5b3g

From Proteopedia

(Difference between revisions)

Revision as of 06:37, 31 May 2023

The crystal structure of the heterodimer of SHORT-ROOT and SCARECROW GRAS domains

Structural highlights

5b3g is a 2 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SCR_ARATH Transcription factor required for quiescent center cells specification and maintenance of surrounding stem cells, and for the asymmetric cell division involved in radial pattern formation in roots. Essential for cell division but not differentiation of the ground tissue. Also required for normal shoot gravitropism. Regulates the radial organization of the shoot axial organs. Binds to the promoter of MGP, NUC, RLK and SCL3. Restricts SHR movment and sequesters it into the nucleus of the endodermis.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

Publication Abstract from PubMed

The plant-specific GAI, RGA and SCR (GRAS) family proteins play critical roles in plant development and signalling. Two GRAS proteins, SHORT-ROOT (SHR) and SCARECROW (SCR), cooperatively direct asymmetric cell division and the patterning of root cell types by transcriptional control in conjunction with BIRD/INDETERMINATE DOMAIN (IDD) transcription factors, although precise details of these specific interactions and actions remain unknown. Here, we present the crystal structures of the SHR-SCR binary and JACKDAW (JKD)/IDD10-SHR-SCR ternary complexes. Each GRAS domain comprises one alpha/beta core subdomain with an alpha-helical cap that mediates heterodimerization by forming an intermolecular helix bundle. The alpha/beta core subdomain of SHR forms the BIRD binding groove, which specifically recognizes the zinc fingers of JKD. We identified a conserved SHR-binding motif in 13 BIRD/IDD transcription factors. Our results establish a structural basis for GRAS-GRAS and GRAS-BIRD interactions and provide valuable clues towards our understanding of these regulators, which are involved in plant-specific signalling networks.

Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD.,Hirano Y, Nakagawa M, Suyama T, Murase K, Shirakawa M, Takayama S, Sun TP, Hakoshima T Nat Plants. 2017 Feb 17;3:17010. doi: 10.1038/nplants.2017.10. PMID:28211915^[12]

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

References

↑ Wysocka-Diller JW, Helariutta Y, Fukaki H, Malamy JE, Benfey PN. Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot. Development. 2000 Feb;127(3):595-603. PMID:10631180
↑ Sabatini S, Heidstra R, Wildwater M, Scheres B. SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem. Genes Dev. 2003 Feb 1;17(3):354-8. PMID:12569126 doi:http://dx.doi.org/10.1101/gad.252503
↑ Sena G, Jung JW, Benfey PN. A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression. Development. 2004 Jun;131(12):2817-26. Epub 2004 May 13. PMID:15142972 doi:http://dx.doi.org/10.1242/dev.01144
↑ Heidstra R, Welch D, Scheres B. Mosaic analyses using marked activation and deletion clones dissect Arabidopsis SCARECROW action in asymmetric cell division. Genes Dev. 2004 Aug 15;18(16):1964-9. PMID:15314023 doi:http://dx.doi.org/10.1101/gad.305504
↑ Levesque MP, Vernoux T, Busch W, Cui H, Wang JY, Blilou I, Hassan H, Nakajima K, Matsumoto N, Lohmann JU, Scheres B, Benfey PN. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol. 2006 May;4(5):e143. Epub 2006 May 2. PMID:16640459 doi:http://dx.doi.org/05-PLBI-RA-1464R2
↑ Cui H, Levesque MP, Vernoux T, Jung JW, Paquette AJ, Gallagher KL, Wang JY, Blilou I, Scheres B, Benfey PN. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science. 2007 Apr 20;316(5823):421-5. PMID:17446396 doi:http://dx.doi.org/316/5823/421
↑ Cruz-Ramirez A, Diaz-Trivino S, Blilou I, Grieneisen VA, Sozzani R, Zamioudis C, Miskolczi P, Nieuwland J, Benjamins R, Dhonukshe P, Caballero-Perez J, Horvath B, Long Y, Mahonen AP, Zhang H, Xu J, Murray JA, Benfey PN, Bako L, Maree AF, Scheres B. A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell. 2012 Aug 31;150(5):1002-15. doi: 10.1016/j.cell.2012.07.017. Epub 2012 Aug , 23. PMID:22921914 doi:http://dx.doi.org/10.1016/j.cell.2012.07.017
↑ Cruz-Ramirez A, Diaz-Trivino S, Wachsman G, Du Y, Arteaga-Vazquez M, Zhang H, Benjamins R, Blilou I, Neef AB, Chandler V, Scheres B. A SCARECROW-RETINOBLASTOMA protein network controls protective quiescence in the Arabidopsis root stem cell organizer. PLoS Biol. 2013 Nov;11(11):e1001724. doi: 10.1371/journal.pbio.1001724. Epub 2013, Nov 26. PMID:24302889 doi:http://dx.doi.org/10.1371/journal.pbio.1001724
↑ Fukaki H, Fujisawa H, Tasaka M. SGR1, SGR2, SGR3: novel genetic loci involved in shoot gravitropism in Arabidopsis thaliana. Plant Physiol. 1996 Mar;110(3):945-55. PMID:8819871
↑ Malamy JE, Benfey PN. Analysis of SCARECROW expression using a rapid system for assessing transgene expression in Arabidopsis roots. Plant J. 1997 Oct;12(4):957-63. PMID:9375406
↑ Fukaki H, Wysocka-Diller J, Kato T, Fujisawa H, Benfey PN, Tasaka M. Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana. Plant J. 1998 May;14(4):425-30. PMID:9670559
↑ Hirano Y, Nakagawa M, Suyama T, Murase K, Shirakawa M, Takayama S, Sun TP, Hakoshima T. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants. 2017 Feb 17;3:17010. doi: 10.1038/nplants.2017.10. PMID:28211915 doi:http://dx.doi.org/10.1038/nplants.2017.10

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5b3g"

Categories: Arabidopsis thaliana | Large Structures | Hakoshima T | Hirano Y | Nakagawa M

@@ Line 3: / Line 3: @@
 <StructureSection load='5b3g' size='340' side='right'caption='[[5b3g]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5b3g]] is a 2 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=5B3G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B3G FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5b3g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B3G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B3G FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5b3h|5b3h]]</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=5b3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b3g OCA], [https://pdbe.org/5b3g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b3g RCSB], [https://www.ebi.ac.uk/pdbsum/5b3g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b3g ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SCR, SGR1, At3g54220, F24B22.180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH]), SHR, SGR7, At4g37650, F19F18.140 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=5b3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b3g OCA], [http://pdbe.org/5b3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b3g RCSB], [http://www.ebi.ac.uk/pdbsum/5b3g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b3g ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SCR_ARATH SCR_ARATH]] Transcription factor required for quiescent center cells specification and maintenance of surrounding stem cells, and for the asymmetric cell division involved in radial pattern formation in roots. Essential for cell division but not differentiation of the ground tissue. Also required for normal shoot gravitropism. Regulates the radial organization of the shoot axial organs. Binds to the promoter of MGP, NUC, RLK and SCL3. Restricts SHR movment and sequesters it into the nucleus of the endodermis.<ref>PMID:10631180</ref> <ref>PMID:12569126</ref> <ref>PMID:15142972</ref> <ref>PMID:15314023</ref> <ref>PMID:16640459</ref> <ref>PMID:17446396</ref> <ref>PMID:22921914</ref> <ref>PMID:24302889</ref> <ref>PMID:8819871</ref> <ref>PMID:9375406</ref> <ref>PMID:9670559</ref>  [[http://www.uniprot.org/uniprot/SHR_ARATH SHR_ARATH]] Transcription factor required for quiescent center cells specification and maintenance of surrounding stem cells, and for the asymmetric cell division involved in radial pattern formation in roots. Essential for both cell division and cell specification. Regulates the radial organization of the shoot axial organs and is required for normal shoot gravitropism. Directly controls the transcription of SCR, and when associated with SCR, of MGP, RLK, TRI, NUC and SCL3.<ref>PMID:10850497</ref> <ref>PMID:12569126</ref> <ref>PMID:15314023</ref> <ref>PMID:16640459</ref> <ref>PMID:17446396</ref> <ref>PMID:9670559</ref>
+[https://www.uniprot.org/uniprot/SCR_ARATH SCR_ARATH] Transcription factor required for quiescent center cells specification and maintenance of surrounding stem cells, and for the asymmetric cell division involved in radial pattern formation in roots. Essential for cell division but not differentiation of the ground tissue. Also required for normal shoot gravitropism. Regulates the radial organization of the shoot axial organs. Binds to the promoter of MGP, NUC, RLK and SCL3. Restricts SHR movment and sequesters it into the nucleus of the endodermis.<ref>PMID:10631180</ref> <ref>PMID:12569126</ref> <ref>PMID:15142972</ref> <ref>PMID:15314023</ref> <ref>PMID:16640459</ref> <ref>PMID:17446396</ref> <ref>PMID:22921914</ref> <ref>PMID:24302889</ref> <ref>PMID:8819871</ref> <ref>PMID:9375406</ref> <ref>PMID:9670559</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Hakoshima, T]]
+[[Category: Hakoshima T]]
-[[Category: Hirano, Y]]
+[[Category: Hirano Y]]
-[[Category: Nakagawa, M]]
+[[Category: Nakagawa M]]
-[[Category: Transcription]]
-[[Category: Transcription cofactor]]

5b3g

From Proteopedia

Revision as of 06:37, 31 May 2023

The crystal structure of the heterodimer of SHORT-ROOT and SCARECROW GRAS domains

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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