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HAMAP rule MF_01379

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General rule information [?]

Accession MF_01379
Dates 18-DEC-2007 (Created)
2-SEP-2024 (Last updated, Version 47)
Name PSII_PsbA_D1
Scope(s) Bacteria
Cyanobacteriota
Plastid
Template(s) P51765 (PSBA_THEVL); P0A444 (PSBA1_THEVB); P69560 (PSBA_SPIOL); P07753 (PSBA_CHLRE); P16033 (PSBA2_SYNY3); [ Recover all ]
Triggered by HAMAP; MF_01379 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier PSBA
Protein name RecName: Full=Photosystem II protein D1;
                 Short=PSII D1 protein;
                 EC=1.10.3.9;
AltName: Full=Photosystem II Q(B) protein;
case <FTTag:Cleavage>
Protein name Flags: Precursor;
end case
Gene name Name=psbA;

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.
CATALYTIC ACTIVITY Reaction=2 a plastoquinone + 4 hnu + 2 H2O = 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. D1 provides most of the ligands for the Mn4-Ca-O5 cluster of the oxygen-evolving complex (OEC). 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
case <FTTag:Cleavage>
PTMC-terminally processed by CtpA; processing is essential to allow assembly of the oxygen-evolving complex and thus photosynthetic growth.
end case
PTM#{Tyr-161} forms a radical intermediate that is referred to as redox-active TyrZ, YZ or Y-Z.
MISCELLANEOUS2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water.
MISCELLANEOUSHerbicides such as atrazine, BNT, diuron or ioxynil bind in the Q(B) binding site and block subsequent electron transfer.
case <OC:Cyanobacteriota>
MISCELLANEOUSCyanobacteriota usually contain more than 2 copies of the psbA gene.
end case
SIMILARITYBelongs to the reaction center PufL/M/PsbA/D family.

Keywords [?]

case <FTTag:phospho>
Phosphoprotein
end case
case <FTTag:acetyl>
Acetylation
end case
Calcium
Chlorophyll
Chromophore
Electron transport
Herbicide resistance
Iron
Manganese
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
GO:0016682; Molecular function:oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
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; 0-3;
NCBIfam TIGR01151; PsbA; 1;

Features [?]

From: PSBA_THEVL (P51765)
Key From To Description Tag Condition FTGroup
TRANSMEM 29 46 /note="Helical"
TRANSMEM 118 133 /note="Helical"
TRANSMEM 142 156 /note="Helical"
TRANSMEM 197 218 /note="Helical"
TRANSMEM 274 288 /note="Helical"
SITE 344 345 /note="Cleavage; by CtpA" Cleavage A-[ACDGSTV]
case <FTTag:Cleavage> and <OC:Viridiplantae>
INIT_MET 1 1 /note="Removed" M
MOD_RES 2 2 /note="N-acetylthreonine" acetyl T
MOD_RES 2 2 /note="Phosphothreonine" phospho T
CHAIN 2 344 /note="Photosystem II protein D1"
PROPEP 345 Cter
else case <FTTag:Cleavage> and not <OC:Viridiplantae>
CHAIN Nter 344 /note="Photosystem II protein D1"
PROPEP 345 Cter
else
CHAIN Nter Cter /note="Photosystem II protein D1"
end case
BINDING 118 118 /ligand="chlorophyll a"
/ligand_id="ChEBI:CHEBI:58416"
/ligand_label="ChlzD1"
/ligand_part="Mg"
/ligand_part_id="ChEBI:CHEBI:25107"
/note="axial binding residue"		 H
BINDING 170 170 /ligand="[CaMn4O5] cluster"
/ligand_id="ChEBI:CHEBI:189552"		 [DE]
BINDING 189 189 /ligand="[CaMn4O5] cluster"
/ligand_id="ChEBI:CHEBI:189552"		 [ED]
BINDING 198 198 /ligand="chlorophyll a"
/ligand_id="ChEBI:CHEBI:58416"
/ligand_label="PD1"
/ligand_part="Mg"
/ligand_part_id="ChEBI:CHEBI:25107"
/note="axial binding residue"		 H
BINDING 215 215 /ligand="Fe cation"
/ligand_id="ChEBI:CHEBI:24875"
/ligand_note="ligand shared with heterodimeric partner"		 H
BINDING 272 272 /ligand="Fe cation"
/ligand_id="ChEBI:CHEBI:24875"
/ligand_note="ligand shared with heterodimeric partner"		 H
BINDING 332 332 /ligand="[CaMn4O5] cluster"
/ligand_id="ChEBI:CHEBI:189552"		 H
BINDING 333 333 /ligand="[CaMn4O5] cluster"
/ligand_id="ChEBI:CHEBI:189552"		 E
BINDING 342 342 /ligand="[CaMn4O5] cluster"
/ligand_id="ChEBI:CHEBI:189552"		 D
BINDING 344 344 /ligand="[CaMn4O5] cluster"
/ligand_id="ChEBI:CHEBI:189552"		 A
BINDING 126 126 /ligand="pheophytin a"
/ligand_id="ChEBI:CHEBI:136840"
/ligand_label="D1"		 [YW]
BINDING 215 215 /ligand="a quinone"
/ligand_id="ChEBI:CHEBI:132124"
/ligand_label="B"		 H
BINDING 264 265 /ligand="a quinone"
/ligand_id="ChEBI:CHEBI:132124"
/ligand_label="B"		 [AS]-F
SITE 161 161 /note="Tyrosine radical intermediate" Y
SITE 190 190 /note="Stabilizes free radical intermediate" H

Additional information [?]

Size range 340-363 amino acids
Related rules None
Fusion Nter: None Cter: None
Comments C-terminal cleavage of D1 by the C-terminal processing protese (CtpA) within the thylakoid lumen is required for ligation of the manganese cluster and association of the oxygen-evolving complex. EUGGR, BIGNA, LEPTE, STAPU and many dinoflagellates are already this length and thus do not seem to be encoded as precursor proteins. One copy in TRIV2 (Q3M5L6) does not have the cleavage site. D1 is very photosensitive and there is a mechanism to replace photodamaged D1.



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