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HAMAP rule MF_01383

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General rule information [?]

Accession MF_01383
Dates 2-DEC-2008 (Created)
20-JUN-2023 (Last updated, Version 27)
Name PSII_PsbD_D2
Scope(s) Bacteria
Cyanobacteriota
Plastid
Template(s) D0VWR8 (PSBD_THEVL); Q8CM25 (PSBD_THEVB); P56761 (PSBD_ARATH); P06005 (PSBD_SPIOL); [ Recover all ]
Triggered by HAMAP; MF_01383 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier PSBD
Protein name RecName: Full=Photosystem II D2 protein;
                 Short=PSII D2 protein;
                 EC=1.10.3.9;
AltName: Full=Photosystem Q(A) protein;
Gene name Name=psbD;

Comments [?]

FUNCTIONPhotosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbD) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors. D2 is needed for assembly of a stable PSII complex.
CATALYTIC ACTIVITY Reaction=2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2; Xref=Rhea:RHEA:36359, Rhea:RHEA-COMP:9561, Rhea:RHEA-COMP:9562, ChEBI:CHEBI:15377, ChEBI:CHEBI:15379, ChEBI:CHEBI:17757, ChEBI:CHEBI:30212, ChEBI:CHEBI:62192; EC=1.10.3.9;
COFACTOR Note=The D1/D2 heterodimer binds P680, chlorophylls that are the primary electron donor of PSII, and subsequent electron acceptors. It shares a non-heme iron and each subunit binds pheophytin, quinone, additional chlorophylls, carotenoids and lipids. There is also a Cl(-1) ion associated with D1 and D2, which is required for oxygen evolution. The PSII complex binds additional chlorophylls, carotenoids and specific lipids.;
case <OC:Cyanobacteriota>
SUBUNITPSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Psb30/Ycf12, peripheral proteins PsbO, CyanoQ (PsbQ), PsbU, PsbV and a large number of cofactors. It forms dimeric complexes.
else
SUBUNITPSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Psb30/Ycf12, at least 3 peripheral proteins of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes.
end case
case <OG:Chloroplast>
SUBCELLULAR LOCATIONPlastid, chloroplast thylakoid membrane; Multi- pass membrane protein.
else case <OC:Gloeobacter>
SUBCELLULAR LOCATIONCell inner membrane; Multi-pass membrane protein.
else
SUBCELLULAR LOCATIONCellular thylakoid membrane; Multi-pass membrane protein.
end case
MISCELLANEOUS2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water.
SIMILARITYBelongs to the reaction center PufL/M/PsbA/D family.

Keywords [?]

Chlorophyll
Chromophore
Electron transport
Iron
Magnesium
Membrane
Metal-binding
Oxidoreductase
Photosynthesis
Photosystem II
case <OC:Gloeobacter>
Cell membrane
Cell inner membrane
else
Thylakoid
end case
Transmembrane
Transport
Transmembrane helix

Gene Ontology [?]

GO:0016168; Molecular function:chlorophyll binding
GO:0009055; Molecular function:electron transfer activity
GO:0005506; Molecular function:iron ion binding
GO:0015979; Biological process:photosynthesis
case <OG:Chloroplast>
GO:0009535; Cellular component:chloroplast thylakoid membrane
else case <OCellular component:Gloeobacter>
GO:0005886; Cellular component:plasma membrane
else; https://www.ebi.ac.uk/QuickGO/term/else
GO:0042651; Cellular component:thylakoid membrane
end case

Cross-references [?]

PROSITE PS00244; REACTION_CENTER; 1;
Pfam PF00124; Photo_RC; 1;
PRINTS PR00256; REACTNCENTRE; 1;
NCBIfam TIGR01152; PsbD; 1;

Features [?]

From: PSBD_THEVL (D0VWR8)
Key From To Description Tag Condition FTGroup
TRANSMEM 30 50 /note="Helical"
TRANSMEM 114 130 /note="Helical"
TRANSMEM 142 155 /note="Helical"
TRANSMEM 197 217 /note="Helical"
TRANSMEM 268 284 /note="Helical"
BINDING 107 107 /ligand="chlorophyll a"
/ligand_id="ChEBI:CHEBI:58416"
/ligand_label="ChlzD2"
/ligand_part="Mg"
/ligand_part_id="ChEBI:CHEBI:25107"
/note="axial binding residue"		 H
BINDING 187 187 /ligand="chlorophyll a"
/ligand_id="ChEBI:CHEBI:58416"
/ligand_label="PD2"
/ligand_part="Mg"
/ligand_part_id="ChEBI:CHEBI:25107"
/note="axial binding residue"		 H
BINDING 204 204 /ligand="Fe cation"
/ligand_id="ChEBI:CHEBI:24875"
/ligand_note="ligand shared with heterodimeric partner"		 H
BINDING 258 258 /ligand="Fe cation"
/ligand_id="ChEBI:CHEBI:24875"
/ligand_note="ligand shared with heterodimeric partner"		 H
BINDING 119 119 /ligand="pheophytin a"
/ligand_id="ChEBI:CHEBI:136840"
/ligand_label="D2"		 Q
BINDING 132 132 /ligand="pheophytin a"
/ligand_id="ChEBI:CHEBI:136840"
/ligand_label="D2"		 N
BINDING 204 204 /ligand="a plastoquinone"
/ligand_id="ChEBI:CHEBI:17757"
/ligand_label="Q(A)"		 H
BINDING 251 251 /ligand="a plastoquinone"
/ligand_id="ChEBI:CHEBI:17757"
/ligand_label="Q(A)"		 F

Additional information [?]

Size range 350-365 amino acids
Related rules None
Fusion Nter: None Cter: None
Comments D2 is phosphorylated in "higer" and "lower eukaryotes" (Ceratodon purpureus, Marchantia polymorpha, Adiantum tenerum, in the last 3 the site was not identified) but not in red algae or cyanobacteria (Ceramium tenuicorne and Synechocystis, see PubMed:9512353). Cyanobacteriota often have more than 1 (often identical) gene for this protein.



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