1s57
From Proteopedia
(New page: 200px<br /><applet load="1s57" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s57, resolution 1.80Å" /> '''crystal structure of...) |
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| - | [[Image:1s57.jpg|left|200px]]<br /><applet load="1s57" size=" | + | [[Image:1s57.jpg|left|200px]]<br /><applet load="1s57" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1s57, resolution 1.80Å" /> | caption="1s57, resolution 1.80Å" /> | ||
'''crystal structure of nucleoside diphosphate kinase 2 from Arabidopsis'''<br /> | '''crystal structure of nucleoside diphosphate kinase 2 from Arabidopsis'''<br /> | ||
==Overview== | ==Overview== | ||
| - | In plants, nucleoside diphosphate kinases (NDPKs) play a key role in the | + | In plants, nucleoside diphosphate kinases (NDPKs) play a key role in the signaling of both stress and light. However, little is known about the structural elements involved in their function. Of the three NDPKs (NDPK1-NDPK3) expressed in Arabidopsis thaliana, NDPK2 is involved in phytochrome-mediated signal transduction. In this study, we found that the binding of dNDP or NTP to NDPK2 strengthens the interaction significantly between activated phytochrome and NDPK2. To better understand the structural basis of the phytochrome-NDPK2 interaction, we determined the X-ray structures of NDPK1, NDPK2, and dGTP-bound NDPK2 from A.thaliana at 1.8A, 2.6A, and 2.4A, respectively. The structures showed that nucleotide binding caused a slight conformational change in NDPK2 that was confined to helices alphaA and alpha2. This suggests that the presence of nucleotide in the active site and/or the evoked conformational change contributes to the recognition of NDPK2 by activated phytochrome. In vitro binding assays showed that only NDPK2 interacted specifically with the phytochrome and the C-terminal regulatory domain of phytochrome is involved in the interaction. A domain swap experiment between NDPK1 and NDPK2 showed that the variable C-terminal region of NDPK2 is important for the activation by phytochrome. The structure of Arabidopsis NDPK1 and NDPK2 showed that the isoforms share common electrostatic surfaces at the nucleotide-binding site, but the variable C-terminal regions have distinct electrostatic charge distributions. These findings suggest that the binding of nucleotide to NDPK2 plays a regulatory role in phytochrome signaling and that the C-terminal extension of NDPK2 provides a potential binding surface for the specific interaction with phytochromes. |
==About this Structure== | ==About this Structure== | ||
| - | 1S57 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with SO4 and EPE as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] Full crystallographic information is available from [http:// | + | 1S57 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=EPE:'>EPE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S57 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Nucleoside-diphosphate kinase]] | [[Category: Nucleoside-diphosphate kinase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Eom, S | + | [[Category: Eom, S H.]] |
| - | [[Category: Han, Y | + | [[Category: Han, Y J.]] |
| - | [[Category: Im, Y | + | [[Category: Im, Y J.]] |
| - | [[Category: Kim, J | + | [[Category: Kim, J I.]] |
| - | [[Category: Kim, S | + | [[Category: Kim, S H.]] |
[[Category: Na, Y.]] | [[Category: Na, Y.]] | ||
[[Category: Shen, Y.]] | [[Category: Shen, Y.]] | ||
| - | [[Category: Song, P | + | [[Category: Song, P S.]] |
[[Category: EPE]] | [[Category: EPE]] | ||
[[Category: SO4]] | [[Category: SO4]] | ||
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[[Category: transferase]] | [[Category: transferase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:58:06 2008'' |
Revision as of 12:58, 21 February 2008
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crystal structure of nucleoside diphosphate kinase 2 from Arabidopsis
Overview
In plants, nucleoside diphosphate kinases (NDPKs) play a key role in the signaling of both stress and light. However, little is known about the structural elements involved in their function. Of the three NDPKs (NDPK1-NDPK3) expressed in Arabidopsis thaliana, NDPK2 is involved in phytochrome-mediated signal transduction. In this study, we found that the binding of dNDP or NTP to NDPK2 strengthens the interaction significantly between activated phytochrome and NDPK2. To better understand the structural basis of the phytochrome-NDPK2 interaction, we determined the X-ray structures of NDPK1, NDPK2, and dGTP-bound NDPK2 from A.thaliana at 1.8A, 2.6A, and 2.4A, respectively. The structures showed that nucleotide binding caused a slight conformational change in NDPK2 that was confined to helices alphaA and alpha2. This suggests that the presence of nucleotide in the active site and/or the evoked conformational change contributes to the recognition of NDPK2 by activated phytochrome. In vitro binding assays showed that only NDPK2 interacted specifically with the phytochrome and the C-terminal regulatory domain of phytochrome is involved in the interaction. A domain swap experiment between NDPK1 and NDPK2 showed that the variable C-terminal region of NDPK2 is important for the activation by phytochrome. The structure of Arabidopsis NDPK1 and NDPK2 showed that the isoforms share common electrostatic surfaces at the nucleotide-binding site, but the variable C-terminal regions have distinct electrostatic charge distributions. These findings suggest that the binding of nucleotide to NDPK2 plays a regulatory role in phytochrome signaling and that the C-terminal extension of NDPK2 provides a potential binding surface for the specific interaction with phytochromes.
About this Structure
1S57 is a Single protein structure of sequence from Arabidopsis thaliana with and as ligands. Active as Nucleoside-diphosphate kinase, with EC number 2.7.4.6 Full crystallographic information is available from OCA.
Reference
Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling., Im YJ, Kim JI, Shen Y, Na Y, Han YJ, Kim SH, Song PS, Eom SH, J Mol Biol. 2004 Oct 22;343(3):659-70. PMID:15465053
Page seeded by OCA on Thu Feb 21 14:58:06 2008
Categories: Arabidopsis thaliana | Nucleoside-diphosphate kinase | Single protein | Eom, S H. | Han, Y J. | Im, Y J. | Kim, J I. | Kim, S H. | Na, Y. | Shen, Y. | Song, P S. | EPE | SO4 | Kinase | Transferase
