PSBD_SPIOL
ID PSBD_SPIOL Reviewed; 353 AA.
AC P06005;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 156.
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 Spinacia oleracea (Spinach).
OG Plastid; Chloroplast.
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC Caryophyllales; Chenopodiaceae; Chenopodioideae; Anserineae; Spinacia.
OX NCBI_TaxID=3562;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6096808; DOI=10.1093/nar/12.23.8819;
RA Holschuh K., Bottomley W., Whitfeld P.R.;
RT "Structure of the spinach chloroplast genes for the D2 and 44 kd reaction-
RT centre proteins of photosystem II and for tRNASer (UGA).";
RL Nucleic Acids Res. 12:8819-8834(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=24177999; DOI=10.1007/bf00395705;
RA Alt J., Morris J., Westhoff P., Herrmann R.G.;
RT "Nucleotide sequence of the clustered genes for the 44kd chlorophyll a
RT apoprotein and the '32kd'-like protein of the photosystem II reaction
RT center in the spinach plastid chromosome.";
RL Curr. Genet. 8:597-606(1984).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Geant d'hiver, and cv. Monatol;
RX PubMed=11292076; DOI=10.1023/a:1006478403810;
RA Schmitz-Linneweber C., Maier R.M., Alcaraz J.-P., Cottet A., Herrmann R.G.,
RA Mache R.;
RT "The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide
RT sequence and gene organization.";
RL Plant Mol. Biol. 45:307-315(2001).
RN [4]
RP PROTEIN SEQUENCE OF 2-7, SUBCELLULAR LOCATION, ACETYLATION AT THR-2, AND
RP PHOSPHORYLATION AT THR-2.
RX PubMed=3121625; DOI=10.1016/s0021-9258(19)57275-1;
RA Michel H., Hunt D.F., Shabanowitz J., Bennett J.;
RT "Tandem mass spectrometry reveals that three photosystem II proteins of
RT spinach chloroplasts contain N-acetyl-O-phosphothreonine at their NH2
RT termini.";
RL J. Biol. Chem. 263:1123-1130(1988).
RN [5]
RP MASS SPECTROMETRY.
RX PubMed=9655347; DOI=10.1002/pro.5560070619;
RA Whitelegge J.P., Gundersen C.B., Faull K.F.;
RT "Electrospray-ionization mass spectrometry of intact intrinsic membrane
RT proteins.";
RL Protein Sci. 7:1423-1430(1998).
RN [6]
RP 3D-STRUCTURE MODELING.
RX PubMed=8931545; DOI=10.1021/bi960764k;
RA Svensson B., Etchebest C., Tuffery P., van Kan P., Smith J., Styring S.;
RT "A model for the photosystem II reaction center core including the
RT structure of the primary donor P680.";
RL Biochemistry 35:14486-14502(1996).
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:3121625}; Multi-
CC pass membrane protein {ECO:0000255|HAMAP-Rule:MF_01383}.
CC -!- MASS SPECTROMETRY: Mass=39418.8; Mass_error=3.9; Method=Electrospray;
CC Note=Non-phosphorylated.; Evidence={ECO:0000269|PubMed:9655347};
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}.
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DR EMBL; M36833; AAA84630.1; -; Genomic_DNA.
DR EMBL; AJ400848; CAB88721.1; -; Genomic_DNA.
DR PIR; A23038; F2SPD2.
DR RefSeq; NP_054928.1; NC_002202.1.
DR PDB; 3JCU; EM; 3.20 A; D/d=1-353.
DR PDBsum; 3JCU; -.
DR AlphaFoldDB; P06005; -.
DR SMR; P06005; -.
DR DIP; DIP-62010N; -.
DR IntAct; P06005; 1.
DR STRING; 3562.P06005; -.
DR iPTMnet; P06005; -.
DR GeneID; 2715610; -.
DR KEGG; soe:2715610; -.
DR OrthoDB; 801765at2759; -.
DR Proteomes; UP000054095; Chloroplast.
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; IBA:GO_Central.
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 Direct protein sequencing; Electron transport; Iron; Magnesium; Membrane;
KW Metal-binding; Oxidoreductase; Phosphoprotein; Photosynthesis;
KW Photosystem II; Plastid; Reference proteome; Thylakoid; Transmembrane;
KW Transmembrane helix; Transport.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:3121625"
FT CHAIN 2..353
FT /note="Photosystem II D2 protein"
FT /id="PRO_0000090521"
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:3121625"
FT MOD_RES 2
FT /note="Phosphothreonine"
FT /evidence="ECO:0000269|PubMed:3121625"
FT HELIX 15..23
FT /evidence="ECO:0007829|PDB:3JCU"
FT STRAND 27..29
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 32..54
FT /evidence="ECO:0007829|PDB:3JCU"
FT TURN 59..62
FT /evidence="ECO:0007829|PDB:3JCU"
FT TURN 68..71
FT /evidence="ECO:0007829|PDB:3JCU"
FT TURN 74..76
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 84..86
FT /evidence="ECO:0007829|PDB:3JCU"
FT TURN 96..98
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 102..107
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 110..136
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 143..158
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 160..164
FT /evidence="ECO:0007829|PDB:3JCU"
FT STRAND 165..167
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 168..170
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 176..190
FT /evidence="ECO:0007829|PDB:3JCU"
FT TURN 192..194
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 196..221
FT /evidence="ECO:0007829|PDB:3JCU"
FT TURN 233..235
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 247..256
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 265..290
FT /evidence="ECO:0007829|PDB:3JCU"
FT TURN 291..293
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 300..308
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 315..334
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 336..338
FT /evidence="ECO:0007829|PDB:3JCU"
FT HELIX 344..346
FT /evidence="ECO:0007829|PDB:3JCU"
SQ SEQUENCE 353 AA; 39507 MW; 288090F22B659EA0 CRC64;
MTIAVGKFTK DEKDLFDSMD DWLRRDRFVF VGWSGLLLFP CAYFALGGWF TGTTFVTSWY
THGLASSYLE GCNFLTAAVS TPANSLAHSL LLLWGPEAQG DFTRWCQLGG LWAFVALHGA
FALIGFMLRQ FELARSVQLR PYNAIAFSGP IAVFVSVFLI YPLGQSGWFF APSFGVAAIF
RFILFFQGFH NWTLNPFHMM GVAGVLGAAL LCAIHGATVE NTLFEDGDGA NTFRAFNPTQ
AEETYSMVTA NRFWSQIFGV AFSNKRWLHF FMLFVPVTGL WMSALGVVGL ALNLRAYDFV
SQEIRAAEDP EFETFYTKNI LLNEGIRAWM AAQDQPHENL IFPEEVLPRG NAL
