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Protein

Photosystem II protein D1

Gene

psbA

Organism
Thermosynechococcus vulcanus (Synechococcus vulcanus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Photosystem II (PSII) is a light-driven water: plastoquinone oxidoreductase that uses light energy to abstract electrons from H2O, generating O2 and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors.UniRule annotation2 Publications

Catalytic activityi

2 H2O + 2 plastoquinone + 4 light = O2 + 2 plastoquinol.UniRule annotation

Cofactori

Note: The D1/D2 heterodimer binds P680, chlorophylls that are the primary electron donor of PSII, and subsequent electron acceptors. It shares a non-heme iron and each subunit binds pheophytin, quinone, additional chlorophylls, carotenoids and lipids. D1 provides most of the ligands for the Mn4-Ca-O5 cluster of the oxygen-evolving complex (OEC). There is also a Cl(-1) ion associated with D1 and D2, which is required for oxygen evolution. The PSII complex binds additional chlorophylls, carotenoids and specific lipids.UniRule annotation4 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi118 – 1181Magnesium (chlorophyll-a ChlzD1 axial ligand); via tele nitrogenUniRule annotation1 Publication
Binding sitei126 – 1261Pheophytin D1UniRule annotation3 Publications
Binding sitei130 – 1301Pheophytin D11 Publication2 Publications
Binding sitei147 – 1471Pheophytin D13 Publications
Sitei161 – 1611Tyrosine radical intermediate2 PublicationsUniRule annotation1 Publication
Metal bindingi170 – 1701Calcium-manganese-oxide [Ca-4Mn-5O]; calcium1 PublicationUniRule annotation2 Publications
Metal bindingi170 – 1701Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 12 PublicationsUniRule annotation2 Publications
Metal bindingi189 – 1891Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 21 PublicationUniRule annotation2 Publications
Sitei190 – 1901Stabilizes free radical intermediateUniRule annotation
Metal bindingi198 – 1981Magnesium (chlorophyll-a PD1 axial ligand); via tele nitrogenUniRule annotation2 Publications
Binding sitei214 – 2141Pheophytin D12 Publications
Metal bindingi215 – 2151Iron; shared with heterodimeric partner; via tele nitrogen1 PublicationUniRule annotation2 Publications
Binding sitei215 – 2151Quinone (B)1 PublicationUniRule annotation2 Publications
Metal bindingi272 – 2721Iron; shared with heterodimeric partner; via tele nitrogen1 PublicationUniRule annotation2 Publications
Metal bindingi332 – 3321Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2; via tele nitrogen1 PublicationUniRule annotation2 Publications
Metal bindingi333 – 3331Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 11 PublicationUniRule annotation2 Publications
Metal bindingi333 – 3331Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 31 PublicationUniRule annotation2 Publications
Metal bindingi342 – 3421Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 21 PublicationUniRule annotation2 Publications
Metal bindingi342 – 3421Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 41 PublicationUniRule annotation2 Publications
Metal bindingi344 – 3441Calcium-manganese-oxide [Ca-4Mn-5O]; calcium; via carboxylate1 PublicationUniRule annotation2 Publications
Metal bindingi344 – 3441Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4; via carboxylate2 PublicationsUniRule annotation2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Herbicide resistance, Photosynthesis, Transport

Keywords - Ligandi

Calcium, Chlorophyll, Chromophore, Iron, Magnesium, Manganese, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Photosystem II protein D1UniRule annotation (EC:1.10.3.9UniRule annotation)
Short name:
PSII D1 proteinUniRule annotation
Alternative name(s):
Photosystem II Q(B) proteinUniRule annotation
Gene namesi
Name:psbAUniRule annotation
Synonyms:psbA-1
OrganismiThermosynechococcus vulcanus (Synechococcus vulcanus)
Taxonomic identifieri32053 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesThermosynechococcus

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 2828Cytoplasmic1 PublicationAdd
BLAST
Transmembranei29 – 4618HelicalUniRule annotation1 PublicationAdd
BLAST
Topological domaini47 – 11771Lumenal1 PublicationAdd
BLAST
Transmembranei118 – 13316HelicalUniRule annotation1 PublicationAdd
BLAST
Topological domaini134 – 1418Cytoplasmic1 Publication
Transmembranei142 – 15615HelicalUniRule annotation1 PublicationAdd
BLAST
Topological domaini157 – 19640Lumenal1 PublicationAdd
BLAST
Transmembranei197 – 21822HelicalUniRule annotation1 PublicationAdd
BLAST
Topological domaini219 – 27355Cytoplasmic1 PublicationAdd
BLAST
Transmembranei274 – 28815HelicalUniRule annotation1 PublicationAdd
BLAST
Topological domaini289 – 36072Lumenal1 PublicationAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane, Photosystem II, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 344344Photosystem II protein D1UniRule annotationPRO_0000090491Add
BLAST
Propeptidei345 – 36016UniRule annotationPRO_0000316426Add
BLAST

Post-translational modificationi

C-terminally processed by CtpA; processing is essential to allow assembly of the oxygen-evolving complex and thus photosynthetic growth.UniRule annotation
Tyr-161 forms a radical intermediate that is referred to as redox-active TyrZ, YZ or Y-Z.2 PublicationsUniRule annotation1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei344 – 3452Cleavage; by CtpAUniRule annotation

Interactioni

Subunit structurei

Cyanobacterial PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Ycf12, at least 3 peripheral proteins PsbO, PsbU, PsbV and a large number of cofactors. It forms dimeric complexes.UniRule annotation4 Publications

Protein-protein interaction databases

DIPiDIP-48859N.

Structurei

Secondary structure

1
360
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi13 – 219Combined sources
Beta strandi26 – 283Combined sources
Helixi31 – 5424Combined sources
Beta strandi62 – 643Combined sources
Helixi71 – 733Combined sources
Turni77 – 793Combined sources
Turni87 – 915Combined sources
Helixi96 – 983Combined sources
Beta strandi99 – 1013Combined sources
Helixi102 – 1076Combined sources
Helixi110 – 13627Combined sources
Helixi143 – 15816Combined sources
Helixi160 – 1656Combined sources
Helixi168 – 1703Combined sources
Helixi176 – 19015Combined sources
Helixi192 – 1943Combined sources
Helixi196 – 22126Combined sources
Helixi233 – 2364Combined sources
Helixi248 – 25811Combined sources
Helixi261 – 2633Combined sources
Helixi268 – 29326Combined sources
Turni294 – 2963Combined sources
Beta strandi297 – 2993Combined sources
Beta strandi309 – 3113Combined sources
Helixi317 – 33115Combined sources
Turni332 – 3365Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IZLX-ray3.70A/J1-360[»]
3A0BX-ray3.70A/a1-344[»]
3A0HX-ray4.00A/a1-344[»]
3WU2X-ray1.90A/a1-344[»]
4IL6X-ray2.10A/a11-344[»]
4UB6X-ray1.95A/a1-344[»]
4UB8X-ray1.95A/a1-344[»]
ProteinModelPortaliP51765.
SMRiP51765. Positions 10-344.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP51765.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni264 – 2652Quinone (B)1 PublicationUniRule annotation2 Publications

Sequence similaritiesi

Belongs to the reaction center PufL/M/PsbA/D family.UniRule annotation

Keywords - Domaini

Transmembrane, Transmembrane helix

Family and domain databases

Gene3Di1.20.85.10. 1 hit.
HAMAPiMF_01379. PSII_PsbA_D1.
InterProiIPR000484. Photo_RC_L/M.
IPR005867. PSII_D1.
[Graphical view]
PfamiPF00124. Photo_RC. 1 hit.
[Graphical view]
SUPFAMiSSF81483. SSF81483. 1 hit.
TIGRFAMsiTIGR01151. psbA. 1 hit.
PROSITEiPS00244. REACTION_CENTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P51765-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTTTLQRRES ANLWERFCNW VTSTDNRLYV GWFGVIMIPT LLAATICFVI
60 70 80 90 100
AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVVPSSNAIG LHFYPIWEAA
110 120 130 140 150
SLDEWLYNGG PYQLIIFHFL LGASCYMGRQ WELSYRLGMR PWICVAYSAP
160 170 180 190 200
LASAFAVFLI YPIGQGSFSD GMPLGISGTF NFMIVFQAEH NILMHPFHQL
210 220 230 240 250
GVAGVFGGAL FCAMHGSLVT SSLIRETTET ESANYGYKFG QEEETYNIVA
260 270 280 290 300
AHGYFGRLIF QYASFNNSRS LHFFLAAWRV VGVWFAALGI STMAFNLNGF
310 320 330 340 350
NFNHSVIDAK GNVINTWADI INRANLGMEV MHERNAHNFP LDLASAESAP
360
VAMIAPSING
Length:360
Mass (Da):39,766
Last modified:October 1, 1996 - v1
Checksum:iD4B7FD7418E3E335
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X79222 Genomic DNA. Translation: CAA55806.1.
PIRiS45009.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X79222 Genomic DNA. Translation: CAA55806.1.
PIRiS45009.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IZLX-ray3.70A/J1-360[»]
3A0BX-ray3.70A/a1-344[»]
3A0HX-ray4.00A/a1-344[»]
3WU2X-ray1.90A/a1-344[»]
4IL6X-ray2.10A/a11-344[»]
4UB6X-ray1.95A/a1-344[»]
4UB8X-ray1.95A/a1-344[»]
ProteinModelPortaliP51765.
SMRiP51765. Positions 10-344.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48859N.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP51765.

Family and domain databases

Gene3Di1.20.85.10. 1 hit.
HAMAPiMF_01379. PSII_PsbA_D1.
InterProiIPR000484. Photo_RC_L/M.
IPR005867. PSII_D1.
[Graphical view]
PfamiPF00124. Photo_RC. 1 hit.
[Graphical view]
SUPFAMiSSF81483. SSF81483. 1 hit.
TIGRFAMsiTIGR01151. psbA. 1 hit.
PROSITEiPS00244. REACTION_CENTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Structure of the D1 subunit of photosystem II in the thermophyllic cyanobacterium Synechococcus vulcanus."
    Dibrov Y., Rahat A., Ohad N., Hirschberg J.
    Submitted (MAY-1994) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Copeland.
  2. "Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-A resolution."
    Kamiya N., Shen J.-R.
    Proc. Natl. Acad. Sci. U.S.A. 100:98-103(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.7 ANGSTROMS) IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
  3. "Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography."
    Kawakami K., Umena Y., Kamiya N., Shen J.R.
    Proc. Natl. Acad. Sci. U.S.A. 106:8567-8572(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.7 ANGSTROMS) OF 1-344 IN COMPLEX WITH CHLOROPHYLL A AND PHEOPHYTIN A IN PHOTOSYSTEM II, FUNCTION, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION, POSSIBLE CL(-) LIGAND.
  4. "Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 A."
    Umena Y., Kawakami K., Shen J.R., Kamiya N.
    Nature 473:55-60(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-344 IN COMPLEX WITH CA-4MN-5O CLUSTER; CHLOROPHYLL A AND PHEOPHYTIN A IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION, TOPOLOGY.
  5. "Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation."
    Koua F.H., Umena Y., Kawakami K., Shen J.R.
    Proc. Natl. Acad. Sci. U.S.A. 110:3889-3894(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 11-344 IN PHOTOSYSTEM II, FUNCTION, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiPSBA_THEVL
AccessioniPrimary (citable) accession number: P51765
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: July 6, 2016
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water.UniRule annotation1 Publication
Cyanobacteria usually contain more than 2 copies of the psbA gene.UniRule annotationCurated
Herbicides such as atrazine, BNT, diuron or ioxynil bind in the Q(B) binding site and block subsequent electron transfer.UniRule annotation

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.