PSBD_ARATH
ID PSBD_ARATH Reviewed; 353 AA.
AC P56761;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 158.
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}; OrderedLocusNames=AtCg00270;
OS Arabidopsis thaliana (Mouse-ear cress).
OG Plastid; Chloroplast.
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10574454; DOI=10.1093/dnares/6.5.283;
RA Sato S., Nakamura Y., Kaneko T., Asamizu E., Tabata S.;
RT "Complete structure of the chloroplast genome of Arabidopsis thaliana.";
RL DNA Res. 6:283-290(1999).
RN [2]
RP PROTEIN SEQUENCE OF 2-7, PHOSPHORYLATION AT THR-2, AND ACETYLATION AT
RP THR-2.
RC STRAIN=cv. Columbia;
RX PubMed=11113141; DOI=10.1074/jbc.m009394200;
RA Vener A.V., Harms A., Sussman M.R., Vierstra R.D.;
RT "Mass spectrometric resolution of reversible protein phosphorylation in
RT photosynthetic membranes of Arabidopsis thaliana.";
RL J. Biol. Chem. 276:6959-6966(2001).
RN [3]
RP INTERACTION WITH PAM68.
RX PubMed=20923938; DOI=10.1105/tpc.110.077453;
RA Armbruster U., Zuhlke J., Rengstl B., Kreller R., Makarenko E., Ruhle T.,
RA Schunemann D., Jahns P., Weisshaar B., Nickelsen J., Leister D.;
RT "The Arabidopsis thylakoid protein PAM68 is required for efficient D1
RT biogenesis and photosystem II assembly.";
RL Plant Cell 22:3439-3460(2010).
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. Interacts with PAM68. {ECO:0000255|HAMAP-Rule:MF_01383,
CC ECO:0000269|PubMed:20923938}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane
CC {ECO:0000255|HAMAP-Rule:MF_01383}; Multi-pass membrane protein
CC {ECO:0000255|HAMAP-Rule:MF_01383}.
CC -!- PTM: Phosphorylation occurs in normal plant growth light conditions.
CC Rapid dephosphorylation occurs during heat shock.
CC {ECO:0000269|PubMed:11113141}.
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; AP000423; BAA84380.1; -; Genomic_DNA.
DR RefSeq; NP_051054.1; NC_000932.1.
DR PDB; 5MDX; EM; 5.30 A; D/d=2-353.
DR PDB; 7OUI; EM; 2.79 A; D/d=2-353.
DR PDBsum; 5MDX; -.
DR PDBsum; 7OUI; -.
DR AlphaFoldDB; P56761; -.
DR SMR; P56761; -.
DR BioGRID; 29974; 16.
DR IntAct; P56761; 2.
DR MINT; P56761; -.
DR STRING; 3702.ATCG00270.1; -.
DR TCDB; 3.E.2.2.3; the photosynthetic reaction center (prc) family.
DR iPTMnet; P56761; -.
DR PaxDb; P56761; -.
DR PRIDE; P56761; -.
DR ProteomicsDB; 224824; -.
DR EnsemblPlants; ATCG00270.1; ATCG00270.1; ATCG00270.
DR GeneID; 844775; -.
DR Gramene; ATCG00270.1; ATCG00270.1; ATCG00270.
DR KEGG; ath:ArthCp017; -.
DR Araport; ATCG00270; -.
DR TAIR; locus:504954651; ATCG00270.
DR eggNOG; ENOG502QWJF; Eukaryota.
DR HOGENOM; CLU_077965_0_0_1; -.
DR InParanoid; P56761; -.
DR OMA; RWFQLGG; -.
DR OrthoDB; 801765at2759; -.
DR BioCyc; MetaCyc:ATCG00270-MON; -.
DR PRO; PR:P56761; -.
DR Proteomes; UP000006548; Chloroplast.
DR ExpressionAtlas; P56761; baseline and differential.
DR Genevisible; P56761; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009534; C:chloroplast thylakoid; HDA:TAIR.
DR GO; GO:0009535; C:chloroplast thylakoid membrane; HDA:TAIR.
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:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0009579; C:thylakoid; HDA:TAIR.
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:0003729; F:mRNA binding; IDA:TAIR.
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:11113141"
FT CHAIN 2..353
FT /note="Photosystem II D2 protein"
FT /id="PRO_0000090498"
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:11113141"
FT MOD_RES 2
FT /note="Phosphothreonine"
FT /evidence="ECO:0000269|PubMed:11113141"
FT HELIX 15..23
FT /evidence="ECO:0007829|PDB:7OUI"
FT STRAND 27..29
FT /evidence="ECO:0007829|PDB:7OUI"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 35..54
FT /evidence="ECO:0007829|PDB:7OUI"
FT TURN 59..61
FT /evidence="ECO:0007829|PDB:7OUI"
FT STRAND 62..64
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 68..70
FT /evidence="ECO:0007829|PDB:7OUI"
FT TURN 74..76
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 84..86
FT /evidence="ECO:0007829|PDB:7OUI"
FT TURN 96..100
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 102..107
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 110..136
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 142..158
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 160..164
FT /evidence="ECO:0007829|PDB:7OUI"
FT STRAND 165..167
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 168..170
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 176..190
FT /evidence="ECO:0007829|PDB:7OUI"
FT TURN 192..194
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 196..221
FT /evidence="ECO:0007829|PDB:7OUI"
FT STRAND 222..224
FT /evidence="ECO:0007829|PDB:7OUI"
FT STRAND 228..230
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 232..234
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 247..257
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 265..291
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 300..308
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 315..334
FT /evidence="ECO:0007829|PDB:7OUI"
FT HELIX 336..338
FT /evidence="ECO:0007829|PDB:7OUI"
FT TURN 344..346
FT /evidence="ECO:0007829|PDB:7OUI"
SQ SEQUENCE 353 AA; 39548 MW; DFCC8807CBAFF178 CRC64;
MTIALGKFTK DEKDLFDIMD 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
