|
|
| Line 3: |
Line 3: |
| | <StructureSection load='2hur' size='340' side='right'caption='[[2hur]], [[Resolution|resolution]] 1.62Å' scene=''> | | <StructureSection load='2hur' size='340' side='right'caption='[[2hur]], [[Resolution|resolution]] 1.62Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2hur]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HUR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2hur]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HUR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 1.62Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nck|2nck]], [[1npk|1npk]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ndk ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [https://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=2hur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hur OCA], [https://pdbe.org/2hur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hur RCSB], [https://www.ebi.ac.uk/pdbsum/2hur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hur 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=2hur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hur OCA], [https://pdbe.org/2hur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hur RCSB], [https://www.ebi.ac.uk/pdbsum/2hur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hur ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/NDK_ECOLI NDK_ECOLI]] 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.[HAMAP-Rule:MF_00451]
| + | [https://www.uniprot.org/uniprot/NDK_ECOLI NDK_ECOLI] 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.[HAMAP-Rule:MF_00451] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 38: |
Line 36: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Nucleoside-diphosphate kinase]]
| + | [[Category: Dautant A]] |
| - | [[Category: Dautant, A]] | + | [[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: Signaling protein]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Type ii tetramer]]
| + | |
| Structural highlights
Function
NDK_ECOLI 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.[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 kinase (NDPK) catalyzes the transfer of gamma-phosphate from nucleoside triphosphates to nucleoside diphosphates. The subunit folding and the dimeric basic structural unit are remarkably the same for available structures but, depending on species, dimers self-associate to form hexamers or tetramers. The crystal structure of the Escherichia coli NDPK reveals a new tetrameric quaternary structure for this protein family. The two tetramers differ by the relative orientation of interacting dimers, which face either the convex or the concave side of their central sheet as in either Myxococcus xanthus (type I) or E. coli (type II), respectively. In the type II tetramer, the subunits interact by a new interface harboring a zone called the Kpn loop as in hexamers, but by the opposite face of this loop. The evolutionary conservation of the interface residues indicates that this new quaternary structure seems to be the most frequent assembly mode in bacterial tetrameric NDP kinases.
The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family.,Moynie L, Giraud MF, Georgescauld F, Lascu I, Dautant A Proteins. 2007 May 15;67(3):755-65. PMID:17330300[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Moynie L, Giraud MF, Georgescauld F, Lascu I, Dautant A. The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family. Proteins. 2007 May 15;67(3):755-65. PMID:17330300 doi:10.1002/prot.21316
|
