3def

From Proteopedia

(Difference between revisions)

Revision as of 07:32, 10 November 2021

Crystal structure of Toc33 from Arabidopsis thaliana, dimerization deficient mutant R130A

Structural highlights

3def is a 1 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	2j3e
Gene:	T7I23.11 (ARATH)
Activity:	Small monomeric GTPase, with EC number 3.6.5.2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TOC33_ARATH] GTPase involved in protein precursor import into chloroplasts. Seems to recognize chloroplast-destined precursor proteins and regulate their presentation to the translocation channel through GTP hydrolysis. Binds GTP, GDP, XTP, but not ATP. Probably specialized in the import of nuclear encoded photosynthetic preproteins from the cytoplasm to the chloroplast, especially during early development stages.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10]

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

Precursor protein translocation across the outer chloroplast membrane depends on the action of the Toc complex, containing GTPases as recognizing receptor components. The G domains of the GTPases are known to dimerize. In the dimeric conformation an arginine contacts the phosphate moieties of bound nucleotide in trans. Kinetic studies suggested that the arginine in itself does not act as an arginine finger of a reciprocal GTPase-activating protein (GAP). Here we investigate the specific function of the residue in two GTPase homologues. Arginine to alanine replacement variants have significantly reduced affinities for dimerization compared with wild-type GTPases. The amino acid exchange does not impact on the overall fold and nucleotide binding, as seen in the monomeric x-ray crystallographic structure of the Arabidopsis Toc33 arginine-alanine replacement variant at 2.0A. We probed the catalytic center with the transition state analogue GDP/AlF(x) using NMR and analytical ultracentrifugation. AlF(x) binding depends on the arginine, suggesting the residue can play a role in catalysis despite the non-GAP nature of the homodimer. Two non-exclusive functional models are discussed: 1) the coGAP hypothesis, in which an additional factor activates the GTPase in homodimeric form; and 2) the switch hypothesis, in which a protein, presumably the large Toc159 GTPase, exchanges with one of the homodimeric subunits, leading to activation.

On the significance of Toc-GTPase homodimers.,Koenig P, Oreb M, Rippe K, Muhle-Goll C, Sinning I, Schleiff E, Tews I J Biol Chem. 2008 Aug 22;283(34):23104-12. Epub 2008 Jun 8. PMID:18541539^[11]

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

References

↑ Yu TS, Li H. Chloroplast protein translocon components atToc159 and atToc33 are not essential for chloroplast biogenesis in guard cells and root cells. Plant Physiol. 2001 Sep;127(1):90-6. PMID:11553737
↑ Jelic M, Soll J, Schleiff E. Two Toc34 homologues with different properties. Biochemistry. 2003 May 20;42(19):5906-16. PMID:12741849 doi:http://dx.doi.org/10.1021/bi034001q
↑ Aronsson H, Combe J, Jarvis P. Unusual nucleotide-binding properties of the chloroplast protein import receptor, atToc33. FEBS Lett. 2003 Jun 5;544(1-3):79-85. PMID:12782294
↑ Weibel P, Hiltbrunner A, Brand L, Kessler F. Dimerization of Toc-GTPases at the chloroplast protein import machinery. J Biol Chem. 2003 Sep 26;278(39):37321-9. Epub 2003 Jul 16. PMID:12869544 doi:http://dx.doi.org/10.1074/jbc.M305946200
↑ Wallas TR, Smith MD, Sanchez-Nieto S, Schnell DJ. The roles of toc34 and toc75 in targeting the toc159 preprotein receptor to chloroplasts. J Biol Chem. 2003 Nov 7;278(45):44289-97. Epub 2003 Sep 1. PMID:12951325 doi:http://dx.doi.org/10.1074/jbc.M307873200
↑ Kubis S, Baldwin A, Patel R, Razzaq A, Dupree P, Lilley K, Kurth J, Leister D, Jarvis P. The Arabidopsis ppi1 mutant is specifically defective in the expression, chloroplast import, and accumulation of photosynthetic proteins. Plant Cell. 2003 Aug;15(8):1859-71. PMID:12897258
↑ Constan D, Patel R, Keegstra K, Jarvis P. An outer envelope membrane component of the plastid protein import apparatus plays an essential role in Arabidopsis. Plant J. 2004 Apr;38(1):93-106. PMID:15053763 doi:http://dx.doi.org/10.1111/j.1365-313X.2004.02024.x
↑ Aronsson H, Combe J, Patel R, Jarvis P. In vivo assessment of the significance of phosphorylation of the Arabidopsis chloroplast protein import receptor, atToc33. FEBS Lett. 2006 Jan 23;580(2):649-55. Epub 2005 Dec 28. PMID:16412428 doi:http://dx.doi.org/S0014-5793(05)01538-3
↑ Hust B, Gutensohn M. Deletion of core components of the plastid protein import machinery causes differential arrest of embryo development in Arabidopsis thaliana. Plant Biol (Stuttg). 2006 Jan;8(1):18-30. PMID:16435266 doi:http://dx.doi.org/10.1055/s-2005-873044
↑ Oreb M, Zoryan M, Vojta A, Maier UG, Eichacker LA, Schleiff E. Phospho-mimicry mutant of atToc33 affects early development of Arabidopsis thaliana. FEBS Lett. 2007 Dec 22;581(30):5945-51. Epub 2007 Dec 3. PMID:18054337 doi:http://dx.doi.org/S0014-5793(07)01225-2
↑ Koenig P, Oreb M, Rippe K, Muhle-Goll C, Sinning I, Schleiff E, Tews I. On the significance of Toc-GTPase homodimers. J Biol Chem. 2008 Aug 22;283(34):23104-12. Epub 2008 Jun 8. PMID:18541539 doi:10.1074/jbc.M710576200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of Toc33 from Arabidopsis thaliana, dimerization deficient mutant R130A==
-<StructureSection load='3def' size='340' side='right' caption='[[3def]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
+<StructureSection load='3def' size='340' side='right'caption='[[3def]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3def]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DEF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3def]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DEF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2j3e|2j3e]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2j3e|2j3e]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">T7I23.11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">T7I23.11 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Small_monomeric_GTPase Small monomeric GTPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.5.2 3.6.5.2] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Small_monomeric_GTPase Small monomeric GTPase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.5.2 3.6.5.2] </span></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=3def FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3def OCA], [http://pdbe.org/3def PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3def RCSB], [http://www.ebi.ac.uk/pdbsum/3def PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3def ProSAT]</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=3def FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3def OCA], [https://pdbe.org/3def PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3def RCSB], [https://www.ebi.ac.uk/pdbsum/3def PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3def ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TOC33_ARATH TOC33_ARATH]] GTPase involved in protein precursor import into chloroplasts. Seems to recognize chloroplast-destined precursor proteins and regulate their presentation to the translocation channel through GTP hydrolysis. Binds GTP, GDP, XTP, but not ATP. Probably specialized in the import of nuclear encoded photosynthetic preproteins from the cytoplasm to the chloroplast, especially during early development stages.<ref>PMID:11553737</ref> <ref>PMID:12741849</ref> <ref>PMID:12782294</ref> <ref>PMID:12869544</ref> <ref>PMID:12951325</ref> <ref>PMID:12897258</ref> <ref>PMID:15053763</ref> <ref>PMID:16412428</ref> <ref>PMID:16435266</ref> <ref>PMID:18054337</ref>
+[[https://www.uniprot.org/uniprot/TOC33_ARATH TOC33_ARATH]] GTPase involved in protein precursor import into chloroplasts. Seems to recognize chloroplast-destined precursor proteins and regulate their presentation to the translocation channel through GTP hydrolysis. Binds GTP, GDP, XTP, but not ATP. Probably specialized in the import of nuclear encoded photosynthetic preproteins from the cytoplasm to the chloroplast, especially during early development stages.<ref>PMID:11553737</ref> <ref>PMID:12741849</ref> <ref>PMID:12782294</ref> <ref>PMID:12869544</ref> <ref>PMID:12951325</ref> <ref>PMID:12897258</ref> <ref>PMID:15053763</ref> <ref>PMID:16412428</ref> <ref>PMID:16435266</ref> <ref>PMID:18054337</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 36: @@
 </StructureSection>
 [[Category: Arath]]
+[[Category: Large Structures]]
 [[Category: Small monomeric GTPase]]
 [[Category: Koenig, P]]

3def

From Proteopedia

Revision as of 07:32, 10 November 2021

Crystal structure of Toc33 from Arabidopsis thaliana, dimerization deficient mutant R130A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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