PSBD_SYNY3
ID PSBD_SYNY3 Reviewed; 352 AA.
AC P09192;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1991, sequence version 2.
DT 03-AUG-2022, entry version 174.
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=sll0849;
OS Synechocystis sp. (strain PCC 6803 / Kazusa).
OC Bacteria; Cyanobacteria; Synechococcales; Merismopediaceae; Synechocystis;
OC unclassified Synechocystis.
OX NCBI_TaxID=1111708;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=24277560; DOI=10.1007/bf00029879;
RA Chisholm D., Williams J.G.K.;
RT "Nucleotide sequence of psbC, the gene encoding the CP-43 chlorophyll a-
RT binding protein of photosystem II, in the cyanobacterium Synechocystis
RT 6803.";
RL Plant Mol. Biol. 10:293-301(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27184 / PCC 6803 / N-1;
RX PubMed=8590279; DOI=10.1093/dnares/2.4.153;
RA Kaneko T., Tanaka A., Sato S., Kotani H., Sazuka T., Miyajima N.,
RA Sugiura M., Tabata S.;
RT "Sequence analysis of the genome of the unicellular cyanobacterium
RT Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region
RT from map positions 64% to 92% of the genome.";
RL DNA Res. 2:153-166(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=8905231; DOI=10.1093/dnares/3.3.109;
RA Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y.,
RA Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T.,
RA Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.,
RA Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence analysis of the genome of the unicellular cyanobacterium
RT Synechocystis sp. strain PCC6803. II. Sequence determination of the entire
RT genome and assignment of potential protein-coding regions.";
RL DNA Res. 3:109-136(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 230-352.
RX PubMed=3130247; DOI=10.1002/j.1460-2075.1988.tb02817.x;
RA Dzelzkalns V.A., Bogorad L.;
RT "Molecular analysis of a mutant defective in photosynthetic oxygen
RT evolution and isolation of a complementing clone by a novel screening
RT procedure.";
RL EMBO J. 7:333-338(1988).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 332-352.
RX PubMed=2105233; DOI=10.1016/0014-5793(90)80085-w;
RA Carpenter S.D., Charite J., Eggers B., Vermaas W.F.;
RT "The psbC start codon in Synechocystis sp. PCC 6803.";
RL FEBS Lett. 260:135-137(1990).
RN [6]
RP SUBCELLULAR LOCATION, AND LACK OF PHOSPHORYLATION.
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=9512353; DOI=10.1016/s0014-5793(98)00088-x;
RA Pursiheimo S., Rintamaeki E., Baena-Gonzalez E., Aro E.-M.;
RT "Thylakoid protein phosphorylation in evolutionally divergent species with
RT oxygenic photosynthesis.";
RL FEBS Lett. 423:178-182(1998).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, AND SUBCELLULAR LOCATION.
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=12069591; DOI=10.1021/bi026012+;
RA Kashino Y., Lauber W.M., Carroll J.A., Wang Q., Whitmarsh J., Satoh K.,
RA Pakrasi H.B.;
RT "Proteomic analysis of a highly active photosystem II preparation from the
RT cyanobacterium Synechocystis sp. PCC 6803 reveals the presence of novel
RT polypeptides.";
RL Biochemistry 41:8004-8012(2002).
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: Cyanobacterial PSII is composed of 1 copy each of membrane
CC proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK,
CC PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral
CC proteins PsbO, PsbU, PsbV and a large number of cofactors. It forms
CC dimeric complexes. {ECO:0000255|HAMAP-Rule:MF_01383,
CC ECO:0000269|PubMed:12069591}.
CC -!- SUBCELLULAR LOCATION: Cellular thylakoid membrane {ECO:0000255|HAMAP-
CC Rule:MF_01383, ECO:0000269|PubMed:12069591,
CC ECO:0000269|PubMed:9512353}; Multi-pass membrane protein
CC {ECO:0000255|HAMAP-Rule:MF_01383}.
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; M21538; AAA85377.1; -; Genomic_DNA.
DR EMBL; BA000022; BAA10851.1; -; Genomic_DNA.
DR EMBL; BA000022; BAA17800.1; -; Genomic_DNA.
DR EMBL; X07018; CAA30070.1; -; Genomic_DNA.
DR PIR; PS0097; PS0097.
DR PDB; 6WJ6; EM; 2.58 A; D=1-352.
DR PDB; 7N8O; EM; 1.93 A; D/d=1-352.
DR PDB; 7RCV; EM; 2.01 A; D/d=1-352.
DR PDBsum; 6WJ6; -.
DR PDBsum; 7N8O; -.
DR PDBsum; 7RCV; -.
DR AlphaFoldDB; P09192; -.
DR SMR; P09192; -.
DR IntAct; P09192; 2.
DR STRING; 1148.1001364; -.
DR TCDB; 3.E.2.2.2; the photosynthetic reaction center (prc) family.
DR PaxDb; P09192; -.
DR EnsemblBacteria; BAA10851; BAA10851; BAA10851.
DR EnsemblBacteria; BAA17800; BAA17800; BAA17800.
DR KEGG; syn:sll0849; -.
DR KEGG; syn:slr0927; -.
DR eggNOG; ENOG502Z8JK; Bacteria.
DR InParanoid; P09192; -.
DR OMA; RWFQLGG; -.
DR PhylomeDB; P09192; -.
DR BioCyc; MetaCyc:PSBD-MON; -.
DR Proteomes; UP000001425; Chromosome.
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:0031676; C:plasma membrane-derived thylakoid membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0030096; C:plasma membrane-derived thylakoid photosystem II; IDA:UniProtKB.
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 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; Chlorophyll; Chromophore; Electron transport; Iron;
KW Magnesium; Membrane; Metal-binding; Oxidoreductase; Photosynthesis;
KW Photosystem II; Reference proteome; Thylakoid; Transmembrane;
KW Transmembrane helix; Transport.
FT CHAIN 1..352
FT /note="Photosystem II D2 protein"
FT /id="PRO_0000090527"
FT TRANSMEM 40..60
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT TRANSMEM 124..140
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT TRANSMEM 152..165
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT TRANSMEM 207..227
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT TRANSMEM 278..294
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT BINDING 117
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 129
FT /ligand="pheophytin a"
FT /ligand_id="ChEBI:CHEBI:136840"
FT /ligand_label="D2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT BINDING 142
FT /ligand="pheophytin a"
FT /ligand_id="ChEBI:CHEBI:136840"
FT /ligand_label="D2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383"
FT BINDING 197
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 214
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 214
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 261
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 268
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 HELIX 14..22
FT /evidence="ECO:0007829|PDB:7N8O"
FT STRAND 26..28
FT /evidence="ECO:0007829|PDB:6WJ6"
FT HELIX 31..54
FT /evidence="ECO:0007829|PDB:7N8O"
FT TURN 58..60
FT /evidence="ECO:0007829|PDB:7N8O"
FT STRAND 61..63
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:7N8O"
FT TURN 73..75
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 83..85
FT /evidence="ECO:0007829|PDB:7N8O"
FT TURN 95..99
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 101..106
FT /evidence="ECO:0007829|PDB:7N8O"
FT TURN 107..109
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 110..136
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 141..157
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 159..163
FT /evidence="ECO:0007829|PDB:7N8O"
FT STRAND 164..166
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 167..169
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 175..189
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 191..193
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 195..220
FT /evidence="ECO:0007829|PDB:7N8O"
FT STRAND 221..223
FT /evidence="ECO:0007829|PDB:7N8O"
FT STRAND 227..229
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 231..234
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 246..257
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 264..290
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 299..307
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 314..333
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 335..337
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 343..345
FT /evidence="ECO:0007829|PDB:7N8O"
FT HELIX 349..351
FT /evidence="ECO:0007829|PDB:6WJ6"
SQ SEQUENCE 352 AA; 39493 MW; 38707947A4A5E243 CRC64;
MTIAVGRAPV ERGWFDVLDD WLKRDRFVFI GWSGLLLFPC AFMALGGWLT GTTFVTSWYT
HGLASSYLEG ANFLTVAVSS PADAFGHSLL FLWGPEAQGN LTRWFQIGGL WPFVALHGAF
GLIGFMLRQF EISRLVGIRP YNAIAFSGPI AVFVSVFLMY PLGQSSWFFA PSFGVAGIFR
FILFLQGFHN WTLNPFHMMG VAGILGGALL CAIHGATVEN TLFEDGEDSN TFRAFEPTQA
EETYSMVTAN RFWSQIFGIA FSNKRWLHFF MLFVPVTGLW MSSVGIVGLA LNLRAYDFVS
QELRAAEDPE FETFYTKNIL LNEGMRAWMA PQDQPHENFI FPEEVLPRGN AL
