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| | ==Crystal structure of nucleoside diphosphate kinase from Haloarcula quadrata== | | ==Crystal structure of nucleoside diphosphate kinase from Haloarcula quadrata== |
| - | <StructureSection load='2zua' size='340' side='right' caption='[[2zua]], [[Resolution|resolution]] 2.59Å' scene=''> | + | <StructureSection load='2zua' size='340' side='right'caption='[[2zua]], [[Resolution|resolution]] 2.59Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zua]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700850 Atcc 700850]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZUA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zua]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_quadrata Haloarcula quadrata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZUA FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ndk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=182779 ATCC 700850])</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]] 2.59Å</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=2zua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zua OCA], [http://pdbe.org/2zua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zua RCSB], [http://www.ebi.ac.uk/pdbsum/2zua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zua ProSAT]</span></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=2zua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zua OCA], [https://pdbe.org/2zua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zua RCSB], [https://www.ebi.ac.uk/pdbsum/2zua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zua ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q401C5_9EURY Q401C5_9EURY]] 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 (By similarity).[HAMAP-Rule:MF_00451] | + | [https://www.uniprot.org/uniprot/Q401C5_9EURY Q401C5_9EURY] 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 (By similarity).[HAMAP-Rule:MF_00451] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Nucleoside diphosphate kinase|Nucleoside diphosphate kinase]] | + | *[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 700850]] | + | [[Category: Haloarcula quadrata]] |
| - | [[Category: Ichimura, T]] | + | [[Category: Large Structures]] |
| - | [[Category: Miyazono, K]] | + | [[Category: Ichimura T]] |
| - | [[Category: Nagata, K]] | + | [[Category: Miyazono K]] |
| - | [[Category: Ohtsuka, J]] | + | [[Category: Nagata K]] |
| - | [[Category: Okai, M]] | + | [[Category: Ohtsuka J]] |
| - | [[Category: Tanokura, M]] | + | [[Category: Okai M]] |
| - | [[Category: Yamamura, A]] | + | [[Category: Tanokura M]] |
| - | [[Category: Ferredoxin fold]]
| + | [[Category: Yamamura A]] |
| - | [[Category: Kinase]]
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| - | [[Category: Kpn loop]]
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| - | [[Category: Transferase]]
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| Structural highlights
Function
Q401C5_9EURY 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 (By similarity).[HAMAP-Rule:MF_00451]
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
Nucleoside diphosphate kinases from haloarchaea Haloarcula quadrata (NDK-q) and H. sinaiiensis (NDK-s) are identical except for one out of 154 residues, i.e., Arg(31) in NDK-q and Cys(31) in NDK-s. However, the salt-dependent activity profiles of NDK-q and NDK-s are quite different: the optimal NaCl concentrations of NDK-q and NDK-s are 1 M and 2 M, respectively. We analyzed the relationships of the secondary, tertiary, and quaternary structures and NDK activity of these NDKs at various salt concentrations, and revealed that 1), NDK-q is present as a hexamer under a wide range of salt concentrations (0.2-4 M NaCl), whereas NDK-s is present as a hexamer at an NaCl concentration above 2 M and as a dimer at NaCl concentrations below 1 M; 2), dimeric NDK-s has lower activity than hexameric NDK-s; and 3), dimeric NDK-s has higher helicity than hexameric NDK-s. We also determined the crystal structure of hexameric NDK-q, and revealed that Arg(31) plays an important role in stabilizing the hexamer. Thus the substitution of Arg (as in NDK-q) to Cys (as in NDK-s) at position 31 destabilizes the hexameric assembly, and causes dissociation to less active dimers at low salt concentrations.
Molecular mechanism of distinct salt-dependent enzyme activity of two halophilic nucleoside diphosphate kinases.,Yamamura A, Ichimura T, Kamekura M, Mizuki T, Usami R, Makino T, Ohtsuka J, Miyazono K, Okai M, Nagata K, Tanokura M Biophys J. 2009 Jun 3;96(11):4692-700. PMID:19486691[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yamamura A, Ichimura T, Kamekura M, Mizuki T, Usami R, Makino T, Ohtsuka J, Miyazono K, Okai M, Nagata K, Tanokura M. Molecular mechanism of distinct salt-dependent enzyme activity of two halophilic nucleoside diphosphate kinases. Biophys J. 2009 Jun 3;96(11):4692-700. PMID:19486691 doi:10.1016/j.bpj.2009.03.012
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