1xtr: Difference between revisions

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New page: left|200px<br /> <applet load="1xtr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1xtr, resolution 2.65Å" /> '''Structure of small ...
 
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[[Image:1xtr.gif|left|200px]]<br />
<applet load="1xtr" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1xtr, resolution 2.65&Aring;" />
'''Structure of small GTPase human Rheb in complex with GppNHp'''<br />


==Overview==
==Structure of small GTPase human Rheb in complex with GppNHp==
The small GTPase Rheb displays unique biological and biochemical, properties different from other small GTPases and functions as an, important mediator between the tumor suppressor proteins TSC1 and TSC2 and, the mammalian target of rapamycin to stimulate cell growth. We report here, the three-dimensional structures of human Rheb in complexes with GDP, GTP, and GppNHp (5'-(beta,gamma-imide)triphosphate), which reveal novel, structural features of Rheb and provide a molecular basis for its distinct, properties. During GTP/GDP cycling, switch I of Rheb undergoes, conformational change while switch II maintains a stable, unusually, extended conformation, which is substantially different from the, alpha-helical conformation seen in other small GTPases. The unique switch, II conformation results in a displacement of Gln64 (equivalent to the, catalytic Gln61 of Ras), making it incapable of participating in GTP, hydrolysis and thus accounting for the low intrinsic GTPase activity of, Rheb. This rearrangement also creates space to accommodate the side chain, of Arg15, avoiding its steric hindrance with the catalytic residue and, explaining its noninvolvement in GTP hydrolysis. Unlike Ras, the phosphate, moiety of GTP in Rheb is shielded by the conserved Tyr35 of switch I, leading to the closure of the GTP-binding site, which appears to prohibit, the insertion of a potential arginine finger from its GTPase-activating, protein. Taking the genetic, biochemical, biological, and structural data, together, we propose that Rheb forms a new group of the Ras/Rap subfamily, and uses a novel GTP hydrolysis mechanism that utilizes Asn1643 of the, tuberous sclerosis complex 2 GTPase-activating protein domain instead of, Gln64 of Rheb as the catalytic residue.
<StructureSection load='1xtr' size='340' side='right'caption='[[1xtr]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1xtr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XTR 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]] 2.65&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=1xtr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xtr OCA], [https://pdbe.org/1xtr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xtr RCSB], [https://www.ebi.ac.uk/pdbsum/1xtr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xtr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RHEB_HUMAN RHEB_HUMAN] Stimulates the phosphorylation of S6K1 and EIF4EBP1 through activation of mTORC1 signaling. Activates the protein kinase activity of mTORC1. Has low intrinsic GTPase activity.<ref>PMID:12271141</ref> <ref>PMID:12869586</ref> <ref>PMID:15340059</ref> <ref>PMID:15854902</ref> <ref>PMID:16098514</ref> <ref>PMID:20381137</ref>
== 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/xt/1xtr_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=1xtr ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The small GTPase Rheb displays unique biological and biochemical properties different from other small GTPases and functions as an important mediator between the tumor suppressor proteins TSC1 and TSC2 and the mammalian target of rapamycin to stimulate cell growth. We report here the three-dimensional structures of human Rheb in complexes with GDP, GTP, and GppNHp (5'-(beta,gamma-imide)triphosphate), which reveal novel structural features of Rheb and provide a molecular basis for its distinct properties. During GTP/GDP cycling, switch I of Rheb undergoes conformational change while switch II maintains a stable, unusually extended conformation, which is substantially different from the alpha-helical conformation seen in other small GTPases. The unique switch II conformation results in a displacement of Gln64 (equivalent to the catalytic Gln61 of Ras), making it incapable of participating in GTP hydrolysis and thus accounting for the low intrinsic GTPase activity of Rheb. This rearrangement also creates space to accommodate the side chain of Arg15, avoiding its steric hindrance with the catalytic residue and explaining its noninvolvement in GTP hydrolysis. Unlike Ras, the phosphate moiety of GTP in Rheb is shielded by the conserved Tyr35 of switch I, leading to the closure of the GTP-binding site, which appears to prohibit the insertion of a potential arginine finger from its GTPase-activating protein. Taking the genetic, biochemical, biological, and structural data together, we propose that Rheb forms a new group of the Ras/Rap subfamily and uses a novel GTP hydrolysis mechanism that utilizes Asn1643 of the tuberous sclerosis complex 2 GTPase-activating protein domain instead of Gln64 of Rheb as the catalytic residue.


==About this Structure==
Structural basis for the unique biological function of small GTPase RHEB.,Yu Y, Li S, Xu X, Li Y, Guan K, Arnold E, Ding J J Biol Chem. 2005 Apr 29;280(17):17093-100. Epub 2005 Feb 23. PMID:15728574<ref>PMID:15728574</ref>
1XTR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with MG, GNP and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1XTR OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structural basis for the unique biological function of small GTPase RHEB., Yu Y, Li S, Xu X, Li Y, Guan K, Arnold E, Ding J, J Biol Chem. 2005 Apr 29;280(17):17093-100. Epub 2005 Feb 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15728574 15728574]
</div>
<div class="pdbe-citations 1xtr" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[GTP-binding protein 3D structures|GTP-binding protein 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Ding, J.]]
[[Category: Ding J]]
[[Category: Yu, Y.]]
[[Category: Yu Y]]
[[Category: GNP]]
[[Category: GOL]]
[[Category: MG]]
[[Category: beta saddle]]
[[Category: p-loop]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 20:10:48 2007''

Latest revision as of 11:09, 25 October 2023

Structure of small GTPase human Rheb in complex with GppNHpStructure of small GTPase human Rheb in complex with GppNHp

Structural highlights

1xtr is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.65Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RHEB_HUMAN Stimulates the phosphorylation of S6K1 and EIF4EBP1 through activation of mTORC1 signaling. Activates the protein kinase activity of mTORC1. Has low intrinsic GTPase activity.[1] [2] [3] [4] [5] [6]

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

The small GTPase Rheb displays unique biological and biochemical properties different from other small GTPases and functions as an important mediator between the tumor suppressor proteins TSC1 and TSC2 and the mammalian target of rapamycin to stimulate cell growth. We report here the three-dimensional structures of human Rheb in complexes with GDP, GTP, and GppNHp (5'-(beta,gamma-imide)triphosphate), which reveal novel structural features of Rheb and provide a molecular basis for its distinct properties. During GTP/GDP cycling, switch I of Rheb undergoes conformational change while switch II maintains a stable, unusually extended conformation, which is substantially different from the alpha-helical conformation seen in other small GTPases. The unique switch II conformation results in a displacement of Gln64 (equivalent to the catalytic Gln61 of Ras), making it incapable of participating in GTP hydrolysis and thus accounting for the low intrinsic GTPase activity of Rheb. This rearrangement also creates space to accommodate the side chain of Arg15, avoiding its steric hindrance with the catalytic residue and explaining its noninvolvement in GTP hydrolysis. Unlike Ras, the phosphate moiety of GTP in Rheb is shielded by the conserved Tyr35 of switch I, leading to the closure of the GTP-binding site, which appears to prohibit the insertion of a potential arginine finger from its GTPase-activating protein. Taking the genetic, biochemical, biological, and structural data together, we propose that Rheb forms a new group of the Ras/Rap subfamily and uses a novel GTP hydrolysis mechanism that utilizes Asn1643 of the tuberous sclerosis complex 2 GTPase-activating protein domain instead of Gln64 of Rheb as the catalytic residue.

Structural basis for the unique biological function of small GTPase RHEB.,Yu Y, Li S, Xu X, Li Y, Guan K, Arnold E, Ding J J Biol Chem. 2005 Apr 29;280(17):17093-100. Epub 2005 Feb 23. PMID:15728574[7]

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

See Also

References

  1. ↑ Tee AR, Fingar DC, Manning BD, Kwiatkowski DJ, Cantley LC, Blenis J. Tuberous sclerosis complex-1 and -2 gene products function together to inhibit mammalian target of rapamycin (mTOR)-mediated downstream signaling. Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13571-6. Epub 2002 Sep 23. PMID:12271141 doi:10.1073/pnas.202476899
  2. ↑ Inoki K, Li Y, Xu T, Guan KL. Rheb GTPase is a direct target of TSC2 GAP activity and regulates mTOR signaling. Genes Dev. 2003 Aug 1;17(15):1829-34. Epub 2003 Jul 17. PMID:12869586 doi:10.1101/gad.1110003
  3. ↑ Li Y, Inoki K, Guan KL. Biochemical and functional characterizations of small GTPase Rheb and TSC2 GAP activity. Mol Cell Biol. 2004 Sep;24(18):7965-75. PMID:15340059 doi:10.1128/MCB.24.18.7965-7975.2004
  4. ↑ Long X, Lin Y, Ortiz-Vega S, Yonezawa K, Avruch J. Rheb binds and regulates the mTOR kinase. Curr Biol. 2005 Apr 26;15(8):702-13. PMID:15854902 doi:S0960-9822(05)00226-5
  5. ↑ Tee AR, Blenis J, Proud CG. Analysis of mTOR signaling by the small G-proteins, Rheb and RhebL1. FEBS Lett. 2005 Aug 29;579(21):4763-8. PMID:16098514 doi:10.1016/j.febslet.2005.07.054
  6. ↑ Sancak Y, Bar-Peled L, Zoncu R, Markhard AL, Nada S, Sabatini DM. Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids. Cell. 2010 Apr 16;141(2):290-303. doi: 10.1016/j.cell.2010.02.024. Epub 2010 Apr , 8. PMID:20381137 doi:10.1016/j.cell.2010.02.024
  7. ↑ Yu Y, Li S, Xu X, Li Y, Guan K, Arnold E, Ding J. Structural basis for the unique biological function of small GTPase RHEB. J Biol Chem. 2005 Apr 29;280(17):17093-100. Epub 2005 Feb 23. PMID:15728574 doi:10.1074/jbc.M501253200

1xtr, resolution 2.65Å

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