|
|
| Line 3: |
Line 3: |
| | <StructureSection load='3b54' size='340' side='right'caption='[[3b54]], [[Resolution|resolution]] 3.10Å' scene=''> | | <StructureSection load='3b54' size='340' side='right'caption='[[3b54]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3b54]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B54 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3b54]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B54 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 3.1Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NDK1, YNK, YNK1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=3b54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b54 OCA], [https://pdbe.org/3b54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b54 RCSB], [https://www.ebi.ac.uk/pdbsum/3b54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b54 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=3b54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b54 OCA], [https://pdbe.org/3b54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b54 RCSB], [https://www.ebi.ac.uk/pdbsum/3b54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b54 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/NDK_YEAST NDK_YEAST]] 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. Required for repair of UV radiation- and etoposide-induced DNA damage.<ref>PMID:18983998</ref>
| + | [https://www.uniprot.org/uniprot/NDK_YEAST NDK_YEAST] 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. Required for repair of UV radiation- and etoposide-induced DNA damage.<ref>PMID:18983998</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 37: |
Line 36: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Nucleoside-diphosphate kinase]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Bao, R]] | + | [[Category: Bao R]] |
| - | [[Category: Cheng, Y X]] | + | [[Category: Cheng YX]] |
| - | [[Category: Wang, H B]] | + | [[Category: Wang HB]] |
| - | [[Category: Alpha/beta sandwich]]
| + | |
| - | [[Category: Atp-binding]]
| + | |
| - | [[Category: Kinase]]
| + | |
| - | [[Category: Magnesium]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Mitochondrion]]
| + | |
| - | [[Category: Nucleotide metabolism]]
| + | |
| - | [[Category: Nucleotide-binding]]
| + | |
| - | [[Category: Phosphorylation]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
NDK_YEAST 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. Required for repair of UV radiation- and etoposide-induced DNA damage.[1]
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 the gamma-phosphate from nucleoside triphosphates to nucleoside diphosphates. In addition to biochemical studies, a number of crystal structures of NDPK from various organisms, including both native proteins and complexes with nucleotides or nucleotide analogues, have been determined. Here, the crystal structure of Ynk1, an NDPK from the yeast Saccharomyces cerevisiae, has been solved at 3.1 A resolution. Structural analysis strongly supports the oligomerization state of this protein being hexameric rather than tetrameric.
Structure of Ynk1 from the yeast Saccharomyces cerevisiae.,Wang H, Bao R, Jiang C, Yang Z, Zhou CZ, Chen Y Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Jul 1;64(Pt, 7):572-6. Epub 2008 Jun 28. PMID:18607079[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yang M, Jarrett SG, Craven R, Kaetzel DM. YNK1, the yeast homolog of human metastasis suppressor NM23, is required for repair of UV radiation- and etoposide-induced DNA damage. Mutat Res. 2009 Jan 15;660(1-2):74-8. Epub 2008 Oct 15. PMID:18983998 doi:http://dx.doi.org/S0027-5107(08)00224-8
- ↑ Wang H, Bao R, Jiang C, Yang Z, Zhou CZ, Chen Y. Structure of Ynk1 from the yeast Saccharomyces cerevisiae. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Jul 1;64(Pt, 7):572-6. Epub 2008 Jun 28. PMID:18607079 doi:10.1107/S1744309108015212
|
