PSBD_PEA
ID PSBD_PEA Reviewed; 353 AA.
AC P06006;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 5.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=Photosystem II D2 protein {ECO:0000255|HAMAP-Rule:MF_01383};
DE Short=PSII D2 protein {ECO:0000255|HAMAP-Rule:MF_01383};
DE EC=1.10.3.9 {ECO:0000255|HAMAP-Rule:MF_01383};
DE AltName: Full=Photosystem Q(A) protein {ECO:0000255|HAMAP-Rule:MF_01383};
GN Name=psbD {ECO:0000255|HAMAP-Rule:MF_01383};
OS Pisum sativum (Garden pea).
OG Plastid; Chloroplast.
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; Hologalegina; IRL clade; Fabeae; Pisum.
OX NCBI_TaxID=3888;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Rosakrone;
RX AGRICOLA=IND84114033; DOI=10.1007/BF00029654;
RA Rasmussen O.F., Bookjans G., Stutmann B.M., Henningsen K.W.;
RT "Localization and nucleotide sequence of the gene for the membrane
RT polypeptide D2 from pea chloroplast DNA.";
RL Plant Mol. Biol. 3:191-199(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Rosakrone;
RX AGRICOLA=IND87019930; DOI=10.1007/BF00034943;
RA Bookjans G.B., Stummann B.M., Rasmussen O.F., Henningsen K.W.;
RT "Structure of a 3.2 kb region of pea chloroplast DNA containing the gene
RT for the 44 kD photosystem II polypeptide.";
RL Plant Mol. Biol. 6:359-366(1986).
RN [3]
RP SUBCELLULAR LOCATION, ACETYLATION AT THR-2, LACK OF PHOSPHORYLATION AT
RP THR-2, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=9407103; DOI=10.1074/jbc.272.52.33158;
RA Sharma J., Panico M., Shipton C.A., Nilsson F., Morris H.R., Barber J.;
RT "Primary structure characterization of the photosystem II D1 and D2
RT subunits.";
RL J. Biol. Chem. 272:33158-33166(1997).
CC -!- FUNCTION: Photosystem II (PSII) is a light-driven water:plastoquinone
CC oxidoreductase that uses light energy to abstract electrons from H(2)O,
CC generating O(2) and a proton gradient subsequently used for ATP
CC formation. It consists of a core antenna complex that captures photons,
CC and an electron transfer chain that converts photonic excitation into a
CC charge separation. The D1/D2 (PsbA/PsbA) reaction center heterodimer
CC binds P680, the primary electron donor of PSII as well as several
CC subsequent electron acceptors. D2 is needed for assembly of a stable
CC PSII complex. {ECO:0000255|HAMAP-Rule:MF_01383}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 a plastoquinone + 2 H2O + 4 hnu = 2 a plastoquinol + O2;
CC Xref=Rhea:RHEA:36359, Rhea:RHEA-COMP:9561, Rhea:RHEA-COMP:9562,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15379, ChEBI:CHEBI:17757,
CC ChEBI:CHEBI:30212, ChEBI:CHEBI:62192; EC=1.10.3.9;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01383};
CC -!- COFACTOR:
CC Note=The D1/D2 heterodimer binds P680, chlorophylls that are the
CC primary electron donor of PSII, and subsequent electron acceptors. It
CC shares a non-heme iron and each subunit binds pheophytin, quinone,
CC additional chlorophylls, carotenoids and lipids. There is also a Cl(-1)
CC ion associated with D1 and D2, which is required for oxygen evolution.
CC The PSII complex binds additional chlorophylls, carotenoids and
CC specific lipids. {ECO:0000255|HAMAP-Rule:MF_01383};
CC -!- SUBUNIT: PSII is composed of 1 copy each of membrane proteins PsbA,
CC PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT,
CC PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins of the oxygen-
CC evolving complex and a large number of cofactors. It forms dimeric
CC complexes. {ECO:0000255|HAMAP-Rule:MF_01383}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane
CC {ECO:0000255|HAMAP-Rule:MF_01383, ECO:0000269|PubMed:9407103}; Multi-
CC pass membrane protein {ECO:0000255|HAMAP-Rule:MF_01383}.
CC -!- MASS SPECTROMETRY: Mass=39456.1; Mass_error=7.7; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:9407103};
CC -!- MISCELLANEOUS: 2 of the reaction center chlorophylls (ChlD1 and ChlD2)
CC are entirely coordinated by water. {ECO:0000255|HAMAP-Rule:MF_01383}.
CC -!- SIMILARITY: Belongs to the reaction center PufL/M/PsbA/D family.
CC {ECO:0000255|HAMAP-Rule:MF_01383}.
CC -!- CAUTION: The submitted nucleotide sequence (AAB59335) does not agree
CC with that shown in (Ref.1) Fig.4 or with that determined in
CC (PubMed:9407103); as amino acid 269 should be H to act as a ligand for
CC the non-heme iron, the sequence shown has been corrected to correspond
CC to that shown in the figure. {ECO:0000305}.
CC -!- CAUTION: Phosphorylated D2 was searched for but not found in
CC (PubMed:9407103).
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DR EMBL; M27309; AAB59335.1; -; Genomic_DNA.
DR PIR; A26059; F2PMD2.
DR RefSeq; YP_003587540.1; NC_014057.1.
DR PDB; 5XNL; EM; 2.70 A; D/d=1-353.
DR PDB; 5XNM; EM; 3.20 A; D/d=1-353.
DR PDB; 6YP7; EM; 3.80 A; D/d=13-353.
DR PDBsum; 5XNL; -.
DR PDBsum; 5XNM; -.
DR PDBsum; 6YP7; -.
DR AlphaFoldDB; P06006; -.
DR SMR; P06006; -.
DR iPTMnet; P06006; -.
DR GeneID; 9073077; -.
DR GO; GO:0009535; C:chloroplast thylakoid membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0009523; C:photosystem II; IEA:UniProtKB-KW.
DR GO; GO:0016168; F:chlorophyll binding; IEA:UniProtKB-UniRule.
DR GO; GO:0045156; F:electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity; IEA:InterPro.
DR GO; GO:0005506; F:iron ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0010242; F:oxygen evolving activity; IEA:UniProtKB-EC.
DR GO; GO:0009772; P:photosynthetic electron transport in photosystem II; IEA:InterPro.
DR CDD; cd09288; Photosystem-II_D2; 1.
DR Gene3D; 1.20.85.10; -; 1.
DR HAMAP; MF_01383; PSII_PsbD_D2; 1.
DR InterPro; IPR036854; Photo_II_D1/D2_sf.
DR InterPro; IPR000484; Photo_RC_L/M.
DR InterPro; IPR005868; PSII_PsbD/D2.
DR PANTHER; PTHR33149; PTHR33149; 1.
DR Pfam; PF00124; Photo_RC; 1.
DR PRINTS; PR00256; REACTNCENTRE.
DR SUPFAM; SSF81483; SSF81483; 1.
DR TIGRFAMs; TIGR01152; psbD; 1.
DR PROSITE; PS00244; REACTION_CENTER; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Chlorophyll; Chloroplast; Chromophore;
KW Electron transport; Iron; Magnesium; Membrane; Metal-binding;
KW Oxidoreductase; Phosphoprotein; Photosynthesis; Photosystem II; Plastid;
KW Thylakoid; Transmembrane; Transmembrane helix; Transport.
FT INIT_MET 1
FT /note="Removed"
FT CHAIN 2..353
FT /note="Photosystem II D2 protein"
FT /id="PRO_0000090516"
FT TRANSMEM 41..61
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT TRANSMEM 125..141
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT TRANSMEM 153..166
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT TRANSMEM 208..228
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT TRANSMEM 279..295
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT BINDING 118
FT /ligand="chlorophyll a"
FT /ligand_id="ChEBI:CHEBI:58416"
FT /ligand_label="ChlzD2"
FT /ligand_part="Mg"
FT /ligand_part_id="ChEBI:CHEBI:25107"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT BINDING 130
FT /ligand="pheophytin a"
FT /ligand_id="ChEBI:CHEBI:136840"
FT /ligand_label="D2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT BINDING 143
FT /ligand="pheophytin a"
FT /ligand_id="ChEBI:CHEBI:136840"
FT /ligand_label="D2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT BINDING 198
FT /ligand="chlorophyll a"
FT /ligand_id="ChEBI:CHEBI:58416"
FT /ligand_label="PD2"
FT /ligand_part="Mg"
FT /ligand_part_id="ChEBI:CHEBI:25107"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT BINDING 215
FT /ligand="a plastoquinone"
FT /ligand_id="ChEBI:CHEBI:17757"
FT /ligand_label="Q(A)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT BINDING 215
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="ligand shared with heterodimeric partner"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT BINDING 262
FT /ligand="a plastoquinone"
FT /ligand_id="ChEBI:CHEBI:17757"
FT /ligand_label="Q(A)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT BINDING 269
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="ligand shared with heterodimeric partner"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT MOD_RES 2
FT /note="N-acetylthreonine"
FT /evidence="ECO:0000269|PubMed:9407103"
FT MOD_RES 2
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P56761"
FT CONFLICT 218
FT /note="T -> I (in Ref. 1; no nucleotide entry and 2;
FT AAB59335)"
FT /evidence="ECO:0000305"
FT CONFLICT 269
FT /note="H -> Y (in Ref. 1; no nucleotide entry and 2;
FT AAB59335)"
FT /evidence="ECO:0000305"
FT HELIX 15..23
FT /evidence="ECO:0007829|PDB:5XNL"
FT STRAND 27..29
FT /evidence="ECO:0007829|PDB:5XNL"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 35..55
FT /evidence="ECO:0007829|PDB:5XNL"
FT TURN 59..62
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 68..70
FT /evidence="ECO:0007829|PDB:5XNL"
FT TURN 74..76
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 84..86
FT /evidence="ECO:0007829|PDB:5XNL"
FT TURN 96..100
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 102..107
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 110..137
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 142..158
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 160..164
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 168..170
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 176..190
FT /evidence="ECO:0007829|PDB:5XNL"
FT TURN 192..194
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 196..221
FT /evidence="ECO:0007829|PDB:5XNL"
FT STRAND 222..224
FT /evidence="ECO:0007829|PDB:5XNL"
FT STRAND 227..230
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 232..235
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 247..257
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 265..291
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 300..308
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 315..329
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 331..334
FT /evidence="ECO:0007829|PDB:5XNL"
FT HELIX 336..338
FT /evidence="ECO:0007829|PDB:5XNL"
FT TURN 344..346
FT /evidence="ECO:0007829|PDB:5XNL"
SQ SEQUENCE 353 AA; 39530 MW; 09339200C9351BBB CRC64;
MTIALGKFTK DQNDLFDIMD DWLRRDRFVF VGWSGLLLFP CAYFAVGGWF TGTTFVTSWY
THGLASSYLE GCNFLTAAVS TPANSLAHSL LLLWGPEAQG DLTRWCQLGG LWTFVALHGA
FGLIGFMLRQ FELARSVQLR PYNAIAFSGP IAVFVSVFLI YPLGQSGWFF APSFGVAAIF
RFILFFQGFH NWTLNPFHMM GVAGVLGAAL LCAIHGATVE NTLFEDGDGA NTFRAFNPTQ
AEETYSMVTA NRFWSQIFGV AFSNKRWLHF FMLFVPVTGL WMSALGVVGL ALNLRAYDFV
SQEIRAAEDP EFETFYTKNI LLNEGIRAWM ATQDQPHENL IFPEEVLPRG NAL
