid, S L]]
[[Category: Endocytosis]]
[[Category: Endocytosis]]
[[Category: Hydrolase]]
[[Category: Hydrolase]]

Latest revision as of 19:48, 3 November 2021

Dynamin GTPase dimer, long axis formDynamin GTPase dimer, long axis form

Structural highlights

2x2e is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , ,
NonStd Res:
Activity:Dynamin GTPase, with EC number 3.6.5.5
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DYN1_HUMAN] Microtubule-associated force-producing protein involved in producing microtubule bundles and able to bind and hydrolyze GTP. Most probably involved in vesicular trafficking processes. Involved in receptor-mediated endocytosis.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Dynamin is an atypical GTPase that catalyses membrane fission during clathrin-mediated endocytosis. The mechanisms of dynamin's basal and assembly-stimulated GTP hydrolysis are unknown, though both are indirectly influenced by the GTPase effector domain (GED). Here we present the 2.0 A resolution crystal structure of a human dynamin 1-derived minimal GTPase-GED fusion protein, which was dimeric in the presence of the transition state mimic GDP.AlF(4)(-).The structure reveals dynamin's catalytic machinery and explains how assembly-stimulated GTP hydrolysis is achieved through G domain dimerization. A sodium ion present in the active site suggests that dynamin uses a cation to compensate for the developing negative charge in the transition state in the absence of an arginine finger. Structural comparison to the rat dynamin G domain reveals key conformational changes that promote G domain dimerization and stimulated hydrolysis. The structure of the GTPase-GED fusion protein dimer provides insight into the mechanisms underlying dynamin-catalysed membrane fission.

G domain dimerization controls dynamin's assembly-stimulated GTPase activity.,Chappie JS, Acharya S, Leonard M, Schmid SL, Dyda F Nature. 2010 May 27;465(7297):435-40. Epub 2010 Apr 28. PMID:20428113[1]

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

References

  1. Chappie JS, Acharya S, Leonard M, Schmid SL, Dyda F. G domain dimerization controls dynamin's assembly-stimulated GTPase activity. Nature. 2010 May 27;465(7297):435-40. Epub 2010 Apr 28. PMID:20428113 doi:10.1038/nature09032

2x2e, resolution 2.00Å

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OCA