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1pku

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[[Image:1pku.gif|left|200px]]<br /><applet load="1pku" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1pku, resolution 2.5&Aring;" />
 
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'''Crystal Structure of Nucleoside Diphosphate Kinase from Rice'''<br />
 
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==Overview==
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==Crystal Structure of Nucleoside Diphosphate Kinase from Rice==
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Nucleoside diphosphate kinase (NDK) is a ubiquitous enzyme found in all organisms and cell types, and catalyzes the transfer of the phosphoryl group from a nucleoside triphosphate to a nucleoside diphosphate. The enzyme is involved in and required for coleoptile elongation in rice as the level of the rice NDK (rNDK) changes during seed germination and the early stages of seedling growth. The expression of rice NDK gene is up-regulated in the growing coleoptiles when the anaerobic stress persists. The rNDK structure determined at 2.5 A resolution consists of a four-stranded anti-parallel beta-sheet, of which the surfaces are partially covered with six alpha-helices; its overall and active site structures are similar to those of homologous enzymes except the major conformation variations of residue 132-138 regions, involving significant structural contacts. The model contains 148 residues of 149 residues in total and averaged 19 water molecules per monomer for 12 molecules in an asymmetric unit. A mold of 12 superimposed molecules shows that the alphaA-alpha2 area has greater variations and higher temperature factors, indicating the flexibility for a substrate entrance. Hexameric molecular packing in both crystal and solution implies that rNDK functions as hexamers. This rNDK structure, which is the first NDK structure from a higher plant system, provides the structural information essential to understand the functional significance of this enzyme during growth and development in both rice and other plants.
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<StructureSection load='1pku' size='340' side='right'caption='[[1pku]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1pku]] is a 12 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=1PKU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PKU FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pku OCA], [https://pdbe.org/1pku PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pku RCSB], [https://www.ebi.ac.uk/pdbsum/1pku PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pku ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NDK1_ORYSJ NDK1_ORYSJ] 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. This NDK is microtubule-associated.[HAMAP-Rule:MF_00451]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pk/1pku_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pku ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1PKU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryza_sativa Oryza sativa]. 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=1PKU OCA].
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*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of nucleoside diphosphate kinase required for coleoptile elongation in rice (Oryza sativa L.)., Huang JY, Chang T, Chang CY, Chen CJ, J Struct Biol. 2005 Jun;150(3):309-18. Epub 2005 Mar 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15890279 15890279]
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[[Category: Large Structures]]
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[[Category: Nucleoside-diphosphate kinase]]
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[[Category: Oryza sativa]]
[[Category: Oryza sativa]]
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[[Category: Single protein]]
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[[Category: Chang C-Y]]
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[[Category: Chang, C Y.]]
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[[Category: Chang T]]
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[[Category: Chang, T.]]
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[[Category: Chen C-J]]
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[[Category: Chen, C J.]]
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[[Category: Huang J-Y]]
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[[Category: Huang, J Y.]]
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[[Category: nucleoside diphosphate kinase]]
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[[Category: rice]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:29:50 2008''
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Current revision

Crystal Structure of Nucleoside Diphosphate Kinase from Rice

PDB ID 1pku

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