7nl4

From Proteopedia

(Difference between revisions)

Current revision

OsNIP2;1 silicon transporter from rice

Structural highlights

7nl4 is a 8 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 3Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NIP21_ORYSJ Silicon influx transporter responsible for silicon transport from the external solution to the root cells (PubMed:16572174). Is coupled with the silicon efflux transporter LSI2 in both exodermal and endodermal root cells for an efficient silicon transport across the cells into the stele (PubMed:17625566). Silicon is beneficial to plant growth and helps plants to overcome abiotic and biotic stresses by preventing lodging (falling over) and increasing resistance to pests and diseases, as well as other stresses (PubMed:16572174). Is coupled with LSI2 transporter in roots for efficient uptake of arsenite, which is further dispatched in shoots and grains (PubMed:18626020). Mediates uptake of methylated arsenic species in roots (PubMed:19542298).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Many of the world's most important food crops such as rice, barley and maize accumulate silicon (Si) to high levels, resulting in better plant growth and crop yields. The first step in Si accumulation is the uptake of silicic acid by the roots, a process mediated by the structurally uncharacterised NIP subfamily of aquaporins, also named metalloid porins. Here, we present the X-ray crystal structure of the archetypal NIP family member from Oryza sativa (OsNIP2;1). The OsNIP2;1 channel is closed in the crystal structure by the cytoplasmic loop D, which is known to regulate channel opening in classical plant aquaporins. The structure further reveals a novel, five-residue extracellular selectivity filter with a large diameter. Unbiased molecular dynamics simulations show a rapid opening of the channel and visualise how silicic acid interacts with the selectivity filter prior to transmembrane diffusion. Our results will enable detailed structure-function studies of metalloid porins, including the basis of their substrate selectivity.

Structural Basis for Silicic Acid Uptake by Higher Plants.,van den Berg B, Pedebos C, Bolla JR, Robinson CV, Basle A, Khalid S J Mol Biol. 2021 Oct 15;433(21):167226. doi: 10.1016/j.jmb.2021.167226. Epub 2021, Sep 3. PMID:34487790^[5]

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

References

↑ Ma JF, Tamai K, Yamaji N, Mitani N, Konishi S, Katsuhara M, Ishiguro M, Murata Y, Yano M. A silicon transporter in rice. Nature. 2006 Mar 30;440(7084):688-91. doi: 10.1038/nature04590. PMID:16572174 doi:http://dx.doi.org/10.1038/nature04590
↑ Ma JF, Yamaji N, Mitani N, Tamai K, Konishi S, Fujiwara T, Katsuhara M, Yano M. An efflux transporter of silicon in rice. Nature. 2007 Jul 12;448(7150):209-12. PMID:17625566 doi:http://dx.doi.org/nature05964
↑ Ma JF, Yamaji N, Mitani N, Xu XY, Su YH, McGrath SP, Zhao FJ. Transporters of arsenite in rice and their role in arsenic accumulation in rice grain. Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):9931-5. doi:, 10.1073/pnas.0802361105. Epub 2008 Jul 14. PMID:18626020 doi:http://dx.doi.org/10.1073/pnas.0802361105
↑ Li RY, Ago Y, Liu WJ, Mitani N, Feldmann J, McGrath SP, Ma JF, Zhao FJ. The rice aquaporin Lsi1 mediates uptake of methylated arsenic species. Plant Physiol. 2009 Aug;150(4):2071-80. doi: 10.1104/pp.109.140350. Epub 2009 Jun, 19. PMID:19542298 doi:http://dx.doi.org/10.1104/pp.109.140350
↑ van den Berg B, Pedebos C, Bolla JR, Robinson CV, Baslé A, Khalid S. Structural Basis for Silicic Acid Uptake by Higher Plants. J Mol Biol. 2021 Oct 15;433(21):167226. PMID:34487790 doi:10.1016/j.jmb.2021.167226

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7nl4"

Categories: Large Structures | Oryza sativa Japonica Group | Van den Berg B

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7nl4 is ON HOLD  until Paper Publication
+==OsNIP2;1 silicon transporter from rice==
+<StructureSection load='7nl4' size='340' side='right'caption='[[7nl4]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7nl4]] is a 8 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=7NL4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NL4 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]] 3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</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=7nl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nl4 OCA], [https://pdbe.org/7nl4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nl4 RCSB], [https://www.ebi.ac.uk/pdbsum/7nl4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nl4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NIP21_ORYSJ NIP21_ORYSJ] Silicon influx transporter responsible for silicon transport from the external solution to the root cells (PubMed:16572174). Is coupled with the silicon efflux transporter LSI2 in both exodermal and endodermal root cells for an efficient silicon transport across the cells into the stele (PubMed:17625566). Silicon is beneficial to plant growth and helps plants to overcome abiotic and biotic stresses by preventing lodging (falling over) and increasing resistance to pests and diseases, as well as other stresses (PubMed:16572174). Is coupled with LSI2 transporter in roots for efficient uptake of arsenite, which is further dispatched in shoots and grains (PubMed:18626020). Mediates uptake of methylated arsenic species in roots (PubMed:19542298).<ref>PMID:16572174</ref> <ref>PMID:17625566</ref> <ref>PMID:18626020</ref> <ref>PMID:19542298</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Many of the world's most important food crops such as rice, barley and maize accumulate silicon (Si) to high levels, resulting in better plant growth and crop yields. The first step in Si accumulation is the uptake of silicic acid by the roots, a process mediated by the structurally uncharacterised NIP subfamily of aquaporins, also named metalloid porins. Here, we present the X-ray crystal structure of the archetypal NIP family member from Oryza sativa (OsNIP2;1). The OsNIP2;1 channel is closed in the crystal structure by the cytoplasmic loop D, which is known to regulate channel opening in classical plant aquaporins. The structure further reveals a novel, five-residue extracellular selectivity filter with a large diameter. Unbiased molecular dynamics simulations show a rapid opening of the channel and visualise how silicic acid interacts with the selectivity filter prior to transmembrane diffusion. Our results will enable detailed structure-function studies of metalloid porins, including the basis of their substrate selectivity.
-Authors: van den Berg, B., van den Berg, B.
+Structural Basis for Silicic Acid Uptake by Higher Plants.,van den Berg B, Pedebos C, Bolla JR, Robinson CV, Basle A, Khalid S J Mol Biol. 2021 Oct 15;433(21):167226. doi: 10.1016/j.jmb.2021.167226. Epub 2021, Sep 3. PMID:34487790<ref>PMID:34487790</ref>
-Description: OsNIP2;1 silicon transporter from rice
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Van Den Berg, B]]
+<div class="pdbe-citations 7nl4" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Aquaporin 3D structures|Aquaporin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Oryza sativa Japonica Group]]
+[[Category: Van den Berg B]]

7nl4

From Proteopedia

Current revision

OsNIP2;1 silicon transporter from rice

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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