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Protein

Photosystem II protein D1 1

Gene

psbA1

Organism
Thermosynechococcus elongatus (strain BP-1)
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 annotation3 Publications

Catalytic activityi

2 H2O + 2 plastoquinone + 4 light = O2 + 2 plastoquinol.UniRule annotation2 Publications

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 (PubMed:19219048, PubMed:21367867). PSII binds additional chlorophylls, carotenoids and specific lipids.UniRule annotation10 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi118 – 1181Magnesium (chlorophyll-a ChlzD1 axial ligand); via tele nitrogen7 PublicationsUniRule annotation2 Publications
Binding sitei126 – 1261Pheophytin D18 PublicationsUniRule annotation2 Publications
Binding sitei130 – 1301Pheophytin D18 Publications2 Publications
Binding sitei147 – 1471Pheophytin D17 Publications2 Publications
Sitei161 – 1611Tyrosine radical intermediate5 PublicationsUniRule annotation
Metal bindingi170 – 1701Calcium-manganese-oxide [Ca-4Mn-5O]; calcium6 PublicationsUniRule annotation1 Publication
Metal bindingi170 – 1701Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 18 PublicationsUniRule annotation1 Publication
Metal bindingi189 – 1891Calcium-manganese-oxide [Ca-4Mn-5O]; calcium5 Publications1 Publication
Metal bindingi189 – 1891Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 28 PublicationsUniRule annotation1 Publication
Sitei190 – 1901Stabilizes free radical intermediateUniRule annotation
Metal bindingi198 – 1981Magnesium (chlorophyll-a PD1 axial ligand); via tele nitrogen7 PublicationsUniRule annotation2 Publications
Metal bindingi215 – 2151Iron; shared with heterodimeric partner; via tele nitrogen8 PublicationsUniRule annotation2 Publications
Binding sitei215 – 2151Quinone (B)5 PublicationsUniRule annotation2 Publications
Metal bindingi272 – 2721Iron; shared with heterodimeric partner; via tele nitrogen8 PublicationsUniRule annotation2 Publications
Metal bindingi332 – 3321Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2; via tele nitrogen8 PublicationsUniRule annotation1 Publication
Metal bindingi333 – 3331Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 18 PublicationsUniRule annotation1 Publication
Metal bindingi333 – 3331Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 39 PublicationsUniRule annotation
Metal bindingi342 – 3421Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 27 PublicationsUniRule annotation1 Publication
Metal bindingi342 – 3421Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 47 PublicationsUniRule annotation1 Publication
Metal bindingi344 – 3441Calcium-manganese-oxide [Ca-4Mn-5O]; calcium; via carboxylate6 PublicationsUniRule annotation1 Publication
Metal bindingi344 – 3441Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4; via carboxylate7 PublicationsUniRule annotation1 Publication

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

Enzyme and pathway databases

BRENDAi1.10.3.9. 7763.

Names & Taxonomyi

Protein namesi
Recommended name:
Photosystem II protein D1 1UniRule annotation (EC:1.10.3.9UniRule annotation2 Publications)
Short name:
PSII D1 protein 1UniRule annotation
Alternative name(s):
Photosystem II Q(B) protein 1UniRule annotation
Gene namesi
Name:psbA1UniRule annotationCurated
Synonyms:psbA-1
Ordered Locus Names:tlr1843
OrganismiThermosynechococcus elongatus (strain BP-1)
Taxonomic identifieri197221 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesThermosynechococcus
Proteomesi
  • UP000000440 Componenti: Chromosome

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini2 – 3130Cytoplasmic1 PublicationAdd
BLAST
Transmembranei32 – 4918Helical1 PublicationAdd
BLAST
Topological domaini50 – 11465Lumenal1 PublicationAdd
BLAST
Transmembranei115 – 13016Helical1 PublicationAdd
BLAST
Topological domaini131 – 14313Cytoplasmic1 PublicationAdd
BLAST
Transmembranei144 – 15613Helical1 PublicationAdd
BLAST
Topological domaini157 – 19640Lumenal1 PublicationAdd
BLAST
Transmembranei197 – 21418Helical1 PublicationAdd
BLAST
Topological domaini215 – 27359Cytoplasmic1 PublicationAdd
BLAST
Transmembranei274 – 28815HelicalUniRule annotation1 PublicationAdd
BLAST
Topological domaini289 – 34456Lumenal1 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
Initiator methionineiRemoved1 Publication
Chaini2 – 344343Photosystem II protein D1 1PRO_0000090485Add
BLAST
Propeptidei345 – 36016UniRule annotationPRO_0000316376Add
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.5 PublicationsUniRule annotation

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 annotation10 Publications

Protein-protein interaction databases

DIPiDIP-48487N.
STRINGi197221.tlr1843.

Structurei

Secondary structure

1
360
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi14 – 218Combined sources
Beta strandi24 – 285Combined 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 – 13728Combined sources
Helixi143 – 15816Combined sources
Helixi160 – 1656Combined sources
Helixi168 – 1703Combined sources
Helixi176 – 19015Combined sources
Helixi192 – 1943Combined sources
Helixi196 – 22126Combined sources
Beta strandi229 – 2313Combined 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 – 32913Combined sources
Turni330 – 3356Combined sources
Beta strandi339 – 3413Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1S5LX-ray3.50A/a1-344[»]
1W5CX-ray3.20A/G1-360[»]
2AXTX-ray3.00A/a1-344[»]
3KZIX-ray3.60A1-344[»]
4FBYX-ray6.56A/G1-344[»]
4IXQX-ray5.70A/a1-360[»]
4IXRX-ray5.90A/a1-360[»]
4PBUX-ray5.00A/a11-344[»]
4PJ0X-ray2.44A/a1-344[»]
4RVYX-ray5.50A/a11-344[»]
4TNHX-ray4.90A/a1-344[»]
4TNIX-ray4.60A/a1-344[»]
4TNJX-ray4.50A/a1-344[»]
4TNKX-ray5.20A/a1-344[»]
4V62X-ray2.90AA/BA1-344[»]
4V82X-ray3.20AA/BA1-344[»]
5E7CX-ray4.50A/a11-344[»]
ProteinModelPortaliP0A444.
SMRiP0A444. Positions 10-344.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A444.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni264 – 2652Quinone (B)5 PublicationsUniRule annotation2 Publications

Sequence similaritiesi

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

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105EY5. Bacteria.
ENOG410XPX5. LUCA.
HOGENOMiHOG000246913.
KOiK02703.
OMAiRESANLW.
OrthoDBiEOG6Q2SGP.

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.

P0A444-1 [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 LHFFLAAWPV VGVWFTALGI STMAFNLNGF
310 320 330 340 350
NFNHSVIDAK GNVINTWADI INRANLGMEV MHERNAHNFP LDLASAESAP
360
VAMIAPSING
Length:360
Mass (Da):39,737
Last modified:March 15, 2005 - v1
Checksum:iD4B45833FA46A4D4
GO

Mass spectrometryi

Molecular mass is 38144±224 Da from positions 2 - 344. Determined by MALDI. Mass for C-terminally truncated D1. The measured protein is probably a mixture of the products of the 3 psbA genes.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000039 Genomic DNA. Translation: BAC09395.1.
RefSeqiNP_682633.1. NC_004113.1.
WP_011057680.1. NC_004113.1.

Genome annotation databases

EnsemblBacteriaiBAC09395; BAC09395; BAC09395.
GeneIDi1010908.
KEGGitel:tlr1843.
PATRICi23929074. VBITheElo119873_1926.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000039 Genomic DNA. Translation: BAC09395.1.
RefSeqiNP_682633.1. NC_004113.1.
WP_011057680.1. NC_004113.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1S5LX-ray3.50A/a1-344[»]
1W5CX-ray3.20A/G1-360[»]
2AXTX-ray3.00A/a1-344[»]
3KZIX-ray3.60A1-344[»]
4FBYX-ray6.56A/G1-344[»]
4IXQX-ray5.70A/a1-360[»]
4IXRX-ray5.90A/a1-360[»]
4PBUX-ray5.00A/a11-344[»]
4PJ0X-ray2.44A/a1-344[»]
4RVYX-ray5.50A/a11-344[»]
4TNHX-ray4.90A/a1-344[»]
4TNIX-ray4.60A/a1-344[»]
4TNJX-ray4.50A/a1-344[»]
4TNKX-ray5.20A/a1-344[»]
4V62X-ray2.90AA/BA1-344[»]
4V82X-ray3.20AA/BA1-344[»]
5E7CX-ray4.50A/a11-344[»]
ProteinModelPortaliP0A444.
SMRiP0A444. Positions 10-344.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48487N.
STRINGi197221.tlr1843.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC09395; BAC09395; BAC09395.
GeneIDi1010908.
KEGGitel:tlr1843.
PATRICi23929074. VBITheElo119873_1926.

Phylogenomic databases

eggNOGiENOG4105EY5. Bacteria.
ENOG410XPX5. LUCA.
HOGENOMiHOG000246913.
KOiK02703.
OMAiRESANLW.
OrthoDBiEOG6Q2SGP.

Enzyme and pathway databases

BRENDAi1.10.3.9. 7763.

Miscellaneous databases

EvolutionaryTraceiP0A444.

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

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: BP-1.
  2. "Crystal structure of photosystem II from Synechococcus elongatus at 3.8 A resolution."
    Zouni A., Witt H.T., Kern J., Fromme P., Krauss N., Saenger W., Orth P.
    Nature 409:739-743(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF 1-360.
  3. "Crystal structure of cyanobacterial photosystem II at 3.2 A resolution: a closer look at the Mn-cluster."
    Biesiadka J., Loll B., Kern J., Irrgang K.-D., Zouni A.
    Phys. Chem. Chem. Phys. 6:4733-4736(2004)
    Cited for: X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS) IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
  4. "Architecture of the photosynthetic oxygen-evolving center."
    Ferreira K.N., Iverson T.M., Maghlaoui K., Barber J., Iwata S.
    Science 303:1831-1838(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF 1-344 IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
  5. "Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II."
    Loll B., Kern J., Saenger W., Zouni A., Biesiadka J.
    Nature 438:1040-1044(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 1-344 IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.
  6. "Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride."
    Guskov A., Kern J., Gabdulkhakov A., Broser M., Zouni A., Saenger W.
    Nat. Struct. Mol. Biol. 16:334-342(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) OF 1-344 IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION, MASS SPECTROMETRY.
    Strain: BP-1.
  7. "Crystal structure of monomeric photosystem II from Thermosynechococcus elongatus at 3.6 A resolution."
    Broser M., Gabdulkhakov A., Kern J., Guskov A., Muh F., Saenger W., Zouni A.
    J. Biol. Chem. 285:26255-26262(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.60 ANGSTROMS) OF 1-344 IN PHOTOSYSTEM II, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.
  8. "Structural basis of cyanobacterial photosystem II inhibition by the herbicide terbutryn."
    Broser M., Glockner C., Gabdulkhakov A., Guskov A., Buchta J., Kern J., Muh F., Dau H., Saenger W., Zouni A.
    J. Biol. Chem. 286:15964-15972(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS) OF 1-344 IN PHOTOSYSTEM II IN COMPLEX WITH HERBICIDE, FUNCTION, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.
  9. Cited for: X-RAY CRYSTALLOGRAPHY (6.56 ANGSTROMS) OF 1-344 IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.
  10. Cited for: X-RAY CRYSTALLOGRAPHY (5.70 ANGSTROMS) IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.
  11. "Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser."
    Kupitz C., Basu S., Grotjohann I., Fromme R., Zatsepin N.A., Rendek K.N., Hunter M.S., Shoeman R.L., White T.A., Wang D., James D., Yang J.H., Cobb D.E., Reeder B., Sierra R.G., Liu H., Barty A., Aquila A.L.
    , Deponte D., Kirian R.A., Bari S., Bergkamp J.J., Beyerlein K.R., Bogan M.J., Caleman C., Chao T.C., Conrad C.E., Davis K.M., Fleckenstein H., Galli L., Hau-Riege S.P., Kassemeyer S., Laksmono H., Liang M., Lomb L., Marchesini S., Martin A.V., Messerschmidt M., Milathianaki D., Nass K., Ros A., Roy-Chowdhury S., Schmidt K., Seibert M., Steinbrener J., Stellato F., Yan L., Yoon C., Moore T.A., Moore A.L., Pushkar Y., Williams G.J., Boutet S., Doak R.B., Weierstall U., Frank M., Chapman H.N., Spence J.C., Fromme P.
    Nature 513:261-265(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (5.00 ANGSTROMS) OF 11-344 IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.
  12. Cited for: X-RAY CRYSTALLOGRAPHY (4.50 ANGSTROMS) OF 1-344 IN PHOTOSYSTEM II, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.

Entry informationi

Entry nameiPSBA1_THEEB
AccessioniPrimary (citable) accession number: P0A444
Secondary accession number(s): P35876
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: March 15, 2005
Last modified: April 13, 2016
This is version 92 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 annotation2 Publications
Herbicides such as terbutryn, atrazine, BNT, diuron or ioxynil bind in the Q(B) binding site and block subsequent electron transfer.UniRule annotation1 Publication
Cyanobacteria usually contain more than 2 copies of the psbA gene; this strain encodes 3.UniRule annotation1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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.