SMART: Bac_rhodopsin domain annotation

Bac_rhodopsin Bacteriorhodopsin-like protein

SMART accession number:	SM01021
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. Some fungal examples are: O74870, P25619, P38079, Q12117.
GO process:	ion transport (GO:0006811)
GO component:	membrane (GO:0016020)
GO function:	ion channel activity (GO:0005216)
Family alignment:	View or

There are 327 Bac_rhodopsin domains in 327 proteins in SMART's nrdb database.

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Evolution (species in which this domain is found)
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Go to specific node: Saccharomyces cerevisiae
Cellular role (predicted cellular role)
Cellular role: signalling
Literature (relevant references for this domain)
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 of halorhodopsin t203v
2jag		L1-intermediate of halorhodopsin t203v
2ntu		Bacteriorhodopsin, wild type, before illumination
2ntw		Bacteriorhodopsin, wild type, after illumination to produce the l intermediate
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
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

Links (links to other resources describing this domain)
PFAM Bac_rhodopsin
INTERPRO IPR001425

PFAM	Bac_rhodopsin
INTERPRO	IPR001425