photosynthetic reaction center family protein is a subunit of a photosynthetic system that utilizes light-induced electron transfer to generate protons that power reactions such as the synthesis of ATP, similar to photosystem II protein D
D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction ...
1-283
0e+00
D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction center; This protein superfamily contains the D1, D2 subunits of the photosystem II (PS II) and the M, L subunits of the bacterial photosynthetic reaction center (RC). These four proteins are highly homologous and share a common fold. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Bacterial photosynthetic reaction center (RC) complex is found in photosynthetic bacteria, such as purple bacteria and other proteobacteria species. It couples light-induced electron transfer to proton pumping across the membrane by reactions of a quinone molecule (QB) that binds two electrons and two protons at the active site. Protons are translocated from the bacterial cytoplasm to the periplasmic space, generating an electrochemical gradient of protons (the protonmotive force) that can be used to power reactions such as the synthesis of ATP.
The actual alignment was detected with superfamily member TIGR01151:
Pssm-ID: 447584 [Multi-domain] Cd Length: 360 Bit Score: 543.76 E-value: 0e+00
photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI ...
1-283
0e+00
photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI subunit (also called Q(B)) in bacterial and its equivalents in chloroplast of algae and higher plants. Photosystem II is many ways functionally equivalent to bacterial reaction center. At the core of Photosystem II are several light harvesting cofactors including plastoquinones, pheophytins, phyloquinones etc. These cofactors are intimately associated with the polypeptides, which principally including subunits DI, DII, Cyt.b, Cyt.f and iron-sulphur protein. Together they participate in the electron transfer reactions that lead to the net production of the reducting equivalents in the form of NADPH, which are used for reduction of CO2 to carbohydrates(C6H1206). Phosystem II operates during oxygenic photosynthesis and principal electron donor is H2O. Although no structural data is presently available, a huge body of literature exits that describes function using a variety of biochemical and biophysical techniques. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis]
Pssm-ID: 130221 [Multi-domain] Cd Length: 360 Bit Score: 543.76 E-value: 0e+00
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
1-283
0e+00
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Molecular dioxygen is released as a by-product. PS II can be described as containing two parts: the photochemical part and the catalytic part. The photochemical portion promotes the fast, efficient light-induced charge separation and stabilization that occur when light is absorbed by chlorophyll. The catalytic portion, where water is oxidized, involves a cluster of Mn ions close to a redox-active tyrosine residue. The Mn cluster and its ligands form a functional unit called the oxygen-evolving complex (OEC) or the water-oxidizing complex (WOC). The D1 and D2 subunits are a pair of interwined polypeptides. They contain all the cofactors involved directly in water oxidation and plastoquinone reduction. The D1 subunit contains the Mn cluster that constitutes the site of water oxidation. D1 and D2 are highly homologous and are also similar to the L and M proteins in bacterial photosynthetic reaction centers.
Pssm-ID: 187747 Cd Length: 338 Bit Score: 536.77 E-value: 0e+00
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II ...
1-283
9.75e-153
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II reaction center D1, PsbA is part of the Pathway/BioSystem: Photosystem II
Pssm-ID: 444426 Cd Length: 356 Bit Score: 430.67 E-value: 9.75e-153
photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI ...
1-283
0e+00
photosystem II, DI subunit (also called Q(B)); This model describes the Photosystem II, DI subunit (also called Q(B)) in bacterial and its equivalents in chloroplast of algae and higher plants. Photosystem II is many ways functionally equivalent to bacterial reaction center. At the core of Photosystem II are several light harvesting cofactors including plastoquinones, pheophytins, phyloquinones etc. These cofactors are intimately associated with the polypeptides, which principally including subunits DI, DII, Cyt.b, Cyt.f and iron-sulphur protein. Together they participate in the electron transfer reactions that lead to the net production of the reducting equivalents in the form of NADPH, which are used for reduction of CO2 to carbohydrates(C6H1206). Phosystem II operates during oxygenic photosynthesis and principal electron donor is H2O. Although no structural data is presently available, a huge body of literature exits that describes function using a variety of biochemical and biophysical techniques. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis]
Pssm-ID: 130221 [Multi-domain] Cd Length: 360 Bit Score: 543.76 E-value: 0e+00
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
1-283
0e+00
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Molecular dioxygen is released as a by-product. PS II can be described as containing two parts: the photochemical part and the catalytic part. The photochemical portion promotes the fast, efficient light-induced charge separation and stabilization that occur when light is absorbed by chlorophyll. The catalytic portion, where water is oxidized, involves a cluster of Mn ions close to a redox-active tyrosine residue. The Mn cluster and its ligands form a functional unit called the oxygen-evolving complex (OEC) or the water-oxidizing complex (WOC). The D1 and D2 subunits are a pair of interwined polypeptides. They contain all the cofactors involved directly in water oxidation and plastoquinone reduction. The D1 subunit contains the Mn cluster that constitutes the site of water oxidation. D1 and D2 are highly homologous and are also similar to the L and M proteins in bacterial photosynthetic reaction centers.
Pssm-ID: 187747 Cd Length: 338 Bit Score: 536.77 E-value: 0e+00
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II ...
1-283
9.75e-153
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II reaction center D1, PsbA is part of the Pathway/BioSystem: Photosystem II
Pssm-ID: 444426 Cd Length: 356 Bit Score: 430.67 E-value: 9.75e-153
D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction ...
78-266
9.90e-55
D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction center; This protein superfamily contains the D1, D2 subunits of the photosystem II (PS II) and the M, L subunits of the bacterial photosynthetic reaction center (RC). These four proteins are highly homologous and share a common fold. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Bacterial photosynthetic reaction center (RC) complex is found in photosynthetic bacteria, such as purple bacteria and other proteobacteria species. It couples light-induced electron transfer to proton pumping across the membrane by reactions of a quinone molecule (QB) that binds two electrons and two protons at the active site. Protons are translocated from the bacterial cytoplasm to the periplasmic space, generating an electrochemical gradient of protons (the protonmotive force) that can be used to power reactions such as the synthesis of ATP.
Pssm-ID: 187745 [Multi-domain] Cd Length: 199 Bit Score: 175.72 E-value: 9.90e-55
D2 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
1-275
6.67e-42
D2 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Molecular dioxygen is released as a by-product. PS II can be described as containing two parts: the photochemical part and the catalytic part. The photochemical portion promotes the fast, efficient light-induced charge separation and stabilization that occur when light is absorbed by chlorophyll. The catalytic portion, where water is oxidized, involves a cluster of Mn ions close to a redox-active tyrosine residue. The Mn cluster and its ligands form a functional unit called the oxygen-evolving complex (OEC) or the water-oxidizing complex (WOC). The D1 and D2 subunits are a pair of intertwined polypeptides. They contain all the cofactors involved directly in water oxidation and plastoquinone reduction. D1 and D2 are highly homologous and are also similar to the L and M proteins in bacterial photosynthetic reaction centers.
Pssm-ID: 187746 Cd Length: 339 Bit Score: 147.05 E-value: 6.67e-42
Subunit L of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction ...
82-194
1.43e-06
Subunit L of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction center (RC) complex, subunit L. The bacterial photosynthetic reaction center couples light-induced electron transfer with pumping protons across the membrane using reactions involving a quinone molecule (QB) that binds two electrons and two protons at the active site. The reaction center consists of three membrane-bound subunits, designated L, M, and H, plus an additional extracellular cytochrome subunit. The L and M subunits are arranged around an axis of 2-fold rotational symmetry perpendicular to the membrane, forming a scaffold that maintains the cofactors in a precise configuration. The L and M subunits have both sequence and structural similarity, suggesting a common evolutionary origin. The L and M subunits bind noncovalently to the nine cofactors in 2-fold symmetric branches: four bacteriochlorophylls (Bchl), two bacteriopheophytins (Bphe), two ubiquinone molecules (QA and QB), and a non-heme iron. Two Bchls on the periplasmic side of the membrane form the 'special pair' or dimer which is the primary electron donor for the photosynthetic reactions. The electron transfer reaction proceeds from the dimer to an intermediate acceptor (PA), a primary quinone (QA), and a secondary quinone (QB). Protons are translocated from the bacterial cytoplasm to the periplasmic space, generating an electrochemical gradient of protons (the protonmotive force) that can be used to power reactions such as ATP synthesis. The RC complex is found in photosynthetic bacteria, such as purple bacteria and other proteobacteria species.
Pssm-ID: 187748 Cd Length: 273 Bit Score: 48.59 E-value: 1.43e-06
Photosystem II reaction center D2, PsbD [Energy production and conversion]; Photosystem II ...
79-194
1.69e-04
Photosystem II reaction center D2, PsbD [Energy production and conversion]; Photosystem II reaction center D2, PsbD is part of the Pathway/BioSystem: Photosystem II
Pssm-ID: 444429 Cd Length: 316 Bit Score: 42.34 E-value: 1.69e-04
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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