TCDB is operated by the Saier Lab Bioinformatics Group
TCIDNameDomainKingdom/PhylumProtein(s)
3.E.2.1.1









Photosynthetic reaction center (RC).  Chromatophores containing the RC and light harvesting complex, LH1, can interface with a conducting support to allow capture and conversion of solar energy as an alternative fuel source (Harrold et al. 2013). This RC may catalyze transmembrane electron transfer, as for members of TC class 5 (Khatypov et al. 2017).

Bacteria
Proteobacteria
PRC of Rhodobacter sphaeroides
3.E.2.1.2









Reaction Center of four subunits, PufC, PufM, PufL and PuhA together with light-harvesting complex 1 of two subunits, LH1α and LH1β. The 3-D structure of the supercomplex with both RC and LH1 has been solved to 1.9 Å resolution (Kishi et al. 2020). The QB quinone binding site is converted to QBH2 upon light-induced reduction and QBH2 is transported to the quinone pool in the membrane through the LH1 ring. Quinone transport in Tch. tepidum occurs through the size-restricted hydrophobic channels in the closed LH1 ring and are consistent with structural studies that have revealed narrow hydrophobic channels in the Tch. tepidum LH1 transmembrane region (Kishi et al. 2020).

Bacteria
Proteobacteria
Reaction Center + light harvesting complex 1 of Thermochromatium tepidum (Chromatium tepidum)
PufC, reaction center cytochrome c subunit, 404 aas, D2Z0P5
PufM, reaction center M subunit, 325 aas and 5 TMSs, A8ASG6
PufL, reaction center L subunit, 281 aas and 5 TMSs, D2Z0P3
PuhA, reaction center H subunit, 259 aas and one N-terminal TMS, D2Z0P9
PufA, LH1α, light harvesting complex subunit α of 61 aas and 1 TMS
PufB, LH1β, light harvesting complex subunit β of 47 aas and 1 TMS
3.E.2.2.1









Cyanobacterial photosystem II in thylakoid membranes (Sarcina et al. 2006). Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S0 to S4). To reveal the mechanism of water oxidation, Suga et al. 2019 analyzed structures of PSII of Thermosynechococcus vulcanus in the S1, S2, and S3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S2, but flipping of D1 Glu189 upon transition to S3 led to the opening of a water channel and provided a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn4CaO6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states revealed cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation (Suga et al. 2019). The oxygen-evolving complex (OEC) is located at a node of five water channels involved in proton release, balancing the net charge of the OEC, and inlet of substrate water (Shen 2015). The PsbJ protein is required for photosystem II activity in centers lacking the PsbO and PsbV lumenal subunits (Choo et al. 2021).

The mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), have been reviewed by Kaur et al. 2021. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons, and gates, which block backflow of the protons. PLS and gates must be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths have different design features (Kaur et al. 2021).

Bacteria
Cyanobacteria
PRC of Synechococcus PCC7942 Photosystem II
PsbA, 360 aas, P04996
PsbC, 461 aas, P11004
PsbD, 352 aas, P11005
PsbE, 83 aas, Q8KPP3
PsbF, 44 aas. Q8KPP2
PsbJ, 39 aas, Q8KPP0
PsbK, 45 aas, Q79AV1
PsbI, 39 aas, Q31MI4
PsbL, 40 aas, Q8KPP1
PsbM, 35 aas, Q31QD8
3.E.2.2.2









Cyanobacterial thylakoid membrane photosystem II.  Biophotovoltaic devices can be used to employ cyanobacteria such as Synechocystis PCC6803 at the anode of a microbial fuel cell to generate electrical power (Cereda et al. 2014).

Bacteria
Cyanobacteria
PRC of Synechocystis PCC6803 Photosystem II