2vx9: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(9 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:2vx9.png|left|200px]]


<!--
==H. salinarum dodecin E45A mutant==
The line below this paragraph, containing "STRUCTURE_2vx9", creates the "Structure Box" on the page.
<StructureSection load='2vx9' size='340' side='right'caption='[[2vx9]], [[Resolution|resolution]] 1.65&Aring;' 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'>[[2vx9]] 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=2VX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VX9 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">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RBF:RIBOFLAVIN'>RBF</scene></td></tr>
{{STRUCTURE_2vx9|  PDB=2vx9  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vx9 OCA], [https://pdbe.org/2vx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vx9 RCSB], [https://www.ebi.ac.uk/pdbsum/2vx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vx9 ProSAT]</span></td></tr>
</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 ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vx/2vx9_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vx9 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Flavins are employed to transform physical input into biological output signals. In this function, flavins catalyze a variety of light-induced reactions and redox processes. However, nature also provides flavoproteins with the ability to uncouple the mediation of signals. Such proteins are the riboflavin-binding proteins (RfBPs) with their function to store riboflavin for fast delivery of FMN and FAD. Here we present in vitro and in vivo data showing that the recently discovered archaeal dodecin is an RfBP, and we reveal that riboflavin storage is not restricted to eukaryotes. However, the function of the prokaryotic RfBP dodecin seems to be adapted to the requirement of a monocellular organism. While in eukaryotes RfBPs are involved in trafficking riboflavin, and dodecin is responsible for the flavin homeostasis of the cell. Although only 68 amino acids in length, dodecin is of high functional versatility in neutralizing riboflavin to protect the cellular environment from uncontrolled flavin reactivity. Besides the predominant ultrafast quenching of excited states, dodecin prevents light-induced riboflavin reactivity by the selective degradation of riboflavin to lumichrome. Coordinated with the high affinity for lumichrome, the directed degradation reaction is neutral to the cellular environment and provides an alternative pathway for suppressing uncontrolled riboflavin reactivity. Intriguingly, the different structural and functional properties of a homologous bacterial dodecin suggest that dodecin has different roles in different kingdoms of life.


===H. SALINARUM DODECIN E45A MUTANT===
Dodecin is the key player in flavin homeostasis of archaea.,Grininger M, Staudt H, Johansson P, Wachtveitl J, Oesterhelt D J Biol Chem. 2009 May 8;284(19):13068-76. Epub 2009 Feb 17. PMID:19224924<ref>PMID:19224924</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<!--
</div>
The line below this paragraph, {{ABSTRACT_PUBMED_19224924}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2vx9" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 19224924 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_19224924}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Halobacterium salinarum R1]]
2VX9 is a [[Single protein]] structure of sequence from [http://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=2VX9 OCA].
[[Category: Large Structures]]
 
[[Category: Grininger M]]
==Reference==
[[Category: Johansson P]]
Dodecin is the key player in flavin homeostasis of archaea., Grininger M, Staudt H, Johansson P, Wachtveitl J, Oesterhelt D, J Biol Chem. 2009 Feb 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19224924 19224924]
[[Category: Oesterhelt D]]
[[Category: Halobacterium salinarum r1]]
[[Category: Staudt H]]
[[Category: Single protein]]
[[Category: Wachtveitl J]]
[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
[[Category: Archaea]]
[[Category: Dodecin]]
[[Category: Flavin]]
[[Category: Flavoprotein]]
[[Category: Lumichrome]]
[[Category: Riboflavin]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar  4 20:10:46 2009''

Latest revision as of 18:36, 13 December 2023

H. salinarum dodecin E45A mutantH. salinarum dodecin E45A mutant

Structural highlights

2vx9 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 1.65Å
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

Flavins are employed to transform physical input into biological output signals. In this function, flavins catalyze a variety of light-induced reactions and redox processes. However, nature also provides flavoproteins with the ability to uncouple the mediation of signals. Such proteins are the riboflavin-binding proteins (RfBPs) with their function to store riboflavin for fast delivery of FMN and FAD. Here we present in vitro and in vivo data showing that the recently discovered archaeal dodecin is an RfBP, and we reveal that riboflavin storage is not restricted to eukaryotes. However, the function of the prokaryotic RfBP dodecin seems to be adapted to the requirement of a monocellular organism. While in eukaryotes RfBPs are involved in trafficking riboflavin, and dodecin is responsible for the flavin homeostasis of the cell. Although only 68 amino acids in length, dodecin is of high functional versatility in neutralizing riboflavin to protect the cellular environment from uncontrolled flavin reactivity. Besides the predominant ultrafast quenching of excited states, dodecin prevents light-induced riboflavin reactivity by the selective degradation of riboflavin to lumichrome. Coordinated with the high affinity for lumichrome, the directed degradation reaction is neutral to the cellular environment and provides an alternative pathway for suppressing uncontrolled riboflavin reactivity. Intriguingly, the different structural and functional properties of a homologous bacterial dodecin suggest that dodecin has different roles in different kingdoms of life.

Dodecin is the key player in flavin homeostasis of archaea.,Grininger M, Staudt H, Johansson P, Wachtveitl J, Oesterhelt D J Biol Chem. 2009 May 8;284(19):13068-76. Epub 2009 Feb 17. PMID:19224924[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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

2vx9, resolution 1.65Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2vx9&oldid=3988482"