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1dze

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Revision as of 07:47, 13 December 2017

Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K

Structural highlights

1dze is a 1 chain structure with sequence from Halobacterium salinarium. The March 2002 RCSB PDB Molecule of the Month feature on Bacteriorhodopsin by David S. Goodsell is 10.2210/rcsb_pdb/mom_2002_3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , , ,
Related:	1c3w, 1brd, 2brd, 1brr, 1bac, 1bad, 1bha, 1bhb, 1bct, 1ap9, 1at9, 1qm8
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[BACR_HALSA] Light-driven proton pump.

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

Structural changes in the proton pumping cycle of wild-type bacteriorhodopsin were investigated by using a 3D crystal (space group P622)prepared by the membrane fusion method. Protein-protein contacts in the crystal elongate the lifetime of the M intermediate by a factor of approximately 100,allowing high levels of the M intermediate to accumulate under continuous illumination. When the M intermediate generated at room temperature was exposed to a low flux of X-rays (approximately 10(14) photons/mm2), this yellow intermediate was converted into a blue species having an absorption maximum at 650 nm. This color change is suggested to accompany a configuration change in the retinal-Lys216 chain. The true conformational change associated with formation of the M intermediate was analyzed by taking the X-radiation-induced structural change into account. Our result indicates that, upon formation of the M intermediate, helix G move stowards the extra-cellular side by, on average, 0.5 angstroms. This movement is coupled with several reactions occurring at distal sites in the protein: (1) reorientation of the side-chain of Leu93 contacting the C13 methyl group of retinal, which is accompanied by detachment of a water molecule from the Schiff base; (2) a significant distortion in the F-G loop, triggering destruction of a hydrogen bonding interaction between a pair of glutamate groups (Glu194 and Glu204); (3) formation of a salt bridge between the carboxylate group of Glu204 and the guanidinium ion of Arg82, which is accompanied by a large distortion in the extra-cellular half of helix C; (4)noticeable movements of the AB loop and the cytoplasmic end of helix B. But, no appreciable change is induced in the peptide backbone of helices A,D, E and F. These structural changes are discussed from the viewpoint of translocation of water molecules.

Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix.,Takeda K, Matsui Y, Kamiya N, Adachi S, Okumura H, Kouyama T J Mol Biol. 2004 Aug 20;341(4):1023-37. PMID:15328615^[1]

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

References

↑ Takeda K, Matsui Y, Kamiya N, Adachi S, Okumura H, Kouyama T. Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix. J Mol Biol. 2004 Aug 20;341(4):1023-37. PMID:15328615

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dze"

@@ Line 1: / Line 1: @@
-==STRUCTURE OF THE M INTERMEDIATE OF BACTERIORHODOPSIN TRAPPED AT 100K==
+==Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K==
 <StructureSection load='1dze' size='340' side='right' caption='[[1dze]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1dze]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. The March 2002 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Bacteriorhodopsin''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2002_3 10.2210/rcsb_pdb/mom_2002_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DZE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DZE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1dze]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarium Halobacterium salinarium]. The March 2002 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Bacteriorhodopsin''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2002_3 10.2210/rcsb_pdb/mom_2002_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DZE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DZE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=L4P:3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL'>L4P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=L4P:3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL'>L4P</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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">[[1c3w|1c3w]], [[1brd|1brd]], [[2brd|2brd]], [[1brr|1brr]], [[1bac|1bac]], [[1bad|1bad]], [[1bha|1bha]], [[1bhb|1bhb]], [[1bct|1bct]], [[1ap9|1ap9]], [[1at9|1at9]], [[1qm8|1qm8]]</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=1dze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dze OCA], [http://pdbe.org/1dze PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dze RCSB], [http://www.ebi.ac.uk/pdbsum/1dze PDBsum]</span></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=1dze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dze OCA], [http://pdbe.org/1dze PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dze RCSB], [http://www.ebi.ac.uk/pdbsum/1dze PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dze ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dz/1dze_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dz/1dze_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 1dze" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Bacteriorhodopsin|Bacteriorhodopsin]]
 == References ==
 <references/>
@@ Line 36: / Line 34: @@
 </StructureSection>
 [[Category: Bacteriorhodopsin]]
-[[Category: Halobacterium salinarum]]
+[[Category: Halobacterium salinarium]]
 [[Category: RCSB PDB Molecule of the Month]]
 [[Category: Adachi, S]]

1dze

From Proteopedia

Revision as of 07:47, 13 December 2017

Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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