7y77

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of rice NAL1

Structural highlights

7y77 is a 3 chain structure with sequence from Oryza sativa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAL1_ORYSJ Involved in the regulation of lateral leaf growth (PubMed:18562767, PubMed:22179305, PubMed:23985993). May be involved in the regulation of basipetal polar auxin transport (PAT) and vascular patterning in leaves (PubMed:18562767). Controls photosynthesis rate by regulating carboxylation efficiency and consequently photosynthesis rate (PubMed:23985993). Controls panicle and spikelet numbers, and grain yield (PubMed:23985993, PubMed:24297875, PubMed:24795339).^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

NARROW LEAF 1 (NAL1) is a breeding-valuable pleiotropic gene that affects multiple agronomic traits in rice, although the molecular mechanism is largely unclear. Here, we report that NAL1 is a serine protease and displays a novel hexameric structure consisting of two ATP-mediated doughnut-shaped trimeric complexes. Moreover, we identified TOPLESS-related corepressor OsTPR2 involved in multiple growth and development processes as the substrate of NAL1. We found that NAL1 degraded OsTPR2, thus modulating the expression of downstream genes related to hormone signalling pathways, eventually achieving its pleiotropic physiological function. An elite allele, NAL1(A), which may have originated from wild rice, could increase grain yield. Furthermore, the NAL1 homologues in different crops have a similar pleiotropic function to NAL1. Our study uncovers a NAL1-OsTPR2 regulatory module and provides gene resources for the design of high-yield crops.

Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice.,Li W, Yan J, Zhang Y, Zhang F, Guan Z, Yao Y, Chang Y, Tu H, Li X, Wang H, Xiong H, Lai X, Yin P, Xiong L Nat Plants. 2023 Jul;9(7):1130-1142. doi: 10.1038/s41477-023-01449-2. Epub 2023 , Jun 22. PMID:37349549^[6]

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

References

↑ Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, Li C. Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol. 2008 Aug;147(4):1947-59. PMID:18562767 doi:10.1104/pp.108.118778
↑ Chen M, Luo J, Shao G, Wei X, Tang S, Sheng Z, Song J, Hu P. Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1. Plant Cell Rep. 2012 May;31(5):863-72. PMID:22179305 doi:10.1007/s00299-011-1207-7
↑ Takai T, Adachi S, Taguchi-Shiobara F, Sanoh-Arai Y, Iwasawa N, Yoshinaga S, Hirose S, Taniguchi Y, Yamanouchi U, Wu J, Matsumoto T, Sugimoto K, Kondo K, Ikka T, Ando T, Kono I, Ito S, Shomura A, Ookawa T, Hirasawa T, Yano M, Kondo M, Yamamoto T. A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate. Sci Rep. 2013;3:2149. PMID:23985993 doi:10.1038/srep02149
↑ Fujita D, Trijatmiko KR, Tagle AG, Sapasap MV, Koide Y, Sasaki K, Tsakirpaloglou N, Gannaban RB, Nishimura T, Yanagihara S, Fukuta Y, Koshiba T, Slamet-Loedin IH, Ishimaru T, Kobayashi N. NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars. Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20431-6. PMID:24297875 doi:10.1073/pnas.1310790110
↑ Zhang GH, Li SY, Wang L, Ye WJ, Zeng DL, Rao YC, Peng YL, Hu J, Yang YL, Xu J, Ren DY, Gao ZY, Zhu L, Dong GJ, Hu XM, Yan MX, Guo LB, Li CY, Qian Q. LSCHL4 from Japonica Cultivar, which is allelic to NAL1, increases yield of indica super rice 93-11. Mol Plant. 2014 Aug;7(8):1350-1364. PMID:24795339 doi:10.1093/mp/ssu055
↑ Li W, Yan J, Zhang Y, Zhang F, Guan Z, Yao Y, Chang Y, Tu H, Li X, Wang H, Xiong H, Lai X, Yin P, Xiong L. Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice. Nat Plants. 2023 Jun 22. PMID:37349549 doi:10.1038/s41477-023-01449-2

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/7y77"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7y77 is ON HOLD
+==Crystal structure of rice NAL1==
+<StructureSection load='7y77' size='340' side='right'caption='[[7y77]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7y77]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Y77 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Y77 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]] 2.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</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=7y77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7y77 OCA], [https://pdbe.org/7y77 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7y77 RCSB], [https://www.ebi.ac.uk/pdbsum/7y77 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7y77 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NAL1_ORYSJ NAL1_ORYSJ] Involved in the regulation of lateral leaf growth (PubMed:18562767, PubMed:22179305, PubMed:23985993). May be involved in the regulation of basipetal polar auxin transport (PAT) and vascular patterning in leaves (PubMed:18562767). Controls photosynthesis rate by regulating carboxylation efficiency and consequently photosynthesis rate (PubMed:23985993). Controls panicle and spikelet numbers, and grain yield (PubMed:23985993, PubMed:24297875, PubMed:24795339).<ref>PMID:18562767</ref> <ref>PMID:22179305</ref> <ref>PMID:23985993</ref> <ref>PMID:24297875</ref> <ref>PMID:24795339</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+NARROW LEAF 1 (NAL1) is a breeding-valuable pleiotropic gene that affects multiple agronomic traits in rice, although the molecular mechanism is largely unclear. Here, we report that NAL1 is a serine protease and displays a novel hexameric structure consisting of two ATP-mediated doughnut-shaped trimeric complexes. Moreover, we identified TOPLESS-related corepressor OsTPR2 involved in multiple growth and development processes as the substrate of NAL1. We found that NAL1 degraded OsTPR2, thus modulating the expression of downstream genes related to hormone signalling pathways, eventually achieving its pleiotropic physiological function. An elite allele, NAL1(A), which may have originated from wild rice, could increase grain yield. Furthermore, the NAL1 homologues in different crops have a similar pleiotropic function to NAL1. Our study uncovers a NAL1-OsTPR2 regulatory module and provides gene resources for the design of high-yield crops.
-Authors:
+Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice.,Li W, Yan J, Zhang Y, Zhang F, Guan Z, Yao Y, Chang Y, Tu H, Li X, Wang H, Xiong H, Lai X, Yin P, Xiong L Nat Plants. 2023 Jul;9(7):1130-1142. doi: 10.1038/s41477-023-01449-2. Epub 2023 , Jun 22. PMID:37349549<ref>PMID:37349549</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 7y77" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Oryza sativa]]
+[[Category: Guan ZY]]
+[[Category: Xiong LZ]]
+[[Category: Yan JJ]]
+[[Category: Yin P]]

7y77

From Proteopedia

Current revision

Crystal structure of rice NAL1

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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