5gij

From Proteopedia

(Difference between revisions)

Revision as of 06:43, 13 May 2020

Crystal structure of TDR-TDIF complex

Structural highlights

5gij is a 2 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:
Gene:	TDR, PXY, At5g61480, MCI2.4 (ARATH)
Activity:	Non-specific serine/threonine protein kinase, with EC number 2.7.11.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TDR_ARATH] Acts with CLE41p and CLE44p peptides as a ligand-receptor pair in a signal transduction pathway involved in the regulation of procambium maintenance and polarity during vascular-tissue development. Mediates repression of tracheary element differentiation and the promotion of procambial cells formation and polar division adjacent to phloem cells in the veins.^[1] ^[2] [CLE41_ARATH] Extracellular signal peptide that regulates cell fate. May act with TDR as a ligand-receptor pair in a signal transduction pathway that represses tracheary element differentiation but promotes the formation of procambial cells adjacent to phloem cells in the veins in an auxin-dependent manner.^[3] ^[4] ^[5]

Publication Abstract from PubMed

In plants, leucine-rich repeat receptor-like kinases (LRR-RKs) perceive ligands, including peptides and small molecules, to regulate various physiological processes. TDIF, a member of the CLE peptide family, specifically interacts with the LRR-RK TDR to inhibit meristem differentiation into tracheary elements, and promotes cell proliferation. Here we report the crystal structure of the extracellular domain of TDR in complex with the TDIF peptide. The extracellular domain of TDR adopts a superhelical structure comprising 22 LRRs, and specifically recognizes TDIF by its inner concave surface. Together with our biochemical and sequence analyses, our structure reveals a conserved TDIF-recognition mechanism of TDR among plant species. Furthermore, a structural comparison of TDR with other plant LRR-RKs suggested the activation mechanism of TDR by TDIF. The structure of this CLE peptide receptor provides insights into the recognition mechanism of the CLE family peptides.

Crystal structure of the plant receptor-like kinase TDR in complex with the TDIF peptide.,Morita J, Kato K, Nakane T, Kondo Y, Fukuda H, Nishimasu H, Ishitani R, Nureki O Nat Commun. 2016 Aug 8;7:12383. doi: 10.1038/ncomms12383. PMID:27498761^[6]

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

References

↑ Fisher K, Turner S. PXY, a receptor-like kinase essential for maintaining polarity during plant vascular-tissue development. Curr Biol. 2007 Jun 19;17(12):1061-6. PMID:17570668 doi:http://dx.doi.org/10.1016/j.cub.2007.05.049
↑ Hirakawa Y, Shinohara H, Kondo Y, Inoue A, Nakanomyo I, Ogawa M, Sawa S, Ohashi-Ito K, Matsubayashi Y, Fukuda H. Non-cell-autonomous control of vascular stem cell fate by a CLE peptide/receptor system. Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):15208-13. doi:, 10.1073/pnas.0808444105. Epub 2008 Sep 23. PMID:18812507 doi:http://dx.doi.org/10.1073/pnas.0808444105
↑ Ito Y, Nakanomyo I, Motose H, Iwamoto K, Sawa S, Dohmae N, Fukuda H. Dodeca-CLE peptides as suppressors of plant stem cell differentiation. Science. 2006 Aug 11;313(5788):842-5. PMID:16902140 doi:http://dx.doi.org/10.1126/science.1128436
↑ Hirakawa Y, Shinohara H, Kondo Y, Inoue A, Nakanomyo I, Ogawa M, Sawa S, Ohashi-Ito K, Matsubayashi Y, Fukuda H. Non-cell-autonomous control of vascular stem cell fate by a CLE peptide/receptor system. Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):15208-13. doi:, 10.1073/pnas.0808444105. Epub 2008 Sep 23. PMID:18812507 doi:http://dx.doi.org/10.1073/pnas.0808444105
↑ Whitford R, Fernandez A, De Groodt R, Ortega E, Hilson P. Plant CLE peptides from two distinct functional classes synergistically induce division of vascular cells. Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18625-30. doi:, 10.1073/pnas.0809395105. Epub 2008 Nov 14. PMID:19011104 doi:http://dx.doi.org/10.1073/pnas.0809395105
↑ Morita J, Kato K, Nakane T, Kondo Y, Fukuda H, Nishimasu H, Ishitani R, Nureki O. Crystal structure of the plant receptor-like kinase TDR in complex with the TDIF peptide. Nat Commun. 2016 Aug 8;7:12383. doi: 10.1038/ncomms12383. PMID:27498761 doi:http://dx.doi.org/10.1038/ncomms12383

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/5gij"

@@ Line 1: / Line 1: @@
 ==Crystal structure of TDR-TDIF complex==
-<StructureSection load='5gij' size='340' side='right' caption='[[5gij]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='5gij' size='340' side='right'caption='[[5gij]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gij]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GIJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GIJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gij]] 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=5GIJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GIJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TDR, PXY, At5g61480, MCI2.4 ([http://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/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </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=5gij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gij OCA], [http://pdbe.org/5gij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gij RCSB], [http://www.ebi.ac.uk/pdbsum/5gij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gij ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gij OCA], [http://pdbe.org/5gij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gij RCSB], [http://www.ebi.ac.uk/pdbsum/5gij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gij ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 24: / Line 25: @@
 __TOC__
 </StructureSection>
+[[Category: Arath]]
+[[Category: Large Structures]]
 [[Category: Non-specific serine/threonine protein kinase]]
 [[Category: Ishitani, R]]

5gij

From Proteopedia

Revision as of 06:43, 13 May 2020

Crystal structure of TDR-TDIF complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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