3zts: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:3zts.png|left|200px]]
-<!--
+==Hexagonal form P6122 of the Aquifex aeolicus nucleoside diphosphate kinase (FINAL STAGE OF RADIATION DAMAGE)==
-The line below this paragraph, containing "STRUCTURE_3zts", creates the "Structure Box" on the page.
+<StructureSection load='3zts' size='340' side='right'caption='[[3zts]], [[Resolution|resolution]] 2.30&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'>[[3zts]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZTS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZTS 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]] 2.3&#8491;</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=3zts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zts OCA], [https://pdbe.org/3zts PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zts RCSB], [https://www.ebi.ac.uk/pdbsum/3zts PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zts ProSAT]</span></td></tr>
-{{STRUCTURE_3zts|  PDB=3zts  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDK_AQUAE NDK_AQUAE] 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).
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The nucleoside diphosphate kinase (Ndk) catalyzes the reversible transfer of the gamma-phosphate from nucleoside triphosphate to nucleoside diphosphate. Ndks form hexamers or two types of tetramers made of the same building block, namely, the common dimer. The secondary interfaces of the Type I tetramer found in Myxococcus xanthus Ndk and of the Type II found in Escherichia coli Ndk involve the opposite sides of subunits. Up to now, the few available structures of Ndk from thermophiles were hexameric. Here, we determined the X-ray structures of four crystal forms of the Ndk from the hyperthermophilic bacterium Aquifex aeolicus (Aa-Ndk). Aa-Ndk displays numerous features of thermostable proteins and is made of the common dimer but it is a tetramer of Type I. Indeed, the insertion of three residues in a surface-exposed spiral loop, named the Kpn-loop, leads to the formation of a two-turn alpha-helix that prevents both hexamer and Type II tetramer assembly. Moreover, the side chain of the cysteine at position 133, which is not present in other Ndk sequences, adopts two alternate conformations. Through the secondary interface, each one forms a disulfide bridge with the equivalent Cys133 from the neighboring subunit. This disulfide bridge was progressively broken during X-ray data collection by radiation damage. Such crosslinks counterbalance the weakness of the common-dimer interface. A 40% decrease of the kinase activity at 60 degrees C after reduction and alkylation of the protein corroborates the structural relevance of the disulfide bridge on the tetramer assembly and enzymatic function. Proteins 2012. (c) 2012 Wiley Periodicals, Inc.
-===Hexagonal form P6122 of the Aquifex aeolicus nucleoside diphosphate kinase (FINAL STAGE OF RADIATION DAMAGE)===
+An intersubunit disulfide bridge stabilizes the tetrameric nucleoside diphosphate kinase of Aquifex aeolicus.,Boissier F, Georgescauld F, Moynie L, Dupuy JW, Sarger C, Podar M, Lascu I, Giraud MF, Dautant A Proteins. 2012 Jun;80(6):1658-68. doi: 10.1002/prot.24062. Epub 2012 Mar 29. PMID:22467275<ref>PMID:22467275</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_22467275}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3zts" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 22467275 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_22467275}}
-==About this Structure==
-[[3zts]] is a 12 chain structure of [[Nucleoside diphosphate kinase]] with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZTS OCA].
 ==See Also==
-*[[Nucleoside diphosphate kinase|Nucleoside diphosphate kinase]]
+*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:022467275</ref><ref group="xtra">PMID:017330300</ref><ref group="xtra">PMID:008263923</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Aquifex aeolicus]]
-[[Category: Nucleoside-diphosphate kinase]]
+[[Category: Large Structures]]
-[[Category: Boissier, F.]]
+[[Category: Boissier F]]
-[[Category: Dautant, A.]]
+[[Category: Dautant A]]
-[[Category: Dupuy, J W.]]
+[[Category: Dupuy J-W]]
-[[Category: Georgescauld, F.]]
+[[Category: Georgescauld F]]
-[[Category: Giraud, M F.]]
+[[Category: Giraud M-F]]
-[[Category: Lascu, I.]]
+[[Category: Lascu I]]
-[[Category: Moynie, L.]]
+[[Category: Moynie L]]
-[[Category: Podar, M.]]
+[[Category: Podar M]]
-[[Category: Sarger, C.]]
+[[Category: Sarger C]]
-[[Category: Disulfide bridge]]
-[[Category: Transferase]]