PSBD_THEVL
ID PSBD_THEVL Reviewed; 342 AA.
AC D0VWR8;
DT 29-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 29-MAY-2013, sequence version 2.
DT 03-AUG-2022, entry version 57.
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};
DE Flags: Fragment;
GN Name=psbD {ECO:0000255|HAMAP-Rule:MF_01383};
OS Thermostichus vulcanus (Synechococcus vulcanus).
OC Bacteria; Cyanobacteria; Thermostichales; Thermostichaceae; Thermostichus.
OX NCBI_TaxID=32053;
RN [1]
RP X-RAY CRYSTALLOGRAPHY (3.7 ANGSTROMS) IN PHOTOSYSTEM II, COFACTOR, SUBUNIT,
RP AND SUBCELLULAR LOCATION.
RX PubMed=12518057; DOI=10.1073/pnas.0135651100;
RA Kamiya N., Shen J.-R.;
RT "Crystal structure of oxygen-evolving photosystem II from
RT Thermosynechococcus vulcanus at 3.7-A resolution.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:98-103(2003).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (3.70 ANGSTROMS) OF 3-342 IN COMPLEX WITH CHLOROPHYLL
RP A AND IRON IN PHOTOSYSTEM II, FUNCTION, COFACTOR, SUBUNIT, SUBCELLULAR
RP LOCATION, AND POSSIBLE CL(-) LIGAND.
RX PubMed=19433803; DOI=10.1073/pnas.0812797106;
RA Kawakami K., Umena Y., Kamiya N., Shen J.R.;
RT "Location of chloride and its possible functions in oxygen-evolving
RT photosystem II revealed by X-ray crystallography.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:8567-8572(2009).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 3-342 IN COMPLEX WITH CHLOROPHYLL
RP A; BETA-CAROTENE AND PHEOPHYTIN A IN PHOTOSYSTEM II, COFACTOR, SUBUNIT,
RP SUBCELLULAR LOCATION, AND TOPOLOGY.
RX PubMed=21499260; DOI=10.1038/nature09913;
RA Umena Y., Kawakami K., Shen J.R., Kamiya N.;
RT "Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9
RT A.";
RL Nature 473:55-60(2011).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN PHOTOSYSTEM II, FUNCTION,
RP COFACTOR, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=23426624; DOI=10.1073/pnas.1219922110;
RA Koua F.H., Umena Y., Kawakami K., Shen J.R.;
RT "Structure of Sr-substituted photosystem II at 2.1 A resolution and its
RT implications in the mechanism of water oxidation.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:3889-3894(2013).
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 (PubMed:19433803, PubMed:23426624). D2 is
CC needed for assembly of a stable PSII complex. {ECO:0000255|HAMAP-
CC Rule:MF_01383, ECO:0000269|PubMed:19433803,
CC ECO:0000269|PubMed:23426624}.
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 ECO:0000269|PubMed:12518057, ECO:0000269|PubMed:19433803,
CC ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624};
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:12518057, ECO:0000269|PubMed:19433803,
CC ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624}.
CC -!- SUBCELLULAR LOCATION: Cellular thylakoid membrane {ECO:0000255|HAMAP-
CC Rule:MF_01383, ECO:0000269|PubMed:12518057,
CC ECO:0000269|PubMed:19433803, ECO:0000269|PubMed:21499260,
CC ECO:0000269|PubMed:23426624}; Multi-pass membrane protein
CC {ECO:0000255|HAMAP-Rule:MF_01383, ECO:0000269|PubMed:12518057,
CC ECO:0000269|PubMed:19433803, ECO:0000269|PubMed:21499260,
CC ECO:0000269|PubMed:23426624}.
CC -!- MISCELLANEOUS: 2 of the reaction center chlorophylls (ChlD1 and ChlD2)
CC are entirely coordinated by water. {ECO:0000255|HAMAP-Rule:MF_01383,
CC ECO:0000269|PubMed:21499260}.
CC -!- SIMILARITY: Belongs to the reaction center PufL/M/PsbA/D family.
CC {ECO:0000255|HAMAP-Rule:MF_01383}.
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DR PDB; 1IZL; X-ray; 3.70 A; D/N=1-342.
DR PDB; 3A0B; X-ray; 3.70 A; D/d=3-342.
DR PDB; 3A0H; X-ray; 4.00 A; D/d=3-342.
DR PDB; 3WU2; X-ray; 1.90 A; D/d=1-342.
DR PDB; 4IL6; X-ray; 2.10 A; D/d=1-342.
DR PDB; 4UB6; X-ray; 1.95 A; D/d=1-342.
DR PDB; 4UB8; X-ray; 1.95 A; D/d=1-342.
DR PDB; 5B5E; X-ray; 1.87 A; D/d=1-342.
DR PDB; 5B66; X-ray; 1.85 A; D/d=1-342.
DR PDB; 5GTH; X-ray; 2.50 A; D/d=1-342.
DR PDB; 5GTI; X-ray; 2.50 A; D/d=1-342.
DR PDB; 5V2C; X-ray; 1.90 A; D/d=1-342.
DR PDB; 5WS5; X-ray; 2.35 A; D/d=1-342.
DR PDB; 5WS6; X-ray; 2.35 A; D/d=1-342.
DR PDB; 6JLJ; X-ray; 2.15 A; D/d=1-342.
DR PDB; 6JLK; X-ray; 2.15 A; D/d=1-342.
DR PDB; 6JLL; X-ray; 2.15 A; D/d=1-342.
DR PDB; 6JLM; X-ray; 2.35 A; D/d=1-342.
DR PDB; 6JLN; X-ray; 2.40 A; D/d=1-342.
DR PDB; 6JLO; X-ray; 2.40 A; D/d=1-342.
DR PDB; 6JLP; X-ray; 2.50 A; D/d=1-342.
DR PDB; 7CJI; X-ray; 2.35 A; D/d=1-342.
DR PDB; 7CJJ; X-ray; 2.40 A; D/d=1-342.
DR PDB; 7COU; X-ray; 2.25 A; D/d=1-342.
DR PDB; 7CZL; EM; 3.78 A; D/d=3-341.
DR PDB; 7D1T; EM; 1.95 A; D/d=1-342.
DR PDB; 7D1U; EM; 2.08 A; D/d=1-342.
DR PDB; 7DXA; EM; 3.14 A; d=1-342.
DR PDB; 7DXH; EM; 3.14 A; d=1-342.
DR PDB; 7EDA; EM; 2.78 A; D=2-342.
DR PDBsum; 1IZL; -.
DR PDBsum; 3A0B; -.
DR PDBsum; 3A0H; -.
DR PDBsum; 3WU2; -.
DR PDBsum; 4IL6; -.
DR PDBsum; 4UB6; -.
DR PDBsum; 4UB8; -.
DR PDBsum; 5B5E; -.
DR PDBsum; 5B66; -.
DR PDBsum; 5GTH; -.
DR PDBsum; 5GTI; -.
DR PDBsum; 5V2C; -.
DR PDBsum; 5WS5; -.
DR PDBsum; 5WS6; -.
DR PDBsum; 6JLJ; -.
DR PDBsum; 6JLK; -.
DR PDBsum; 6JLL; -.
DR PDBsum; 6JLM; -.
DR PDBsum; 6JLN; -.
DR PDBsum; 6JLO; -.
DR PDBsum; 6JLP; -.
DR PDBsum; 7CJI; -.
DR PDBsum; 7CJJ; -.
DR PDBsum; 7COU; -.
DR PDBsum; 7CZL; -.
DR PDBsum; 7D1T; -.
DR PDBsum; 7D1U; -.
DR PDBsum; 7DXA; -.
DR PDBsum; 7DXH; -.
DR PDBsum; 7EDA; -.
DR AlphaFoldDB; D0VWR8; -.
DR SMR; D0VWR8; -.
DR DIP; DIP-61466N; -.
DR IntAct; D0VWR8; 1.
DR EvolutionaryTrace; D0VWR8; -.
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:0031676; C:plasma membrane-derived thylakoid membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016168; F:chlorophyll binding; IEA:UniProtKB-KW.
DR GO; GO:0045156; F:electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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; Chlorophyll; Chromophore; Electron transport; Iron;
KW Magnesium; Membrane; Metal-binding; Oxidoreductase; Photosynthesis;
KW Photosystem II; Thylakoid; Transmembrane; Transmembrane helix; Transport.
FT CHAIN 1..342
FT /note="Photosystem II D2 protein"
FT /id="PRO_0000422602"
FT TOPO_DOM 1..29
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:21499260"
FT TRANSMEM 30..50
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383,
FT ECO:0000269|PubMed:21499260"
FT TOPO_DOM 51..113
FT /note="Lumenal"
FT /evidence="ECO:0000269|PubMed:21499260"
FT TRANSMEM 114..130
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383,
FT ECO:0000269|PubMed:21499260"
FT TOPO_DOM 131..141
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:21499260"
FT TRANSMEM 142..155
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383,
FT ECO:0000269|PubMed:21499260"
FT TOPO_DOM 156..196
FT /note="Lumenal"
FT /evidence="ECO:0000269|PubMed:21499260"
FT TRANSMEM 197..217
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383,
FT ECO:0000269|PubMed:21499260"
FT TOPO_DOM 218..267
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:21499260"
FT TRANSMEM 268..284
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383,
FT ECO:0000269|PubMed:21499260"
FT TOPO_DOM 285..342
FT /note="Lumenal"
FT /evidence="ECO:0000269|PubMed:21499260"
FT BINDING 107
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 ECO:0000269|PubMed:23426624"
FT BINDING 119
FT /ligand="pheophytin a"
FT /ligand_id="ChEBI:CHEBI:136840"
FT /ligand_label="D2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383,
FT ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624"
FT BINDING 132
FT /ligand="pheophytin a"
FT /ligand_id="ChEBI:CHEBI:136840"
FT /ligand_label="D2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383,
FT ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624,
FT ECO:0000303|PubMed:19433803"
FT BINDING 187
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 ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624"
FT BINDING 204
FT /ligand="a plastoquinone"
FT /ligand_id="ChEBI:CHEBI:17757"
FT /ligand_label="Q(A)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383,
FT ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624,
FT ECO:0000303|PubMed:19433803"
FT BINDING 204
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 ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624,
FT ECO:0000303|PubMed:19433803"
FT BINDING 251
FT /ligand="a plastoquinone"
FT /ligand_id="ChEBI:CHEBI:17757"
FT /ligand_label="Q(A)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01383,
FT ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624"
FT BINDING 258
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 ECO:0000269|PubMed:21499260, ECO:0000269|PubMed:23426624,
FT ECO:0000303|PubMed:19433803"
FT NON_TER 1
FT HELIX 4..12
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 21..44
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 48..51
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 57..59
FT /evidence="ECO:0007829|PDB:5B66"
FT TURN 63..65
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:5B66"
FT TURN 85..89
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 91..96
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 99..126
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 131..147
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 149..153
FT /evidence="ECO:0007829|PDB:5B66"
FT STRAND 154..156
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 165..179
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 181..183
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 185..210
FT /evidence="ECO:0007829|PDB:5B66"
FT STRAND 211..213
FT /evidence="ECO:0007829|PDB:5B66"
FT STRAND 216..220
FT /evidence="ECO:0007829|PDB:7COU"
FT HELIX 221..224
FT /evidence="ECO:0007829|PDB:3WU2"
FT HELIX 226..228
FT /evidence="ECO:0007829|PDB:7DXA"
FT TURN 229..232
FT /evidence="ECO:0007829|PDB:7DXA"
FT HELIX 236..247
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 254..280
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 289..297
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 304..323
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 325..327
FT /evidence="ECO:0007829|PDB:5B66"
FT HELIX 333..335
FT /evidence="ECO:0007829|PDB:5B66"
SQ SEQUENCE 342 AA; 38379 MW; 3CD88A6D811BB788 CRC64;
ERGWFDILDD WLKRDRFVFV GWSGILLFPC AYLALGGWLT GTTFVTSWYT HGLASSYLEG
CNFLTVAVST PANSMGHSLL LLWGPEAQGD FTRWCQLGGL WTFIALHGAF GLIGFMLRQF
EIARLVGVRP YNAIAFSAPI AVFVSVFLIY PLGQSSWFFA PSFGVAAIFR FLLFFQGFHN
WTLNPFHMMG VAGVLGGALL CAIHGATVEN TLFQDGEGAS TFRAFNPTQA EETYSMVTAN
RFWSQIFGIA FSNKRWLHFF MLFVPVTGLW MSAIGVVGLA LNLRSYDFIS QEIRAAEDPE
FETFYTKNLL LNEGIRAWMA PQDQPHENFV FPEEVLPRGN AL
