Reviewed, UniProtKB/Swiss-Prot P02945 (BACR_HALSA)

Names and origin

Protein names

Recommended name:
    Bacteriorhodopsin
      Short name=BR

Gene names

Name:	bop
Ordered Locus Names:	VNG_1467G

Organism

Halobacterium salinarium (Halobacterium halobium) [Complete proteome] [HAMAP]

Taxonomic identifier

2242 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Halobacteria › Halobacteriales › Halobacteriaceae › Halobacterium

Protein attributes

Sequence length	262 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Light-driven proton pump.
Subunit structure	Homotrimer.
Subcellular location	Cell membrane; Multi-pass membrane protein.
Sequence similarities	Belongs to the archaeal/bacterial/fungal opsin family.
Mass spectrometry	Molecular mass is 27052.5±2.7 Da from positions 14 - 261. Determined by ESI. Ref.10

Ontologies

Keywords
Biological process	Hydrogen ion transport Ion transport Sensory transduction Transport
Cellular component	Cell membrane Membrane
Domain	Transmembrane
Ligand	Chromophore
Molecular function	Photoreceptor protein Receptor Retinal protein
PTM	Pyrrolidone carboxylic acid
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	phototransduction Inferred from electronic annotation. Source: UniProtKB-KW protein-chromophore linkage Inferred from electronic annotation. Source: UniProtKB-KW proton transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	integral to membrane Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ion channel activity Inferred from electronic annotation. Source: InterPro photoreceptor activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Propeptide

1 – 13

13

PRO_0000020246

Chain

14 – 262

249

Bacteriorhodopsin

PRO_0000020247

Regions

Topological domain

14 – 23

10

Extracellular

Transmembrane

24 – 42

19

Helix A

Topological domain

43 – 56

14

Cytoplasmic

Transmembrane

57 – 75

19

Helix B

Topological domain

76 – 91

16

Extracellular

Transmembrane

92 – 109

18

Helix C

Topological domain

110 – 120

11

Cytoplasmic

Transmembrane

121 – 140

20

Helix D

Topological domain

141 – 147

7

Extracellular

Transmembrane

148 – 167

20

Helix E

Topological domain

168 – 185

18

Cytoplasmic

Transmembrane

186 – 204

19

Helix F

Topological domain

205 – 216

12

Extracellular

Transmembrane

217 – 236

20

Helix G

Topological domain

237 – 262

26

Cytoplasmic

Sites

Site

98

1

Primary proton acceptor

Amino acid modifications

Modified residue

14

1

Pyrrolidone carboxylic acid

Modified residue

229

1

N6-(retinylidene)lysine

Experimental info

Sequence conflict

118

1

Q → E AA sequence Ref.6

Sequence conflict

124

1

L → I AA sequence Ref.6

Sequence conflict

130

1

I → L AA sequence Ref.6

Sequence conflict

151

1

Missing AA sequence Ref.6

Sequence conflict

159

1

L → S AA sequence Ref.6

Sequence conflict

219

1

L → A AA sequence Ref.6

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

262

Helix Strand Turn

Details...

Helix

23 – 43

21

Turn

44 – 46

3

Helix

50 – 74

25

Turn

75 – 78

4

Beta strand

80 – 84

5

Beta strand

87 – 91

5

Helix

94 – 113

20

Helix

118 – 140

23

Helix

144 – 167

24

Helix

178 – 204

27

Turn

206 – 209

4

Helix

214 – 238

25

Helix

240 – 242

3

Sequences

	Sequence		Length	Mass (Da)
	P02945-1 [UniParc]. Last modified July 1, 1989. Version 2. Checksum: 38AC8A364C8C7F21	FASTA	262	28,256
	10 20 30 40 50 60 MLELLPTAVE GVSQAQITGR PEWIWLALGT ALMGLGTLYF LVKGMGVSDP DAKKFYAITT 70 80 90 100 110 120 LVPAIAFTMY LSMLLGYGLT MVPFGGEQNP IYWARYADWL FTTPLLLLDL ALLVDADQGT 130 140 150 160 170 180 ILALVGADGI MIGTGLVGAL TKVYSYRFVW WAISTAAMLY ILYVLFFGFT SKAESMRPEV 190 200 210 220 230 240 ASTFKVLRNV TVVLWSAYPV VWLIGSEGAG IVPLNIETLL FMVLDVSAKV GFGLILLRSR 250 260 AIFGEAEAPE PSAGDGAAAT SD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The bacteriorhodopsin gene." Dunn R.J., McCoy J., Simsek M., Majumdar A., Chang S.H., RajBhandary U.L., Khorana H.G. Proc. Natl. Acad. Sci. U.S.A. 78:6744-6748(1981) [PubMed: 12049093] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: S9.
[2]	"Studies on the light-transducing pigment bacteriorhodopsin." Dunn R.J., Hackett N.R., Huang K.-S., Jones S., Khorana H.G., Lee D.-S., Liao M.-J., Lo K.-M., McCoy J., Noguchi S., Radhakrishnan R., RajBhandary U.L. Cold Spring Harb. Symp. Quant. Biol. 48:853-862(1983) [PubMed: 6327180] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Bacterioopsin, haloopsin, and sensory opsin I of the halobacterial isolate Halobacterium sp. strain SG1: three new members of a growing family." Soppa J., Duschl J., Oesterhelt D. J. Bacteriol. 175:2720-2726(1993) [PubMed: 8478333] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: SG1.
[4]	"Bacteriorhodopsin precursor. Characterization and its integration into the purple membrane." Seehra J.S., Khorana H.G. J. Biol. Chem. 259:4187-4193(1984) [PubMed: 6706999] [Abstract] Cited for: PROTEIN SEQUENCE.
[5]	"Genome sequence of Halobacterium species NRC-1." Ng W.V., Kennedy S.P., Mahairas G.G., Berquist B., Pan M., Shukla H.D., Lasky S.R., Baliga N.S., Thorsson V., Sbrogna J., Swartzell S., Weir D., Hall J., Dahl T.A., Welti R., Goo Y.A., Leithauser B., Keller K. , Cruz R., Danson M.J., Hough D.W., Maddocks D.G., Jablonski P.E., Krebs M.P., Angevine C.M., Dale H., Isenbarger T.A., Peck R.F., Pohlschroder M., Spudich J.L., Jung K.-H., Alam M., Freitas T., Hou S., Daniels C.J., Dennis P.P., Omer A.D., Ebhardt H., Lowe T.M., Liang P., Riley M., Hood L., DasSarma S. Proc. Natl. Acad. Sci. U.S.A. 97:12176-12181(2000) [PubMed: 11016950] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700922 / JCM 11081 / NRC-1.
[6]	"The amino acid sequence of bacteriorhodopsin." Ovchinnikov Y.A., Abdulaev N.G., Feigina M.Y., Kiselev A.V., Lobanov N.A., Nasimov I.V. Bioorg. Khim. 4:1573-1574(1978) Cited for: PROTEIN SEQUENCE OF 14-261.
[7]	"Amino acid sequence of bacteriorhodopsin." Khorana H.G., Gerber G.E., Herlihy W.C., Gray C.P., Anderegg R.J., Nihei K., Biemann K. Proc. Natl. Acad. Sci. U.S.A. 76:5046-5050(1979) [PubMed: 291920] [Abstract] Cited for: PROTEIN SEQUENCE OF 14-261.
[8]	"Mass spectrometric analysis of integral membrane proteins: application to complete mapping of bacteriorhodopsins and rhodopsin." Ball L.E., Oatis J.E. Jr., Dharmasiri K., Busman M., Wang J., Cowden L.B., Galijatovic A., Chen N., Crouch R.K., Knapp D.R. Protein Sci. 7:758-764(1998) [PubMed: 9541408] [Abstract] Cited for: PROTEIN SEQUENCE OF 14-248, PYROGLUTAMATE FORMATION AT GLN-14.
[9]	"Attachment site(s) of retinal in bacteriorhodopsin." Katre N.V., Wolber P.K., Stoeckenius W., Stroud R.M. Proc. Natl. Acad. Sci. U.S.A. 78:4068-4072(1981) [PubMed: 6794028] [Abstract] Cited for: RETINAL-BINDING SITE.
[10]	"Electrospray-ionization mass spectrometry of intact intrinsic membrane proteins." Whitelegge J.P., Gundersen C.B., Faull K.F. Protein Sci. 7:1423-1430(1998) [PubMed: 9655347] [Abstract] Cited for: MASS SPECTROMETRY.
[11]	"Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure." Faham S., Bowie J.U. J. Mol. Biol. 316:1-6(2002) [PubMed: 11829498] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 14-244.
[12]	"Tertiary structure of bacteriorhodopsin. Positions and orientations of helices A and B in the structural map determined by neutron diffraction." Popot J.-L., Engleman D.M., Gurel O., Zaccai G. J. Mol. Biol. 210:829-847(1989) [PubMed: 2614846] [Abstract] Cited for: STRUCTURE BY NEUTRON DIFFRACTION.
[13]	"Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy." Henderson R., Baldwin J.M., Ceska T.A., Zemlin F., Beckmann E., Downing K.H. J. Mol. Biol. 213:899-929(1990) [PubMed: 2359127] [Abstract] Cited for: STRUCTURE BY ELECTRON MICROSCOPY (3.5 ANGSTROMS) OF 15-261.
[14]	"Electron-crystallographic refinement of the structure of bacteriorhodopsin." Grigorieff N., Ceska T.A., Downing K.H., Baldwin J.M., Henderson R. J. Mol. Biol. 259:393-421(1996) [PubMed: 8676377] [Abstract] Cited for: STRUCTURE BY ELECTRON MICROSCOPY (3.5 ANGSTROMS) OF 14-260.
[15]	"Three-dimensional structure of proteolytic fragment 163-231 of bacterioopsin determined from nuclear magnetic resonance data in solution." Barsukov I.L., Nolde D.E., Lomize A.L., Arseniev A.S. Eur. J. Biochem. 206:665-672(1992) [PubMed: 1606953] [Abstract] Cited for: STRUCTURE BY NMR OF 176-244.
[16]	"1H-15N-NMR studies of bacteriorhodopsin Halobacterium halobium. Conformational dynamics of the four-helical bundle." Orekhov V.Y., Abdulaeva G.V., Musina L.Y., Arseniev A.S. Eur. J. Biochem. 210:223-229(1992) [PubMed: 1332860] [Abstract] Cited for: STRUCTURE BY NMR OF 1-231.
[17]	"Surface of bacteriorhodopsin revealed by high-resolution electron crystallography." Kimura Y., Vassylyev D.G., Miyazawa A., Kidera A., Matsushima M., Mitsuoka K., Murata K., Hirai T., Fujiyoshi Y. Nature 389:206-211(1997) [PubMed: 9296502] [Abstract] Cited for: STRUCTURE BY ELECTRON MICROSCOPY (3.0 ANGSTROMS) OF 15-244.
[18]	"X-ray structure of bacteriorhodopsin at 2.5-A from microcrystals grown in lipidic cubic phases." Pebay-Peyroula E., Rummel G., Rosenbusch J.P., Landau E.M. Science 277:1676-1681(1997) [PubMed: 9287223] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 20-238.
[19]	"Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex." Essen L.-O., Siegert R., Lehmann W.D., Oesterhelt D. Proc. Natl. Acad. Sci. U.S.A. 95:11673-11678(1998) [PubMed: 9751724] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 15-245.
[20]	"Proton transfer pathways in bacteriorhodopsin at 2.3 Angstrom resolution." Luecke H., Richter H.-T., Lanyi J.K. Science 280:1934-1937(1998) [PubMed: 9632391] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 19-165.
[21]	"Structure of bacteriorhodopsin at 1.55-A resolution." Luecke H., Schobert B., Richter H.-T., Cartailler J.-P., Lanyi J.K. J. Mol. Biol. 291:899-911(1999) [PubMed: 10452895] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 18-244.
[22]	"High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle." Edman K., Nollert P., Royant A., Belrhali H., Pebay-Peyroula E., Hajdu J., Neutze R., Landau E.M. Nature 401:822-826(1999) [PubMed: 10548112] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 18-245.
[23]	"Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 A resolution." Belrhali H., Nollert P., Royant A., Menzel C., Rosenbusch J.P., Landau E.M., Pebay-Peyroula E. Structure 7:909-917(1999) [PubMed: 10467143] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 14-261.
[24]	"Coupling photoisomerization of retinal to directional transport in bacteriorhodopsin." Luecke H., Schobert B., Cartailler J.-P., Richter H.T., Rosengarth A., Needleman R., Lanyi J.K. J. Mol. Biol. 300:1237-1255(2000) [PubMed: 10903866] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 18-245.
[25]	"Helix deformation is coupled to vectorial proton transport in the photocycle of bacteriorhodopsin." Royant A., Edman K., Ursby T., Pebay-Peyroula E., Landau E.M., Neutze R. Nature 406:645-648(2000) [PubMed: 10949307] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 18-245.
[26]	"Molecular mechanism of vectorial proton translocation by bacteriorhodopsin." Subramaniam S., Henderson R. Nature 406:653-657(2000) [PubMed: 10949309] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF 14-262.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

V00474 Genomic DNA. Translation: CAA23744.1.
M11720 Genomic DNA. Translation: AAA72504.1.
X70293 Genomic DNA. Translation: CAA49774.1.
AE004437 Genomic DNA. Translation: AAG19772.1.

PIR

RAHSB. A93898.
H84300.

RefSeq

NP_280292.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AP9	X-ray	2.35	A	14-261	[»]
1AT9	X-ray	3.00	A	15-261	[»]
1BAC	model	-	A	14-261	[»]
1BAD	model	-	A	14-261	[»]
1BCT	NMR	-	A	176-244	[»]
1BHA	NMR	-	A	14-84	[»]
1BHB	NMR	-	A	14-84	[»]
1BM1	X-ray	3.50	A	15-253	[»]
1BRD	electron microscopy	-	A	15-261	[»]
1BRR	X-ray	2.90	A/B/C	15-253	[»]
1BRX	X-ray	2.30	A	15-261	[»]
1C3W	X-ray	1.55	A	18-244	[»]
1C8R	X-ray	1.80	A	14-262	[»]
1C8S	X-ray	2.00	A	18-235	[»]
1CWQ	X-ray	2.25	A/B	15-247	[»]
1DZE	X-ray	2.50	A	14-261	[»]
1E0P	X-ray	2.10	A	18-245	[»]
1F4Z	X-ray	1.80	A	18-244	[»]
1F50	X-ray	1.70	A	18-244	[»]
1FBB	X-ray	3.20	A	14-261	[»]
1FBK	X-ray	3.20	A	14-261	[»]
1IW6	X-ray	2.30	A	14-261	[»]
1IW9	X-ray	2.50	A	14-261	[»]
1IXF	X-ray	2.60	A	14-261	[»]
1JV6	X-ray	2.00	A	14-262	[»]
1JV7	X-ray	2.25	A	14-262	[»]
1KG8	X-ray	2.00	A	14-243	[»]
1KG9	X-ray	1.81	A	14-243	[»]
1KGB	X-ray	1.65	A	14-243	[»]
1KME	X-ray	2.00	A/B	14-244	[»]
1L0M	NMR	-	A	20-231	[»]
1M0K	X-ray	1.43	A	1-262	[»]
1M0L	X-ray	1.47	A	1-262	[»]
1M0M	X-ray	1.43	A	1-262	[»]
1MGY	X-ray	2.00	A	14-262	[»]
1O0A	X-ray	1.62	A	14-262	[»]
1P8H	X-ray	1.52	A	14-262	[»]
1P8I	X-ray	1.86	A	14-262	[»]
1P8U	X-ray	1.62	A	14-262	[»]
1PXR	X-ray	1.70	A/B	14-262	[»]
1PXS	X-ray	2.20	A/B	14-262	[»]
1PY6	X-ray	1.80	A/B	14-262	[»]
1Q5I	X-ray	2.30	A/B	14-262	[»]
1Q5J	X-ray	2.10	A/B	14-262	[»]
1QHJ	X-ray	1.90	A	14-261	[»]
1QKO	X-ray	2.10	A	14-261	[»]
1QKP	X-ray	2.10	A	14-261	[»]
1QM8	X-ray	2.50	A	14-261	[»]
1R2N	NMR	-	A	14-262	[»]
1R84	NMR	-	A	14-245	[»]
1S51	X-ray	2.00	A/B	18-244	[»]
1S52	X-ray	2.30	A/B	18-244	[»]
1S53	X-ray	2.00	A/B	18-244	[»]
1S54	X-ray	2.20	A/B	18-244	[»]
1S8J	X-ray	2.30	A	14-262	[»]
1S8L	X-ray	2.30	A	14-262	[»]
1TN0	X-ray	2.50	A/B	14-262	[»]
1TN5	X-ray	2.20	A/B	14-262	[»]
1UCQ	X-ray	2.40	A	14-262	[»]
1VJM	X-ray	2.30	A	14-262	[»]
1X0I	X-ray	2.30	1	14-261	[»]
1X0K	X-ray	2.60	1	14-261	[»]
1X0S	X-ray	2.50	A	14-261	[»]
1XJI	X-ray	2.20	A	15-261	[»]
2AT9	X-ray	3.00	A	15-253	[»]
2BRD	X-ray	3.50	A	15-261	[»]
2I1X	X-ray	2.00	A	14-262	[»]
2I20	X-ray	2.08	A	14-262	[»]
2I21	X-ray	1.84	A	14-262	[»]
2NTU	X-ray	1.53	A	14-262	[»]
2NTW	X-ray	1.53	A	14-262	[»]
2ZFE	X-ray	2.50	A	1-262	[»]
2ZZL	X-ray	2.03	A	1-262	[»]
3COC	X-ray	2.31	A/B	14-262	[»]
3COD	X-ray	2.70	A/B	14-262	[»]
3HAN	X-ray	2.75	A	14-262	[»]
3HAO	X-ray	2.49	A/B	14-262	[»]
3HAP	X-ray	1.60	A	14-262	[»]
3HAQ	X-ray	2.30	A	14-262	[»]
3HAR	X-ray	1.70	A	14-262	[»]
3HAS	X-ray	1.90	A	14-262	[»]

ModBase

Search...

Protein family/group databases

TCDB

3.E.1.1.1. ion-translocating microbial rhodopsin (MR) family.

Genome annotation databases

GeneID

1448071.

GenomeReviews

Gene locus VNG_1467G in contig AE004437_GR.

KEGG

hal:VNG1467G.

NMPDR

fig|64091.1.peg.1312.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

HBG498017.

OMA

FWTISTI.

Enzyme and pathway databases

BioCyc

HSP64091:VNG1467G-MON.

Family and domain databases

InterPro

IPR001425. Rhodopsin_bac.
IPR018229. Rhodopsin_retinal_BS.
[Graphical view]

Pfam

PF01036. Bac_rhodopsin. 1 hit.
[Graphical view]

PRINTS

PR00251. BACTRLOPSIN.

PROSITE

PS00950. BACTERIAL_OPSIN_1. 1 hit.
PS00327. BACTERIAL_OPSIN_RET. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

BACR_HALSA

Accession

Primary (citable) accession number: P02945
Secondary accession number(s): Q9HPU5

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 1, 1989
Last modified:	December 15, 2009
This is version 123 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)