TCDB is operated by the Saier Lab Bioinformatics Group
TCIDNameOrganismal TypeExample
3.E.1.1.1









Bacteriorhodopsin. Proton efflux occurs via a transient linear water-molecule chain in a hydrophobic section of the Brho channel between Asp96 and Asp85 (Freier et al., 2011).  It can be converted to a chloride uptake pump by a single amino acid substitution at position 85.  However, halorhodopsin (3.E.1.2.1), which pumps chloride ions (Cl-) into the cell, apparently does not use hydrogen-bonded water molecules for Cl- transport (Muroda et al. 2012).

Archaea

Bacteriorhodopsin of Halobacterium salinarum
3.E.1.1.2









Archaerhodopsin-2 (aR2) (a retinal protein-carotenoid complex) (Yoshimura and Kouyama, 2007).
Euryarchaeota
aR2 of Halorubrum sp. aus-2 (P29563)
3.E.1.1.3









"Middle" rhodopsin or Brhol; has 11-cis-retinal and shows intermediate properties between Brho and sensory rhodopsin II (Sudo et al., 2011).

Euryarchaeota

Middle rhodopsin of Haloquadratum walsbyi (G0LFX8)
3.E.1.1.4









Archaerhodopsin 3, AR3.  Pumps protons in response to light absorption (Saint Clair et al. 2012). 86% identical to 3.E.1.1.2.

Archaea

AR3 of Halorubrum sodomense
3.E.1.2.1









Halorhodopsin Cl- uptake pump; homologous to bacteriorhodopsin (3.E.1.1.1) which can be converted from a proton pump with outwardly directed polarity into a chloride pump with inwardly directed polarity via a single amino acid substitution at position 85.  Cl- transport does not depend on water hydrogen bonded to the chromophore as in the case of bacteriorhodopsin (Muroda et al. 2012).

Archaea

Halorhodopsin of Halobacterium salinarum
3.E.1.2.2









Halorhodopsin (a trimer with the carotenoid, bacterioruberin, binding to crevices between adjacent protein subunits in the trimeric assembly; Sasaki et al., 2012). Structure known to 2.0 Å resolution (Kouyama et al., 2010) (PDB# 3A7K)).

Archaea

Halorhodopsin of Natronomonas pharaonis (P15647)
3.E.1.3.1









Sensory rhodopsin I
Archaea
Sensory rhodopsin I of Halobacterium salinarum
3.E.1.3.2









Sensory rhodopsin II.  The 3-d structure has been solved by NMR (Gautier and Nietlispach 2012).

Archaea

Sensory rhodopsin II (phoborhodopsin) of Halobacterium salinarum
3.E.1.3.3









Sensory rhodopsin II, SR2 (Sop2). The NMR solution structure of the detergent solubilized protein is in good agreement with the x-ray structure (Gautier et al. 2010).

Archaea

SRII of Natronomonas pharaonis (P42196)
3.E.1.4.1









Heat shock protein HSP30
Yeast
HSP30 of Saccharomyces cerevisiae
3.E.1.4.2









Retinal binding protein, NOP-1
Fungi
NOP-1 of Neurospora crassa
3.E.1.4.3









H+ pumping rhodopsin (Waschuk et al., 2005)
Fungi
Rhodopsin of Leptosphaeria maculans (AAG01180)
3.E.1.4.4









Bacteriorhodopsin-like protein, c102333

Plants (Chlorophyta)

c102333 of Acetabularia acetabulum (Q1AJZ3)
3.E.1.4.5









Opsin 1, Bacteriorhodopsin-like protein

Cryptophyta

Opsin 1 of Guillardia theta (Q2QCJ4)
3.E.1.4.6









Probable chaparone membrane protein related to Hsp30, Mrh1 (320 aas; 33% identical to Hsp30p). This protein and its two paralogues, Hsp30 and YR02, are induced by heat shock and are present primarily in the plasma membrane (Wu et al. 2000).

Fungi

Mrh1p of Saccharomyces cerevisiae (Q12117)
3.E.1.4.7









Cyanorhodopsin of 334 aas and 7 TMSs, Ops1 (Frassanito et al. 2010).

Algae (Glycophyta)

Cyanorhodopsin of Cyanophora paradoxa
3.E.1.5.1









Pentachlorophenone-induced protein, FDD123
Fungi
FDD123 of Coriolus versicolor
3.E.1.6.1









Proteorhopdopsin (exhibits variable vectorality: H+ is pumped out at basic pH but not at acidic pH; see Friedrich et al., 2002) Proteorbodopsin has been used to measure membrane potentials and electrical spiking in E. coli (Kralj et al., 2011; Ward et al., 2011).

Bacteria

Proteorhodopsin from an uncultured γ-proteobacterium EOAC 31A08
3.E.1.6.2









Xanthorhodopsin, a proton pump with a carotenoid antenna, salinixanthin (Lanyi and Balashov 2008). A crystal structure (1.9 Å resolution) is available (Luecke et al., 2008).

Bacteroidetes
Xanthorhodopsin with a salinixanthin chromophore of Salinibacter ruber (Q2S2F8)
3.E.1.6.3









Rhodopsin (associates with salinixanthin, the light-harvesting carotenoid antenna of xanthorhodopsin; Imasheva et al., 2009Hashimoto et al., 2010).

Bacteria

Rhodopsin of Gloeobacter violaceus (Q7NP59)
3.E.1.6.4









Bacteriorhodopsin-like circadian clock related protein (Okamoto and Hastings, 2003)

Dinoflagellates (Alveolata)

BacRhodopsin of Pyrocystis lunula (Q8GZE7)
3.E.1.6.5









H+-pumping bacteriorhodopsin, Brho (Petrovskaya et al. 2010).

Bacteria

Brho of Exiguobacterium sibiricum (B1YFV8)
3.E.1.6.6









Proton pumping proteorhodopsin of 253 aas (Kimura et al. 2011).

Bacteroidetes

Proteorhodopsin of Nonlabens dokdonensis (Donghaeana dokdonensis)
3.E.1.7.1









Channelrhodopsin-1 (chlamyrhodopsin-3) (ChR1; Cop3; CSOA) (light-gated proton channel) (Nagel et al., 2003)
Algae
Channelrhodopsin-1 of Chlamydomonas reinhardtii
3.E.1.7.2









Channelrhodopsin-2 (chlamyrhodopsin-4; ChR2; Cop4; CSOB) (light-gated cation-selective ion channel (both monovalent and divalent cations are transported)) (Nagel et al., 2003). Berndt et al. (2010) showed that ChR2 has two open states with differing ion selectivities. The channel is fairly nonspecific at the beginning of a light pulse, and becomes more specific for protons during longer periods of light exposure. Residues involved in channel closure have been identified (Bamann et al. 2010).  ChR2 is 712 aas long; the MR domain is N-terminal. Homologues of the C-terminal domain of about 400aas is found fused to other porters or alone in many phyla of eukaryotes. This domain is found in TC entries 9.A.14.1.1 (MLP1 and 2 of the nuclear pore complex) and 3.A.18.1.1 (pinin of the nuclear mRNA export complex) and many other proteins. 

Blue light illumination of ChR2 activates an intrinsic leak channel conductive for cations. Sequence comparison of ChR2 with the related ChR1 protein revealed a cluster of charged amino acids within the predicted transmembrane domain 2 (TM2), which includes glutamates E90, E97 and E101. Charge inversion substitutions altered ChR2 function, replacement of E90 by lysine or alanine resulted in differential effects on H+- and Na+-mediated currents. These results are consistent with this glutamate side chain within TMS2 contributing to ion flux through and the cation selectivity of ChR2 (Ruffert et al., 2011). Glutamate residue-97 lies in the outer pore where it interacts with a cation to facilitate dehydration. This residue is also the primary binding target of Gd3+(Tanimoto et al., 2012). 

Algae

Channelrhodopsin-2 of Chlamydomonas reinhardtii (Q8RUT8)
3.E.1.7.3









Channelrhodopsin-2 light-gated ion channel. A 6Å projection map is available (Müller et al., 2011). Glutamate residue-97 lies in the outer pore where it interacts with a cation to facilitate dehydration. This residue is also the primary binding target of Gd3+ (Tanimoto et al., 2012).

Channelrhodopsin-2 of Volvox carteri (B4Y105)
3.E.1.7.4









Channelopsin, MChR1 (Govorunova et al., 2011).

Plants

MChR1 of Mesostigma viride (F8UVI5)
3.E.1.8.1









Sensory rhodopsin (geen-light-activated photoreceptor; does not transport ions) (Jung et al., 2003). Has all-trans-retinal when dark adapted, but 11-cis-retinal when light adapted due to reversible interconversion (Sineshchekov et al., 2005)

Bacteria
Sensory rhodopsin of Anabaena (Nostoc) sp. PCC7120