2zua: Difference between revisions

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{{Seed}}
[[Image:2zua.png|left|200px]]


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==Crystal structure of nucleoside diphosphate kinase from Haloarcula quadrata==
The line below this paragraph, containing "STRUCTURE_2zua", creates the "Structure Box" on the page.
<StructureSection load='2zua' size='340' side='right'caption='[[2zua]], [[Resolution|resolution]] 2.59&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.59&#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=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>
{{STRUCTURE_2zua|  PDB=2zua  |  SCENE=  }}
</table>
== Function ==
[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 ==
[[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/zu/2zua_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2zua ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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.


===Crystal structure of nucleoside diphosphate kinase from Haloarcula quadrata===
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<ref>PMID:19486691</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2zua" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_19486691}}, adds the Publication Abstract to the page
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 19486691 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_19486691}}
__TOC__
 
</StructureSection>
==About this Structure==
2ZUA is a 4 chains structure of sequences from [http://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].
 
==Reference==
<ref group="xtra">PMID:19486691</ref><references group="xtra"/>
[[Category: Haloarcula quadrata]]
[[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]]
[[Category: Kpn loop]]
[[Category: Transferase]]
 
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Retrieved from "https://proteopedia.org/2zua"