8pml: Difference between revisions

Latest revision as of 05:57, 5 June 2024

Structure of Nal1 protein , SPIKE allele from japonica rice, construct 46-458

Structural highlights

8pml is a 6 chain structure with sequence from Oryza sativa Japonica Group. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.95Å
Ligands:	ATP, MG
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 LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that unlike suggested previously, H234 instead of H233 is a component of the catalytic triad alongside residues D291 and S385 in NAL1. Remarkably, residue 233 unexpectedly plays a pivotal role in regulating NAL1's proteolytic activity. These findings establish a strong foundation for utilizing NAL1 in breeding programs aimed at improving crop yield.

The catalytic triad of rice NARROW LEAF1 involves H234.,Huang LY, Liu NN, Chen WF, Ai X, Li HH, Zhang ZL, Hou XM, Fosse P, Mauffret O, Lei DS, Rety S, Xi XG Nat Plants. 2024 May;10(5):743-748. doi: 10.1038/s41477-024-01668-1. Epub 2024 , Apr 10. PMID:38600265^[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
↑ Huang LY, Liu NN, Chen WF, Ai X, Li HH, Zhang ZL, Hou XM, Fossé P, Mauffret O, Lei DS, Rety S, Xi XG. The catalytic triad of rice NARROW LEAF1 involves H234. Nat Plants. 2024 May;10(5):743-748. PMID:38600265 doi:10.1038/s41477-024-01668-1

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OCA

[1] 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

[2] 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

[3] 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

[4] 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

[5] 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

[6] Huang LY, Liu NN, Chen WF, Ai X, Li HH, Zhang ZL, Hou XM, Fossé P, Mauffret O, Lei DS, Rety S, Xi XG. The catalytic triad of rice NARROW LEAF1 involves H234. Nat Plants. 2024 May;10(5):743-748. PMID:38600265 doi:10.1038/s41477-024-01668-1

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[2]

[3]

[4]

[5]

[6]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8pml is ON HOLD
+==Structure of Nal1 protein , SPIKE allele from japonica rice, construct 46-458==
+<StructureSection load='8pml' size='340' side='right'caption='[[8pml]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8pml]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PML 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]] 2.95&#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>, <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=8pml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pml OCA], [https://pdbe.org/8pml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pml RCSB], [https://www.ebi.ac.uk/pdbsum/8pml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pml 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 LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that unlike suggested previously, H234 instead of H233 is a component of the catalytic triad alongside residues D291 and S385 in NAL1. Remarkably, residue 233 unexpectedly plays a pivotal role in regulating NAL1's proteolytic activity. These findings establish a strong foundation for utilizing NAL1 in breeding programs aimed at improving crop yield.
-Authors: Huang, L.Y., Rety, S., Xi, X.G.
+The catalytic triad of rice NARROW LEAF1 involves H234.,Huang LY, Liu NN, Chen WF, Ai X, Li HH, Zhang ZL, Hou XM, Fosse P, Mauffret O, Lei DS, Rety S, Xi XG Nat Plants. 2024 May;10(5):743-748. doi: 10.1038/s41477-024-01668-1. Epub 2024 , Apr 10. PMID:38600265<ref>PMID:38600265</ref>
-Description: Structure of Nal1 protein , SPIKE allele from japonica rice, construct 46-458
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Xi, X.G]]
+<div class="pdbe-citations 8pml" style="background-color:#fffaf0;"></div>
-[[Category: Rety, S]]
+== References ==
-[[Category: Huang, L.Y]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Oryza sativa Japonica Group]]
+[[Category: Huang LY]]
+[[Category: Rety S]]
+[[Category: Xi XG]]

8pml: Difference between revisions

Latest revision as of 05:57, 5 June 2024

Structure of Nal1 protein , SPIKE allele from japonica rice, construct 46-458

Structural highlights

Function

Publication Abstract from PubMed

References

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