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Conserved domains on  [gi|2223788631|gb|UOX28094|]
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photosystem II protein D1, partial (chloroplast) [Harveylithon sp. 9]

Protein Classification

photosynthetic reaction center family protein( domain architecture ID 607)

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

Gene Ontology:  GO:0045156|GO:0009772|GO:0016168|GO:0046872
PubMed:  15313239|11115630

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Photo_RC super family cl08220
D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction ...
 1-89 3.57e-60

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 cd09289:

Pssm-ID: 447584  Cd Length: 338  Bit Score: 186.24  E-value: 3.57e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223788631   1 AEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIRETTESESANNGYKFGQEEETYNIVAAHGYFGRLIFQYASFNN 80
Cdd:cd09289   182 AEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANAGYKFGQEEETYNIVAAHGYFGRLIFQYASFNN 261


                  ....*....
gi 2223788631  81 SRSLHFFLG 89
Cdd:cd09289   262 SRSLHFFLA 270
 
Name Accession Description Interval E-value
Photosystem-II_D1 cd09289
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 1-89 3.57e-60

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: 186.24  E-value: 3.57e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223788631   1 AEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIRETTESESANNGYKFGQEEETYNIVAAHGYFGRLIFQYASFNN 80
Cdd:cd09289   182 AEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANAGYKFGQEEETYNIVAAHGYFGRLIFQYASFNN 261


                  ....*....
gi 2223788631  81 SRSLHFFLG 89
Cdd:cd09289   262 SRSLHFFLA 270
PLN00056 PLN00056
photosystem Q(B) protein; Provisional
 1-89 3.02e-52

photosystem Q(B) protein; Provisional


Pssm-ID: 177687  Cd Length: 353  Bit Score: 166.46  E-value: 3.02e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223788631   1 AEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIRETTESESANNGYKFGQEEETYNIVAAHGYFGRLIFQYASFNN 80
Cdd:PLN00056  188 AEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFGQEEETYNIVAAHGYFGRLIFQYASFNN 267


                  ....*....
gi 2223788631  81 SRSLHFFLG 89
Cdd:PLN00056  268 SRSLHFFLA 276
PsbA COG5716
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II ...
 1-88 1.21e-44

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: 146.78  E-value: 1.21e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223788631   1 AEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIRETTESESANNGYKFGQEEETYNIVAAH-GYFGRLIFQYASFN 79
Cdd:COG5716   191 ADHNILMNPFHMLGVAGVYGGALLFAMHGSLVTSVLRRETTESESINAGYFGGQRELTYIVDRGTaGERARLFWRWTMGF 270


                  ....*....
gi 2223788631  80 NSRSLHFFL 88
Cdd:COG5716   271 NARSIHFWL 279
Photo_RC pfam00124
Photosynthetic reaction centre protein;
4-88 1.63e-23

Photosynthetic reaction centre protein;


Pssm-ID: 425477  Cd Length: 260  Bit Score: 89.61  E-value: 1.63e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223788631   4 NILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR-ETTESESANNGYKFGQEEETYnivaahgYFGRLIFQYasfnNSR 82
Cdd:pfam00124 147 NFLYNPFHMLGIAFLFGSALLLAMHGALVLSVLRPgGTREVESINDRGTAGEREATF-------WRWTMGFNA----NSR 215


                  ....*.
gi 2223788631  83 SLHFFL 88
Cdd:pfam00124 216 SIHRWG 221
 
Name Accession Description Interval E-value
Photosystem-II_D1 cd09289
D1 subunit of photosystem II (PS II); Photosystem II (PS II), D2 subunit. PS II is a ...
 1-89 3.57e-60

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: 186.24  E-value: 3.57e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223788631   1 AEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIRETTESESANNGYKFGQEEETYNIVAAHGYFGRLIFQYASFNN 80
Cdd:cd09289   182 AEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANAGYKFGQEEETYNIVAAHGYFGRLIFQYASFNN 261


                  ....*....
gi 2223788631  81 SRSLHFFLG 89
Cdd:cd09289   262 SRSLHFFLA 270
PLN00056 PLN00056
photosystem Q(B) protein; Provisional
 1-89 3.02e-52

photosystem Q(B) protein; Provisional


Pssm-ID: 177687  Cd Length: 353  Bit Score: 166.46  E-value: 3.02e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223788631   1 AEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIRETTESESANNGYKFGQEEETYNIVAAHGYFGRLIFQYASFNN 80
Cdd:PLN00056  188 AEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFGQEEETYNIVAAHGYFGRLIFQYASFNN 267


                  ....*....
gi 2223788631  81 SRSLHFFLG 89
Cdd:PLN00056  268 SRSLHFFLA 276
psbA CHL00003
photosystem II protein D1
 1-89 3.38e-49

photosystem II protein D1


Pssm-ID: 176948  Cd Length: 338  Bit Score: 158.12  E-value: 3.38e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223788631   1 AEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIRETTESESANNGYKFGQEEETYNIVAAHGYFGRLIFQYASFNN 80
Cdd:CHL00003  182 AEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANLGYKFGQEEETYNIVAAHGYFGRLIFQYASFNN 261


                  ....*....
gi 2223788631  81 SRSLHFFLG 89
Cdd:CHL00003  262 SRSLHFFLA 270
PsbA COG5716
Photosystem II reaction center D1, PsbA [Energy production and conversion]; Photosystem II ...
 1-88 1.21e-44

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: 146.78  E-value: 1.21e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223788631   1 AEHNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIRETTESESANNGYKFGQEEETYNIVAAH-GYFGRLIFQYASFN 79
Cdd:COG5716   191 ADHNILMNPFHMLGVAGVYGGALLFAMHGSLVTSVLRRETTESESINAGYFGGQRELTYIVDRGTaGERARLFWRWTMGF 270


                  ....*....
gi 2223788631  80 NSRSLHFFL 88
Cdd:COG5716   271 NARSIHFWL 279
Photo_RC pfam00124
Photosynthetic reaction centre protein;
4-88 1.63e-23

Photosynthetic reaction centre protein;


Pssm-ID: 425477  Cd Length: 260  Bit Score: 89.61  E-value: 1.63e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223788631   4 NILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIR-ETTESESANNGYKFGQEEETYnivaahgYFGRLIFQYasfnNSR 82
Cdd:pfam00124 147 NFLYNPFHMLGIAFLFGSALLLAMHGALVLSVLRPgGTREVESINDRGTAGEREATF-------WRWTMGFNA----NSR 215


                  ....*.
gi 2223788631  83 SLHFFL 88
Cdd:pfam00124 216 SIHRWG 221
Photo_RC cd09223
D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction ...
 4-88 6.51e-22

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: 84.43  E-value: 6.51e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2223788631   4 NILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIRETTESEsanngykfGQEEETYNIVAAHGYFGRLIFQYASFNnsRS 83
Cdd:cd09223   107 NWHYNPFHMLGVAFVFGGALLCAMHGALVLSVLNPEGEETE--------GQEAEEYNTAEHANYFWRDIFGYAIGN--RS 176


                  ....*
gi 2223788631  84 LHFFL 88
Cdd:cd09223   177 IHRFG 181
PRK14505 PRK14505
bifunctional photosynthetic reaction center subunit L/M; Provisional
 3-42 2.42e-03

bifunctional photosynthetic reaction center subunit L/M; Provisional


Pssm-ID: 172976  Cd Length: 643  Bit Score: 35.02  E-value: 2.42e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2223788631   3 HNILMHPFHQLGVAGVFGGSLFSAMHGSLVTSSLIRETTE 42
Cdd:PRK14505  204 YNFFYNPFHAIGITLLFASTLFLHMHGSAVLSEAKRNISD 243
Photo-RC_L cd09290
Subunit L of bacterial photosynthetic reaction center; Bacterial photosynthetic reaction ...
 4-34 6.33e-03

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: 33.95  E-value: 6.33e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2223788631   4 NILMHPFHQLGVAGVFGGSLFSAMHGSLVTS 34
Cdd:cd09290   167 NFHYNPAHMIAITFLFTNTLALSMHGSLILS 197
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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.
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