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1s59

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Structure of nucleoside diphosphate kinase 2 with bound dGTP from Arabidopsis

Structural highlights

1s59 is a 6 chain structure with sequence from Arabidopsis thaliana. 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

NDK2_ARATH Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. May activate MPK3 and MPK6. May be involved in the regulation of cellular redox state and hydrogen peroxide-mediated MAP kinase signaling.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[2]

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

References

↑ Moon H, Lee B, Choi G, Shin D, Prasad DT, Lee O, Kwak SS, Kim DH, Nam J, Bahk J, Hong JC, Lee SY, Cho MJ, Lim CO, Yun DJ. NDP kinase 2 interacts with two oxidative stress-activated MAPKs to regulate cellular redox state and enhances multiple stress tolerance in transgenic plants. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):358-63. Epub 2002 Dec 27. PMID:12506203 doi:http://dx.doi.org/10.1073/pnas.252641899
↑ Im YJ, Kim JI, Shen Y, Na Y, Han YJ, Kim SH, Song PS, Eom SH. Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling. J Mol Biol. 2004 Oct 22;343(3):659-70. PMID:15465053 doi:10.1016/j.jmb.2004.08.054

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1s59"

@@ Line 1: / Line 1: @@
 ==Structure of nucleoside diphosphate kinase 2 with bound dGTP from Arabidopsis==
-<StructureSection load='1s59' size='340' side='right' caption='[[1s59]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='1s59' size='340' side='right'caption='[[1s59]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1s59]] is a 6 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=1S59 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S59 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1s59]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S59 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S59 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGI:2-DEOXYGUANOSINE-5-DIPHOSPHATE'>DGI</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1s57|1s57]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGI:2-DEOXYGUANOSINE-5-DIPHOSPHATE'>DGI</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NDPK2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=1s59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s59 OCA], [https://pdbe.org/1s59 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s59 RCSB], [https://www.ebi.ac.uk/pdbsum/1s59 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s59 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=1s59 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s59 OCA], [http://pdbe.org/1s59 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s59 RCSB], [http://www.ebi.ac.uk/pdbsum/1s59 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NDK2_ARATH NDK2_ARATH]] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. May activate MPK3 and MPK6. May be involved in the regulation of cellular redox state and hydrogen peroxide-mediated MAP kinase signaling.<ref>PMID:12506203</ref>
+[https://www.uniprot.org/uniprot/NDK2_ARATH NDK2_ARATH] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. May activate MPK3 and MPK6. May be involved in the regulation of cellular redox state and hydrogen peroxide-mediated MAP kinase signaling.<ref>PMID:12506203</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s5/1s59_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s5/1s59_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 31: @@
 ==See Also==
-*[[Nucleoside diphosphate kinase|Nucleoside diphosphate kinase]]
+*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Nucleoside-diphosphate kinase]]
+[[Category: Large Structures]]
-[[Category: Eom, S H]]
+[[Category: Eom SH]]
-[[Category: Han, Y J]]
+[[Category: Han Y-J]]
-[[Category: Im, Y J]]
+[[Category: Im YJ]]
-[[Category: Kim, J I]]
+[[Category: Kim J-I]]
-[[Category: Kim, S H]]
+[[Category: Kim S-H]]
-[[Category: Na, Y]]
+[[Category: Na Y]]
-[[Category: Shen, Y]]
+[[Category: Shen Y]]
-[[Category: Song, P S]]
+[[Category: Song P-S]]
-[[Category: Kinase]]
-[[Category: Transferase]]

1s59

From Proteopedia

Current revision

Structure of nucleoside diphosphate kinase 2 with bound dGTP from Arabidopsis

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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