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| | ==Orthorhombic crystal form P21212 of the Aquifex aeolicus nucleoside diphosphate kinase== | | ==Orthorhombic crystal form P21212 of the Aquifex aeolicus nucleoside diphosphate kinase== |
| - | <StructureSection load='3ztp' size='340' side='right' caption='[[3ztp]], [[Resolution|resolution]] 1.37Å' scene=''> | + | <StructureSection load='3ztp' size='340' side='right'caption='[[3ztp]], [[Resolution|resolution]] 1.37Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ztp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZTP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZTP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ztp]] is a 2 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=3ZTP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZTP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.37Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3zts|3zts]], [[3ztr|3ztr]], [[3ztq|3ztq]], [[3zto|3zto]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=3ztp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ztp OCA], [https://pdbe.org/3ztp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ztp RCSB], [https://www.ebi.ac.uk/pdbsum/3ztp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ztp ProSAT]</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=3ztp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ztp OCA], [http://pdbe.org/3ztp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ztp RCSB], [http://www.ebi.ac.uk/pdbsum/3ztp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ztp ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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). | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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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: Aquifex aeolicus huber and stetter 2001]] | + | [[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: Transferase]]
| + | |
| Structural highlights
Function
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).
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Boissier F, Georgescauld F, Moynie L, Dupuy JW, Sarger C, Podar M, Lascu I, Giraud MF, Dautant A. An intersubunit disulfide bridge stabilizes the tetrameric nucleoside diphosphate kinase of Aquifex aeolicus. Proteins. 2012 Jun;80(6):1658-68. doi: 10.1002/prot.24062. Epub 2012 Mar 29. PMID:22467275 doi:10.1002/prot.24062
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