Bac_rhodopsinBacteriorhodopsin-like protein |
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| SMART accession number: | SM01021 |
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| Description: | The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria (PUBMED:2468194), (PUBMED:2591367). They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). |
| Interpro abstract (IPR001425): | Bacterial rhodopsins are a family of bacterial opsins. They are retinal-binding proteins that provide light-dependent ion transport and sensory functions to a family of halophilic bacteria [ (PUBMED:2468194) (PUBMED:2591367) ]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal binding (a conserved lysine). The archaeal/bacterial/fungal rhodopsin family includes bacteriorhodopsin and archaerhodopsin, which are light-driven proton pumps; halorhodopsin, a light-driven chloride pump; and sensory rhodopsin, which mediates both photoattractant (in the red) and photophobic (in the UV) responses. This family also includes distantly related proteins that do not contain the retinal binding lysine and so cannot function as opsins. |
| GO process: | ion transport (GO:0006811) |
| GO component: | membrane (GO:0016020) |
| GO function: | ion channel activity (GO:0005216) |
| Family alignment: |
There are 3028 Bac_rhodopsin domains in 3027 proteins in SMART's nrdb database.
Click on the following links for more information.
- Evolution (species in which this domain is found)
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Taxonomic distribution of proteins containing Bac_rhodopsin domain.
This tree includes only several representative species. The complete taxonomic breakdown of all proteins with Bac_rhodopsin domain is also avaliable.
Click on the protein counts, or double click on taxonomic names to display all proteins containing Bac_rhodopsin domain in the selected taxonomic class.
- Cellular role (predicted cellular role)
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Cellular role: signalling
- Literature (relevant references for this domain)
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Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Grigorieff N, Ceska TA, Downing KH, Baldwin JM, Henderson R
- Electron-crystallographic refinement of the structure ofbacteriorhodopsin.
- J Mol Biol. 1996; 259: 393-421
- Display abstract
Using electron diffraction data corrected for diffuse scattering togetherwith additional phase information from 30 new images of tilted specimens,an improved experimental density map has been calculated forbacteriorhodopsin. The atomic model has then been rebuilt into this newmap with particular attention to the surface loops. All the residues from7 to 227 as well as ten lipid molecules are now included, although a fewamino acid residues in three of the six surface loops, about half of thelipid hydrophobic chains and all of the lipid head groups are disordered.The model has then been refined against the experimental diffractionamplitudes to an R-factor of 28% at 3.5 angstrom resolution with strictgeometry (0.005 angstrom) bond length deviation) using the improvement ofthe "free" phase residual between calculated and experimental phases fromimages as an objective criterion of accuracy. For the refinement some newprograms were developed to restrain the number of parameters, to becompatible with the limited resolution of our data. In the final refinedmodel of the protein (2BRD), compared with earlier co-ordinates (1BRD),helix D has been moved towards the cytoplasm by almost 4 angstrom, and theoverall accuracy of the co-ordinates of residues in the other six heliceshas been improved. As a result the positions of nearly all the importantresidues in bacteriorhodopsin are now well determined. In particular, theburied, protonated Asp115 is 7 angstrom from, and so not in contact with,the retinal and Met118 forms a cap on the pocket occupied by thebeta-ionone ring. No clear density exists for the side-chain of Arg82,which forms a central part of the extracellular half-channel. The onlyarginine side-chain built into good density is that of Arg134 at theextracellular end of helix E, the others being disordered near one of thetwo surfaces. The interpretation of the end of helix F on theextracellular surface is now clearer; an extra loose helical turn has beenbuilt bringing the side-chain of Glu194 close to Arg134 to form a probablesalt bridge. The model provides an improved framework for understandingthe mechanism of the light-driven proton pumping. A number of cavitiesthat could contain water molecules were found by searching the refinedmodel, most of them above or below the Schiff base in the half-channelsleading to the two surfaces. The ordered and disordered regions of thestructure are described by the temperature factor distribution.
- Blanck A, Oesterhelt D, Ferrando E, Schegk ES, Lottspeich F
- Primary structure of sensory rhodopsin I, a prokaryotic photoreceptor.
- EMBO J. 1989; 8: 3963-71
- Display abstract
The gene coding for sensory rhodopsin I (SR-I) has been identified in arestriction fragment of genomic DNA from the Halobacterium halobium strainL33. Of the 1014 nucleotides whose sequence was determined, 720 belong tothe structural gene of SR-I. In the 5' non-coding region two putativepromoter elements and a ribosomal binding site have been identified. The3' flanking region bears a potential terminator structure. The SR-Iprotein moiety carries no signal peptide and is not processed at its Nterminus. The C terminus, however, lacks the last aspartic acid residueencoded by the gene. Analysis of the primary structure of SR-I reveals noconsistent homology with the eukaryotic photoreceptor rhodopsin, but 14%homology with the halobacterial ion pumps, bacteriorhodopsin (BR) andhalorhodopsin (HR). Residues conserved in all three proteins are discussedwith respect to their contribution to secondary structure, retinal bindingand ion translocation. The aspartic acid residue which mediates in BR thereprotonation of the Schiff base (D96) is replaced in SR-I by a tyrosine(Y87). This amino acid replacement is proposed to be of crucial importancein the evolution of the slow-cycling photosensing pigment SR-I.
- Oesterhelt D, Tittor J
- Two pumps, one principle: light-driven ion transport in halobacteria.
- Trends Biochem Sci. 1989; 14: 57-61
- Display abstract
Comparison of the primary structure of the chloride pump halorhodopsinwith that of the proton pump bacteriorhodopsin provides insight intolight-driven ion transport by retinal proteins. Several conserved aminoacid residues in the membrane-spanning region of both proteins and theirinteraction with different isomerization states of retinal are suggestedto be the key element for ion transport in both proteins.
- Structure (3D structures containing this domain)
3D Structures of Bac_rhodopsin domains in PDB
PDB code Main view Title 1ap9 
X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES 1at9 
STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY 1bm1 
CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN THE LIGHT-ADAPTED STATE 1brd 
Model for the structure of Bacteriorhodopsin based on high-resolution Electron Cryo-microscopy 1brr 
X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX 1brx 
BACTERIORHODOPSIN/LIPID COMPLEX 1c3w 
BACTERIORHODOPSIN/LIPID COMPLEX AT 1.55 A RESOLUTION 1c8r 
BACTERIORHODOPSIN D96N BR STATE AT 2.0 A RESOLUTION 1c8s 
BACTERIORHODOPSIN D96N LATE M STATE INTERMEDIATE 1cwq 
M INTERMEDIATE STRUCTURE OF THE WILD TYPE BACTERIORHODOPSIN IN COMBINATION WITH THE GROUND STATE STRUCTURE 1dze 
Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K 1e0p 
L intermediate of bacteriorhodopsin 1e12 
Halorhodopsin, a light-driven chloride pump 1f4z 
BACTERIORHODOPSIN-M PHOTOINTERMEDIATE STATE OF THE E204Q MUTANT AT 1.8 ANGSTROM RESOLUTION 1f50 
BACTERIORHODOPSIN-BR STATE OF THE E204Q MUTANT AT 1.7 ANGSTROM RESOLUTION 1fbb 
CRYSTAL STRUCTURE OF NATIVE CONFORMATION OF BACTERIORHODOPSIN 1fbk 
CRYSTAL STRUCTURE OF CYTOPLASMICALLY OPEN CONFORMATION OF BACTERIORHODOPSIN 1gu8 
SENSORY RHODOPSIN II 1gue 
SENSORY RHODOPSIN II 1h2s 
Molecular basis of transmenbrane signalling by sensory rhodopsin II-transducer complex 1h68 
sensory rhodopsin II 1iw6 
Crystal Structure of the Ground State of Bacteriorhodopsin 1iw9 
Crystal Structure of the M Intermediate of Bacteriorhodopsin 1ixf 
Crystal Structure of the K intermediate of bacteriorhodopsin 1jgj 
CRYSTAL STRUCTURE OF SENSORY RHODOPSIN II AT 2.4 ANGSTROMS: INSIGHTS INTO COLOR TUNING AND TRANSDUCER INTERACTION 1jv6 
BACTERIORHODOPSIN D85S/F219L DOUBLE MUTANT AT 2.00 ANGSTROM RESOLUTION 1jv7 
BACTERIORHODOPSIN O-LIKE INTERMEDIATE STATE OF THE D85S MUTANT AT 2.25 ANGSTROM RESOLUTION 1kg8 
X-ray structure of an early-M intermediate of bacteriorhodopsin 1kg9 
Structure of a ""mock-trapped"" early-M intermediate of bacteriorhosopsin 1kgb 
structure of ground-state bacteriorhodopsin 1kme 
CRYSTAL STRUCTURE OF BACTERIORHODOPSIN CRYSTALLIZED FROM BICELLES 1l0m 
Solution structure of Bacteriorhodopsin 1m0k 
BACTERIORHODOPSIN K INTERMEDIATE AT 1.43 A RESOLUTION 1m0l 
BACTERIORHODOPSIN/LIPID COMPLEX AT 1.47 A RESOLUTION 1m0m 
BACTERIORHODOPSIN M1 INTERMEDIATE AT 1.43 A RESOLUTION 1mgy 
Structure of the D85S mutant of bacteriorhodopsin with bromide bound 1o0a 
BACTERIORHODOPSIN L INTERMEDIATE AT 1.62 A RESOLUTION 1p8h 
BACTERIORHODOPSIN M1 INTERMEDIATE PRODUCED AT ROOM TEMPERATURE 1p8i 
F219L BACTERIORHODOPSIN MUTANT 1p8u 
BACTERIORHODOPSIN N' INTERMEDIATE AT 1.62 A RESOLUTION 1pxr 
Structure of Pro50Ala mutant of Bacteriorhodopsin 1pxs 
Structure of Met56Ala mutant of Bacteriorhodopsin 1py6 
Bacteriorhodopsin crystallized from bicells 1q5i 
Crystal structure of bacteriorhodopsin mutant P186A crystallized from bicelles 1q5j 
Crystal structure of bacteriorhodopsin mutant P91A crystallized from bicelles 1qhj 
X-RAY STRUCTURE OF BACTERIORHODOPSIN GROWN IN LIPIDIC CUBIC PHASES 1qko 
HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE 1qkp 
HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE 1qm8 
Structure of Bacteriorhodopsin at 100 K 1r2n 
NMR structure of the all-trans retinal in dark-adapted Bacteriorhodopsin 1r84 
NMR structure of the 13-cis-15-syn retinal in dark_adapted bacteriorhodopsin 1s51 
Thr24Ser Bacteriorhodopsin 1s52 
Thr24Val Bacteriorhodopsin 1s53 
Thr46Ser Bacteriorhodopsin 1s54 
Thr24Ala Bacteriorhodopsin 1s8j 
Nitrate-bound D85S mutant of bacteriorhodopsin 1s8l 
Anion-free form of the D85S mutant of bacteriorhodopsin from crystals grown in the presence of halide 1tn0 
Structure of bacterorhodopsin mutant A51P 1tn5 
Structure of bacterorhodopsin mutant K41P 1uaz 
Crystal structure of archaerhodopsin-1 1ucq 
Crystal structure of the L intermediate of bacteriorhodopsin 1vgo 
Crystal Structure of Archaerhodopsin-2 1vjm 
Deformation of helix C in the low-temperature L-intermediate of bacteriorhodopsin 1x0i 
Crystal Structure of the Acid Blue Form of Bacteriorhodopsin 1x0k 
Crystal Structure of Bacteriorhodopsin at pH 10 1x0s 
Crystal structure of the 13-cis isomer of bacteriorhodopsin 1xio 
Anabaena sensory rhodopsin 1xji 
Bacteriorhodopsin crystallized in bicelles at room temperature 2at9 
STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM BY ELECTRON CRYSTALLOGRAPHY 2brd 
CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN PURPLE MEMBRANE 2ei4 
Trimeric complex of archaerhodopsin-2 2f93 
K Intermediate Structure of Sensory Rhodopsin II/Transducer Complex in Combination with the Ground State Structure 2f95 
M intermediate structure of sensory rhodopsin II/transducer complex in combination with the ground state structure 2i1x 
Bacteriorhodopsin/lipid complex, D96A mutant 2i20 
Bacteriorhodopsin/lipid complex, M state of D96A mutant 2i21 
Bacteriorhodopsin/lipid complex, T46V mutant 2jaf 
ground state and L1 intermediate of halorhodopsin 2jag 
ground state and L1 intermediate of halorhodopsin 2ksy 
Solution nmr structure of sensory rhodopsin II 2l6x 
Solution NMR Structure of Proteorhodopsin. 2m3g 
Structure of Anabaena Sensory Rhodopsin Determined by Solid State NMR Spectroscopy 2ntu 
Bacteriorhodopsin, wild type, before illumination 2ntw 
Bacteriorhodopsin, wild type, after illumination to produce the L intermediate 2wjk 
Bacteriorhodopsin mutant E204D 2wjl 
Bacteriorhodopsin mutant E194D 2z55 
Bacterioruberin in the trimeric structure of archaerhodopsin-2 2zfe 
Crystal structure of bacteriorhodopsin-xenon complex 2zzl 
Structure of bacteriorhodopsin's M intermediate at pH 7 3a7k 
Crystal structure of halorhodopsin from Natronomonas pharaonis 3abw 
Crystal structure of pharaonis halorhodopsin in complex with azide ion 3am6 
Crystal structure of the proton pumping rhodopsin AR2 from marine alga Acetabularia acetabulum 3coc 
Crystal Structure of D115A mutant of Bacteriorhodopsin 3cod 
Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin 3ddl 
Crystallographic Structure of Xanthorhodopsin, a Light-Driven Ion Pump with Dual Chromophore 3han 
Crystal structure of bacteriorhodopsin mutant V49A crystallized from bicelles 3hao 
Crystal structure of bacteriorhodopsin mutant L94A crystallized from bicelles 3hap 
Crystal structure of bacteriorhodopsin mutant L111A crystallized from bicelles 3haq 
Crystal structure of bacteriorhodopsin mutant I148A crystallized from bicelles 3har 
Crystal structure of bacteriorhodopsin mutant I148V crystallized from bicelles 3has 
Crystal structure of bacteriorhodopsin mutant L152A crystallized from bicelles 3mbv 
Structure of bacterirhodopsin crystallized in betta-XylOC(16+4) meso phase 3ns0 
X-ray structure of bacteriorhodopsin 3nsb 
Structure of bacteriorhodopsin ground state before and after X-ray modification 3qap 
Crystal structure of Natronomonas pharaonis sensory rhodopsin II in the ground state 3qbg 
Anion-free blue form of pharaonis halorhodopsin 3qbi 
Crystal structure of an anion-free yellow form of pharaonis halorhodopsin 3qbk 
Bromide-bound form of pharaonis halorhodopsin 3qbl 
Pharaonis halorhodopsin complexed with nitrate 3qdc 
Crystal structure of Natronomonas pharaonis sensory rhodopsin II in the active state 3t45 
Crystal structure of bacteriorhodopsin mutant A215T, a phototaxis signaling mutant at 3.0 A resolution 3ug9 
Crystal Structure of the Closed State of Channelrhodopsin 3utv 
Crystal structure of bacteriorhodopsin mutant Y57F 3utw 
Crystal structure of bacteriorhodopsin mutant P50A/Y57F 3utx 
Crystal structure of bacteriorhodopsin mutant T46A 3uty 
Crystal structure of bacteriorhodopsin mutant P50A/T46A 3vhz 
Crystal structure of the trans isomer of the L93A mutant of bacteriorhodopsin 3vi0 
Crystal structure of the O intermediate of the L93A mutant of bacteriorhodopsin 3vvk 
An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin 3wqj 
3WQJ 3x3b 
3X3B 3x3c 
3X3C 4fbz 
Crystal structure of deltarhodopsin from Haloterrigena thermotolerans 4fpd 
Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway 4gyc 
Structure of the SRII(D75N mutant)/HtrII Complex in I212121 space group ("U" shape) 4hwl 
Crystal Structure Analysis of the Bacteriorhodopsin in Facial Amphiphile-7 DMPC Bicelle 4hyj 
Crystal structure of Exiguobacterium sibiricum rhodopsin 4hyx 
Crystal Structure Analysis of the Bacteriorhodopsin in Facial Amphiphile-4 DMPC Bicelle 4jq6 
Crystal structure of blue light-absorbing proteorhodopsin from Med12 at 2.3 Angstrom 4jr8 
Crystal structure of cruxrhodopsin-3 from Haloarcula vallismortis at 2.3 angstrom resolution 4kly 
Crystal structure of a blue-light absorbing proteorhodopsin mutant D97N from HOT75 4knf 
Crystal structure of a blue-light absorbing proteorhodopsin double-mutant D97N/Q105L from HOT75 4l35 
4L35 4md1 
4MD1 4md2 
4MD2 4ov0 
4OV0 4pxk 
4PXK 4qi1 
4QI1 4qid 
4QID 4qry 
4QRY 4tl3 
4TL3 4wav 
4WAV 4x31 
4X31 4x32 
4X32 4xtl 
4XTL 4xtn 
4XTN 4xto 
4XTO 4xxj 
4XXJ 4y9h 
4Y9H 4yzi 
4YZI 5a44 
5A44 5a45 
5A45 5ahy 
5AHY 5ahz 
5AHZ 5awz 
5AWZ 5ax0 
5AX0 5ax1 
5AX1 5azd 
5AZD 5b0w 
5B0W 5b2n 
5B2N 5b34 
5B34 5b35 
5B35 5br2 
5BR2 5br5 
5BR5 5etz 
5ETZ 5fjg 
5FJG 5g28 
5G28 5g2a 
5G2A 5g2c 
5G2C 5g2d 
5G2D 5g36 
5G36 5g54 
5G54 5j7a 
5J7A - Links (links to other resources describing this domain)
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PFAM Bac_rhodopsin INTERPRO IPR001425