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| | <StructureSection load='2cc6' size='340' side='right'caption='[[2cc6]], [[Resolution|resolution]] 1.27Å' scene=''> | | <StructureSection load='2cc6' size='340' side='right'caption='[[2cc6]], [[Resolution|resolution]] 1.27Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2cc6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hals3 Hals3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CC6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CC6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2cc6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum_R1 Halobacterium salinarum R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CC6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CC6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=LUM:LUMICHROME'>LUM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.27Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1mog|1mog]], [[2cc7|2cc7]], [[2cc8|2cc8]], [[2cc9|2cc9]], [[2ccb|2ccb]], [[2ccc|2ccc]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=LUM:LUMICHROME'>LUM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2cc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cc6 OCA], [https://pdbe.org/2cc6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cc6 RCSB], [https://www.ebi.ac.uk/pdbsum/2cc6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cc6 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=2cc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cc6 OCA], [https://pdbe.org/2cc6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cc6 RCSB], [https://www.ebi.ac.uk/pdbsum/2cc6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cc6 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DODEC_HALS3 DODEC_HALS3] May function as storage protein that sequesters riboflavin and related compounds, thereby protecting the cell against undesirable reactions mediated by the free flavins. Binds and sequesters riboflavin, lumiflavin and lumichrome. Can also bind FAD and FMN (in vitro), but has low affinity for FAD and even lower affinity for FMN. Protects bound flavins against light damage; Trp-36 rapidly quenches the flavin excited state. Promotes the conversion of bound riboflavin to lumichrome.<ref>PMID:12679016</ref> <ref>PMID:16460756</ref> <ref>PMID:17027852</ref> <ref>PMID:19224924</ref> <ref>PMID:20408700</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Hals3]] | + | [[Category: Halobacterium salinarum R1]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Grininger, M]] | + | [[Category: Grininger M]] |
| - | [[Category: Oesterhelt, D]] | + | [[Category: Oesterhelt D]] |
| - | [[Category: Zeth, K]] | + | [[Category: Zeth K]] |
| - | [[Category: Flavin]]
| + | |
| - | [[Category: Flavin-like ligand]]
| + | |
| - | [[Category: Flavoprotein]]
| + | |
| Structural highlights
2cc6 is a 1 chain structure with sequence from Halobacterium salinarum R1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.27Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
DODEC_HALS3 May function as storage protein that sequesters riboflavin and related compounds, thereby protecting the cell against undesirable reactions mediated by the free flavins. Binds and sequesters riboflavin, lumiflavin and lumichrome. Can also bind FAD and FMN (in vitro), but has low affinity for FAD and even lower affinity for FMN. Protects bound flavins against light damage; Trp-36 rapidly quenches the flavin excited state. Promotes the conversion of bound riboflavin to lumichrome.[1] [2] [3] [4] [5]
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
Dodecin is a small dodecameric flavoprotein from Halobacterium salinarum that contains two flavins stacked between two tryptophan residues to form an aromatic tetrade. The functional properties of heterologously expressed dodecin were investigated by fluorescence spectroscopy, which allowed the determination of dissociation constants for a number of protein-ligand complexes. The values obtained were in the nanomolar to micromolar range and correlate positively with the ligand size. These data were supplemented by X-ray crystal structures of the apododecin and holocomplexes with lumichrome, lumiflavin, riboflavin and FMN at resolutions between 1.55 to 1.95 A to unravel a gating mechanism as the structural basis for the preferential binding of the small ligands lumichrome and lumiflavin. The detailed analysis of the dodecin manifold for preferential binding of lumichrome and lumiflavin provides insight on a subatom level into a protein's strategy to gain selectivity for low molecular mass compounds by steric restrictions rather than specific interactions. Investigations on the ligand composition of a wild-type dodecin crystal (1.32 A resolution) support conclusions of functional and structural investigations on heterologously expressed dodecin, and strongly suggest that lumichrome, a molecule associated with the flavin metabolism, is a ligand of dodecin in vivo. Studies on mutant protein and a Halorhodospira halophila homologue spread the idea of a lumichrome binding system as a possible "waste"-trapping device, widely distributed in prokaryotes.
Dodecins: a family of lumichrome binding proteins.,Grininger M, Zeth K, Oesterhelt D J Mol Biol. 2006 Mar 31;357(3):842-57. Epub 2006 Jan 18. PMID:16460756[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bieger B, Essen LO, Oesterhelt D. Crystal structure of halophilic dodecin: a novel, dodecameric flavin binding protein from Halobacterium salinarum. Structure. 2003 Apr;11(4):375-85. PMID:12679016
- ↑ Grininger M, Zeth K, Oesterhelt D. Dodecins: a family of lumichrome binding proteins. J Mol Biol. 2006 Mar 31;357(3):842-57. Epub 2006 Jan 18. PMID:16460756 doi:10.1016/j.jmb.2005.12.072
- ↑ Grininger M, Seiler F, Zeth K, Oesterhelt D. Dodecin sequesters FAD in closed conformation from the aqueous solution. J Mol Biol. 2006 Dec 8;364(4):561-6. Epub 2006 Sep 5. PMID:17027852 doi:10.1016/j.jmb.2006.08.083
- ↑ Grininger M, Staudt H, Johansson P, Wachtveitl J, Oesterhelt D. Dodecin is the key player in flavin homeostasis of archaea. J Biol Chem. 2009 May 8;284(19):13068-76. Epub 2009 Feb 17. PMID:19224924 doi:10.1074/jbc.M808063200
- ↑ Grininger M, Noll G, Trawoger S, Sinner EK, Oesterhelt D. Electrochemical switching of the flavoprotein dodecin at gold surfaces modified by flavin-DNA hybrid linkers. Biointerphases. 2008 Sep;3(3):51-8. PMID:20408700 doi:10.1116/1.2965134
- ↑ Grininger M, Zeth K, Oesterhelt D. Dodecins: a family of lumichrome binding proteins. J Mol Biol. 2006 Mar 31;357(3):842-57. Epub 2006 Jan 18. PMID:16460756 doi:10.1016/j.jmb.2005.12.072
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