This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5dys

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal Structure of T94I rhodopsin mutant

Structural highlights

5dys is a 1 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	, , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OPSD_BOVIN Photoreceptor required for image-forming vision at low light intensity. Required for photoreceptor cell viability after birth. Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal (By similarity).^[1] ^[2]

Publication Abstract from PubMed

Congenital stationary night blindness (CSNB) is an inherited and non-progressive retinal dysfunction. Here, we present the crystal structure of CSNB-causing T94I2.61 rhodopsin in the active conformation at 2.3 A resolution. The introduced hydrophobic side chain prolongs the lifetime of the G protein activating metarhodopsin-II state by establishing a direct van der Waals contact with K2967.43, the site of retinal attachment. This is in stark contrast to the light-activated state of the CSNB-causing G90D2.57 mutation, where the charged mutation forms a salt bridge with K2967.43 To find the common denominator between these two functional modifications, we combined our structural data with a kinetic biochemical analysis and molecular dynamics simulations. Our results indicate that both the charged G90D2.57 and the hydrophobic T94I2.61 mutation alter the dark state by weakening the interaction between the Schiff base (SB) and its counterion E1133.28 We propose that this interference with the tight regulation of the dim light photoreceptor rhodopsin increases background noise in the visual system and causes the loss of night vision characteristic for CSNB patients.

Structural role of the T94I rhodopsin mutation in congenital stationary night blindness.,Singhal A, Guo Y, Matkovic M, Schertler G, Deupi X, Yan EC, Standfuss J EMBO Rep. 2016 Jul 25. pii: e201642671. PMID:27458239^[3]

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

References

↑ Nakamichi H, Okada T. Local peptide movement in the photoreaction intermediate of rhodopsin. Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12729-34. Epub 2006 Aug 14. PMID:16908857
↑ Salom D, Lodowski DT, Stenkamp RE, Le Trong I, Golczak M, Jastrzebska B, Harris T, Ballesteros JA, Palczewski K. Crystal structure of a photoactivated deprotonated intermediate of rhodopsin. Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16123-8. Epub 2006 Oct 23. PMID:17060607
↑ Singhal A, Guo Y, Matkovic M, Schertler G, Deupi X, Yan EC, Standfuss J. Structural role of the T94I rhodopsin mutation in congenital stationary night blindness. EMBO Rep. 2016 Jul 25. pii: e201642671. PMID:27458239 doi:http://dx.doi.org/10.15252/embr.201642671

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5dys"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of T94I rhodopsin mutant==
-<StructureSection load='5dys' size='340' side='right' caption='[[5dys]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='5dys' size='340' side='right'caption='[[5dys]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5dys]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DYS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5dys]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DYS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DYS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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]] 2.3&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5dys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dys OCA], [http://pdbe.org/5dys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dys RCSB], [http://www.ebi.ac.uk/pdbsum/5dys PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dys 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=5dys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dys OCA], [https://pdbe.org/5dys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dys RCSB], [https://www.ebi.ac.uk/pdbsum/5dys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dys ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/OPSD_BOVIN OPSD_BOVIN]] Photoreceptor required for image-forming vision at low light intensity. Required for photoreceptor cell viability after birth. Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal (By similarity).<ref>PMID:16908857</ref> <ref>PMID:17060607</ref>
+[https://www.uniprot.org/uniprot/OPSD_BOVIN OPSD_BOVIN] Photoreceptor required for image-forming vision at low light intensity. Required for photoreceptor cell viability after birth. Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal (By similarity).<ref>PMID:16908857</ref> <ref>PMID:17060607</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5dys" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Deupi, X]]
+[[Category: Bos taurus]]
-[[Category: Guo, Y]]
+[[Category: Large Structures]]
-[[Category: Matkovic, M]]
+[[Category: Deupi X]]
-[[Category: Schertler, G]]
+[[Category: Guo Y]]
-[[Category: Singhal, A]]
+[[Category: Matkovic M]]
-[[Category: Standfuss, J]]
+[[Category: Schertler G]]
-[[Category: Yan, E]]
+[[Category: Singhal A]]
-[[Category: Congenital stationary night blindness]]
+[[Category: Standfuss J]]
-[[Category: Constitutive activity]]
+[[Category: Yan E]]
-[[Category: G protein-coupled receptor]]
-[[Category: Rhodopsin]]
-[[Category: Signaling protein]]

5dys

From Proteopedia

Current revision

Crystal Structure of T94I rhodopsin mutant

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox