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Annotation rule MF_01379
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General rule information [?]

Accession MF_01379
Dates 18-DEC-2007 (Created)
19-NOV-2019 (Last updated, Version 37)
Name PSII_PsbA_D1
Scope
Bacteria; Cyanobacteria
Plastid
Templates P51765 (PSBA_THEVL); P0A444 (PSBA1_THEEB); P69560 (PSBA_SPIOL); P07753 (PSBA_CHLRE); P16033 (PSBA2_SYNY3): [Recover all]

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
psbA

Comments [?]

Function Photosystem 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/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors.
Catalytic activity RHEA:36359: 2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2
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:Cyanobacteria>
Subunit Cyanobacterial PSII 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, Ycf12, at least 3 peripheral proteins PsbO, PsbU, PsbV and a large number of cofactors. It forms dimeric complexes.
else
Subunit PSII 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, 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 location Plastid, chloroplast thylakoid membrane; Multi-pass membrane protein.
else case <OC:Gloeobacter>
Subcellular location Cell inner membrane; Multi-pass membrane protein.
else
Subcellular location Cellular thylakoid membrane; Multi-pass membrane protein.
end case
case <FTTag:Cleavage>
Ptm C-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.
Miscellaneous 2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water.
Herbicides such as atrazine, BNT, diuron or ioxynil bind in the Q(B) binding site and block subsequent electron transfer.
case <OC:Cyanobacteria>
Miscellaneous Cyanobacteria usually contain more than 2 copies of the psbA gene.
end case
Similarity Belongs to the reaction center PufL/M/PsbA/D family.

Keywords [?]

case <FTTag:phospho>
end case
case <FTTag:acetyl>
end case
case <OC:Gloeobacter>
else
end case

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 <OC:Gloeobacter>
GO:0005886; Cellular component: plasma membrane.
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;
TIGRFAMs TIGR01151; PsbA; 1;

Features [?]

From: PSBA_THEVL (P51765)
Key     From     To       Description   Tag   Condition   FTGroup
TRANSMEM     29     46       Helical        
TRANSMEM     118     133       Helical        
TRANSMEM     142     156       Helical        
TRANSMEM     197     218       Helical        
TRANSMEM     274     288       Helical        
SITE (Optional)     344     345       Cleavage; by CtpA   Cleavage   A-[ACDGSTV]  
case <FTTag:Cleavage> and <OC:Viridiplantae>
INIT_MET     1     1       Removed     M  
MOD_RES     2     2       N-acetylthreonine   acetyl   T  
MOD_RES     2     2       Phosphothreonine   phospho   T  
CHAIN     2     344       Photosystem II protein D1        
PROPEP     345     Cter                
else case <FTTag:Cleavage> and not <OC:Viridiplantae>
CHAIN     Nter     344       Photosystem II protein D1        
PROPEP     345     Cter                
else
CHAIN     Nter     Cter       Photosystem II protein D1        
end case
REGION     264     265       Quinone (B)     [AS]-F  
METAL     118     118       Magnesium (chlorophyll-a ChlzD1 axial ligand); via tele nitrogen     H  
METAL     170     170       Calcium-manganese-oxide [Ca-4Mn-5O]; calcium     [DE]  
METAL     170     170       Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4     [DE]  
METAL     189     189       Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1     [ED]  
METAL     198     198       Magnesium (chlorophyll-a PD1 axial ligand); via tele nitrogen     H  
METAL     215     215       Iron; shared with heterodimeric partner; via tele nitrogen     H  
METAL     272     272       Iron; shared with heterodimeric partner; via tele nitrogen     H  
METAL     332     332       Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1; via tele nitrogen     H  
METAL     333     333       Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 3     E  
METAL     333     333       Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4     E  
METAL     342     342       Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1     D  
METAL     342     342       Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2     D  
METAL     344     344       Calcium-manganese-oxide [Ca-4Mn-5O]; calcium; via carboxylate     A  
METAL     344     344       Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2; via carboxylate     A  
BINDING     126     126       Pheophytin D1     [YW]  
BINDING     215     215       Quinone (B)     H  
SITE     161     161       Tyrosine radical intermediate     Y  
SITE     190     190       Stabilizes free radical intermediate     H  

Additional information [?]

Size range 340-363 amino acids
Related rules None
Fusion 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.