4fpd: Difference between revisions

Revision as of 20:04, 19 October 2022

Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway

Structural highlights

4fpd is a 1 chain structure with sequence from Halobacterium salinarum NRC-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	CL, LI1, RET
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BACR_HALSA Light-driven proton pump.

Publication Abstract from PubMed

Despite extensive investigation, the precise mechanism controlling the opening of the cytoplasmic proton uptake pathway in bacteriorhodopsin (bR) has remained a mystery. From an analysis of the X-ray structure of the D96G/F171C/F219L triple mutant of bR and 60 independent molecular dynamics simulations of bR photointermediates, we report that the deprotonation of D96, a key residue in proton transfer reactions, serves two roles that occur sequentially. First, D96 donates a proton to the Schiff base. Subsequently, the deprotonation of D96 serves to "unlatch" the cytoplasmic side. The latching function of D96 appears to be remarkably robust, functioning to open hydration channels in all photointermediate structures. These results suggest that the protonation state of D96 may be the critical biophysical cue controlling the opening and closing of the cytoplasmic half-channel in bR. We suspect that this protonation-switch mechanism could also be utilized in other proton pumps to minimize backflow and reinforce directionality.

Deprotonation of d96 in bacteriorhodopsin opens the proton uptake pathway.,Wang T, Sessions AO, Lunde CS, Rouhani S, Glaeser RM, Duan Y, Facciotti MT Structure. 2013 Feb 5;21(2):290-7. doi: 10.1016/j.str.2012.12.018. PMID:23394942^[1]

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

References

↑ Wang T, Sessions AO, Lunde CS, Rouhani S, Glaeser RM, Duan Y, Facciotti MT. Deprotonation of d96 in bacteriorhodopsin opens the proton uptake pathway. Structure. 2013 Feb 5;21(2):290-7. doi: 10.1016/j.str.2012.12.018. PMID:23394942 doi:https://dx.doi.org/10.1016/j.str.2012.12.018

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Wang T, Sessions AO, Lunde CS, Rouhani S, Glaeser RM, Duan Y, Facciotti MT. Deprotonation of d96 in bacteriorhodopsin opens the proton uptake pathway. Structure. 2013 Feb 5;21(2):290-7. doi: 10.1016/j.str.2012.12.018. PMID:23394942 doi:https://dx.doi.org/10.1016/j.str.2012.12.018

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='4fpd' size='340' side='right'caption='[[4fpd]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4fpd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halsa Halsa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FPD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4FPD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4fpd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum_NRC-1 Halobacterium salinarum NRC-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FPD 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=LI1:1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL'>LI1</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kgb|1kgb]], [[1kg8|1kg8]], [[1kg9|1kg9]], [[1jv7|1jv7]], [[1fbk|1fbk]]</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=4fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fpd OCA], [https://pdbe.org/4fpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fpd RCSB], [https://www.ebi.ac.uk/pdbsum/4fpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fpd ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4fpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fpd OCA], [http://pdbe.org/4fpd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fpd RCSB], [http://www.ebi.ac.uk/pdbsum/4fpd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fpd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.
+[https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA] Light-driven proton pump.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Halsa]]
+[[Category: Halobacterium salinarum NRC-1]]
 [[Category: Large Structures]]
-[[Category: Duan, Y]]
+[[Category: Duan Y]]
-[[Category: Facciotti, M T]]
+[[Category: Facciotti MT]]
-[[Category: Glaeser, R M]]
+[[Category: Glaeser RM]]
-[[Category: Lunde, C S]]
+[[Category: Lunde CS]]
-[[Category: Rouani, S]]
+[[Category: Rouani S]]
-[[Category: Sessions, A O]]
+[[Category: Sessions AO]]
-[[Category: Wang, T]]
+[[Category: Wang T]]
-[[Category: Helix]]
-[[Category: Deprotonation]]
-[[Category: Ion transport]]
-[[Category: Membrane]]
-[[Category: Proton pump]]
-[[Category: Retinal binding]]
-[[Category: Transmembrane]]
-[[Category: Transport protein]]

4fpd: Difference between revisions

Revision as of 20:04, 19 October 2022

Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway

Structural highlights

Function

Publication Abstract from PubMed

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References

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