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| - | {{Seed}} | |
| - | [[Image:1vfi.png|left|200px]] | |
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| - | <!--
| + | ==Solution Structure of Vanabin2 (RUH-017), a Vanadium-binding Protein from Ascidia sydneiensis samea== |
| - | The line below this paragraph, containing "STRUCTURE_1vfi", creates the "Structure Box" on the page.
| + | <StructureSection load='1vfi' size='340' side='right'caption='[[1vfi]]' 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'>[[1vfi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ascidia_sydneiensis_samea Ascidia sydneiensis samea]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VFI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VFI 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">Solution NMR, 20 models</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=1vfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vfi OCA], [https://pdbe.org/1vfi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vfi RCSB], [https://www.ebi.ac.uk/pdbsum/1vfi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vfi ProSAT], [https://www.topsan.org/Proteins/RSGI/1vfi TOPSAN]</span></td></tr> |
| - | {{STRUCTURE_1vfi| PDB=1vfi | SCENE= }}
| + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/VBP2_ASCSS VBP2_ASCSS] Acts as a vanadium reductase which may form an electron transfer cascade in conjunction with NADPH and glutathione through thiol disulfide exchange reactions. Partial cleavage of its disulfide bonds results in the reduction of V(5+) to V(4+). Binds up to 24 V(4+) ions per protein at pH 7.5. Also binds Fe(3+) and Cu(2+) and, to a lesser extent, Co(2+), Zn(2+) and Ni(2+).<ref>PMID:12697328</ref> <ref>PMID:12785759</ref> <ref>PMID:14602598</ref> <ref>PMID:16631310</ref> <ref>PMID:18466774</ref> <ref>PMID:19336037</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Ascidians belonging to the suborder Phlebobranchia are known to accumulate high levels of a transition metal, vanadium, in their blood cells, called vanadocytes, although the mechanism for this biological phenomenon remains unclear. Recently, we identified vanadium(IV)-binding proteins, designated as Vanabins, from vanadium-accumulating ascidians. Here, we report the first 3D structure of Vanabin2 from an ascidian, Ascidia sydneiensis samea, in an aqueous solution. The structure revealed a novel bow-shaped conformation, with four alpha-helices connected by nine disulfide bonds. There are no structural homologues reported so far. The 15N heteronuclear single-quantum coherence (HSQC) perturbation experiments of Vanabin2 indicated that vanadyl cations, which are exclusively localized on the same face of the molecule, are coordinated by amine nitrogens derived from amino acid residues such as lysines, arginines, and histidines, as suggested by the electron paramagnetic resonance (EPR) results. The present NMR studies provide information that will contribute toward elucidating the mechanism of vanadium accumulation in ascidians. |
| | | | |
| - | ===Solution Structure of Vanabin2 (RUH-017), a Vanadium-binding Protein from Ascidia sydneiensis samea===
| + | Solution structure of Vanabin2, a vanadium(IV)-binding protein from the vanadium-rich ascidian Ascidia sydneiensis samea.,Hamada T, Asanuma M, Ueki T, Hayashi F, Kobayashi N, Yokoyama S, Michibata H, Hirota H J Am Chem Soc. 2005 Mar 30;127(12):4216-22. PMID:15783203<ref>PMID:15783203</ref> |
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| - | | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | <!--
| + | </div> |
| - | The line below this paragraph, {{ABSTRACT_PUBMED_15783203}}, adds the Publication Abstract to the page
| + | <div class="pdbe-citations 1vfi" style="background-color:#fffaf0;"></div> |
| - | (as it appears on PubMed at http://www.pubmed.gov), where 15783203 is the PubMed ID number.
| + | == References == |
| - | -->
| + | <references/> |
| - | {{ABSTRACT_PUBMED_15783203}}
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==About this Structure== | + | |
| - | 1VFI is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Ascidia_sydneiensis_samea Ascidia sydneiensis samea]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VFI OCA].
| + | |
| - | | + | |
| - | ==Reference== | + | |
| - | Solution structure of Vanabin2, a vanadium(IV)-binding protein from the vanadium-rich ascidian Ascidia sydneiensis samea., Hamada T, Asanuma M, Ueki T, Hayashi F, Kobayashi N, Yokoyama S, Michibata H, Hirota H, J Am Chem Soc. 2005 Mar 30;127(12):4216-22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15783203 15783203]
| + | |
| | [[Category: Ascidia sydneiensis samea]] | | [[Category: Ascidia sydneiensis samea]] |
| - | [[Category: Asanuma, M.]] | + | [[Category: Large Structures]] |
| - | [[Category: Hamada, T.]] | + | [[Category: Asanuma M]] |
| - | [[Category: Hayashi, F.]] | + | [[Category: Hamada T]] |
| - | [[Category: Hirota, H.]] | + | [[Category: Hayashi F]] |
| - | [[Category: Kobayashi, N.]] | + | [[Category: Hirota H]] |
| - | [[Category: Michibata, H.]] | + | [[Category: Kobayashi N]] |
| - | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
| + | [[Category: Michibata H]] |
| - | [[Category: Ueki, T.]] | + | [[Category: Ueki T]] |
| - | [[Category: Yokoyama, S.]] | + | [[Category: Yokoyama S]] |
| - | [[Category: Ascidian]]
| + | |
| - | [[Category: Nmr]]
| + | |
| - | [[Category: Riken structural genomics/proteomics initiative]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Vanadium-binding]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 12:42:22 2008''
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| Structural highlights
Function
VBP2_ASCSS Acts as a vanadium reductase which may form an electron transfer cascade in conjunction with NADPH and glutathione through thiol disulfide exchange reactions. Partial cleavage of its disulfide bonds results in the reduction of V(5+) to V(4+). Binds up to 24 V(4+) ions per protein at pH 7.5. Also binds Fe(3+) and Cu(2+) and, to a lesser extent, Co(2+), Zn(2+) and Ni(2+).[1] [2] [3] [4] [5] [6]
Publication Abstract from PubMed
Ascidians belonging to the suborder Phlebobranchia are known to accumulate high levels of a transition metal, vanadium, in their blood cells, called vanadocytes, although the mechanism for this biological phenomenon remains unclear. Recently, we identified vanadium(IV)-binding proteins, designated as Vanabins, from vanadium-accumulating ascidians. Here, we report the first 3D structure of Vanabin2 from an ascidian, Ascidia sydneiensis samea, in an aqueous solution. The structure revealed a novel bow-shaped conformation, with four alpha-helices connected by nine disulfide bonds. There are no structural homologues reported so far. The 15N heteronuclear single-quantum coherence (HSQC) perturbation experiments of Vanabin2 indicated that vanadyl cations, which are exclusively localized on the same face of the molecule, are coordinated by amine nitrogens derived from amino acid residues such as lysines, arginines, and histidines, as suggested by the electron paramagnetic resonance (EPR) results. The present NMR studies provide information that will contribute toward elucidating the mechanism of vanadium accumulation in ascidians.
Solution structure of Vanabin2, a vanadium(IV)-binding protein from the vanadium-rich ascidian Ascidia sydneiensis samea.,Hamada T, Asanuma M, Ueki T, Hayashi F, Kobayashi N, Yokoyama S, Michibata H, Hirota H J Am Chem Soc. 2005 Mar 30;127(12):4216-22. PMID:15783203[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ueki T, Adachi T, Kawano S, Aoshima M, Yamaguchi N, Kanamori K, Michibata H. Vanadium-binding proteins (vanabins) from a vanadium-rich ascidian Ascidia sydneiensis samea. Biochim Biophys Acta. 2003 Apr 15;1626(1-3):43-50. PMID:12697328
- ↑ Fukui K, Ueki T, Ohya H, Michibata H. Vanadium-binding protein in a vanadium-rich ascidian Ascidia sydneiensissamea: CW and pulsed EPR studies. J Am Chem Soc. 2003 May 28;125(21):6352-3. PMID:12785759 doi:http://dx.doi.org/10.1021/ja034507w
- ↑ Ueki T, Sakamoto Y, Yamaguchi N, Michibata H. Bioaccumulation of copper ions by Escherichia coli expressing vanabin genes from the vanadium-rich ascidian Ascidia sydneiensis samea. Appl Environ Microbiol. 2003 Nov;69(11):6442-6. PMID:14602598
- ↑ Kawakami N, Ueki T, Matsuo K, Gekko K, Michibata H. Selective metal binding by Vanabin2 from the vanadium-rich ascidian, Ascidia sydneiensis samea. Biochim Biophys Acta. 2006 Jul;1760(7):1096-101. Epub 2006 Apr 4. PMID:16631310 doi:http://dx.doi.org/10.1016/j.bbagen.2006.03.013
- ↑ Ueki T, Satake M, Kamino K, Michibata H. Sequence variation of Vanabin2-like vanadium-binding proteins in blood cells of the vanadium-accumulating ascidian Ascidia sydneiensis samea. Biochim Biophys Acta. 2008 Jul-Aug;1780(7-8):1010-5. doi:, 10.1016/j.bbagen.2008.04.001. Epub 2008 May 6. PMID:18466774 doi:http://dx.doi.org/10.1016/j.bbagen.2008.04.001
- ↑ Kawakami N, Ueki T, Amata Y, Kanamori K, Matsuo K, Gekko K, Michibata H. A novel vanadium reductase, Vanabin2, forms a possible cascade involved in electron transfer. Biochim Biophys Acta. 2009 Apr;1794(4):674-9. doi: 10.1016/j.bbapap.2009.01.007. , Epub 2009 Feb 3. PMID:19336037 doi:http://dx.doi.org/10.1016/j.bbapap.2009.01.007
- ↑ Hamada T, Asanuma M, Ueki T, Hayashi F, Kobayashi N, Yokoyama S, Michibata H, Hirota H. Solution structure of Vanabin2, a vanadium(IV)-binding protein from the vanadium-rich ascidian Ascidia sydneiensis samea. J Am Chem Soc. 2005 Mar 30;127(12):4216-22. PMID:15783203 doi:http://dx.doi.org/10.1021/ja042687j
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