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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)DescriptionActionsGraphical viewLength
Metal bindingi118Magnesium (chlorophyll-a ChlzD1 axial ligand); via tele nitrogen7 PublicationsUniRule annotation2 Publications1
Binding sitei126Pheophytin D18 PublicationsUniRule annotation2 Publications1
Binding sitei130Pheophytin D18 Publications2 Publications1
Binding sitei147Pheophytin D17 Publications2 Publications1
Sitei161Tyrosine radical intermediate5 PublicationsUniRule annotation1
Metal bindingi170Calcium-manganese-oxide [Ca-4Mn-5O]; calcium6 PublicationsUniRule annotation1 Publication1
Metal bindingi170Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 18 PublicationsUniRule annotation1 Publication1
Metal bindingi189Calcium-manganese-oxide [Ca-4Mn-5O]; calcium5 Publications1 Publication1
Metal bindingi189Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 28 PublicationsUniRule annotation1 Publication1
Sitei190Stabilizes free radical intermediateUniRule annotation1
Metal bindingi198Magnesium (chlorophyll-a PD1 axial ligand); via tele nitrogen7 PublicationsUniRule annotation2 Publications1
Metal bindingi215Iron; shared with heterodimeric partner; via tele nitrogen8 PublicationsUniRule annotation2 Publications1
Binding sitei215Quinone (B)5 PublicationsUniRule annotation2 Publications1
Metal bindingi272Iron; shared with heterodimeric partner; via tele nitrogen8 PublicationsUniRule annotation2 Publications1
Metal bindingi332Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2; via tele nitrogen8 PublicationsUniRule annotation1 Publication1
Metal bindingi333Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 18 PublicationsUniRule annotation1 Publication1
Metal bindingi333Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 39 PublicationsUniRule annotation1
Metal bindingi342Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 27 PublicationsUniRule annotation1 Publication1
Metal bindingi342Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 47 PublicationsUniRule annotation1 Publication1
Metal bindingi344Calcium-manganese-oxide [Ca-4Mn-5O]; calcium; via carboxylate6 PublicationsUniRule annotation1 Publication1
Metal bindingi344Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4; via carboxylate7 PublicationsUniRule annotation1 Publication1

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 lineageiBacteriaCyanobacteriaSynechococcalesSynechococcaceaeThermosynechococcus
Proteomesi
  • UP000000440 Componenti: Chromosome

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini2 – 31Cytoplasmic1 PublicationAdd BLAST30
Transmembranei32 – 49Helical1 PublicationAdd BLAST18
Topological domaini50 – 114Lumenal1 PublicationAdd BLAST65
Transmembranei115 – 130Helical1 PublicationAdd BLAST16
Topological domaini131 – 143Cytoplasmic1 PublicationAdd BLAST13
Transmembranei144 – 156Helical1 PublicationAdd BLAST13
Topological domaini157 – 196Lumenal1 PublicationAdd BLAST40
Transmembranei197 – 214Helical1 PublicationAdd BLAST18
Topological domaini215 – 273Cytoplasmic1 PublicationAdd BLAST59
Transmembranei274 – 288HelicalUniRule annotation1 PublicationAdd BLAST15
Topological domaini289 – 344Lumenal1 PublicationAdd BLAST56

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane, Photosystem II, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000904852 – 344Photosystem II protein D1 1Add BLAST343
PropeptideiPRO_0000316376345 – 360UniRule annotationAdd BLAST16

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)DescriptionActionsGraphical viewLength
Sitei344 – 345Cleavage; by CtpAUniRule annotation2

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

1360
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi14 – 21Combined sources8
Beta strandi24 – 28Combined sources5
Helixi31 – 54Combined sources24
Beta strandi62 – 64Combined sources3
Helixi71 – 73Combined sources3
Turni77 – 79Combined sources3
Turni87 – 91Combined sources5
Helixi96 – 98Combined sources3
Beta strandi99 – 101Combined sources3
Helixi102 – 107Combined sources6
Helixi110 – 137Combined sources28
Helixi143 – 158Combined sources16
Helixi160 – 165Combined sources6
Helixi168 – 170Combined sources3
Helixi176 – 190Combined sources15
Helixi192 – 194Combined sources3
Helixi196 – 221Combined sources26
Beta strandi229 – 231Combined sources3
Helixi233 – 236Combined sources4
Helixi248 – 258Combined sources11
Helixi261 – 263Combined sources3
Helixi268 – 293Combined sources26
Turni294 – 296Combined sources3
Beta strandi297 – 299Combined sources3
Beta strandi309 – 311Combined sources3
Helixi317 – 329Combined sources13
Turni330 – 335Combined sources6
Beta strandi339 – 341Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A444.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni264 – 265Quinone (B)5 PublicationsUniRule annotation2 Publications2

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.
OrthoDBiPOG091H15P4.

Family and domain databases

CDDicd09289. Photosystem-II_D1. 1 hit.
Gene3Di1.20.85.10. 1 hit.
HAMAPiMF_01379. PSII_PsbA_D1. 1 hit.
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
PDB 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.
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.
OrthoDBiPOG091H15P4.

Enzyme and pathway databases

BRENDAi1.10.3.9. 7763.

Miscellaneous databases

EvolutionaryTraceiP0A444.

Family and domain databases

CDDicd09289. Photosystem-II_D1. 1 hit.
Gene3Di1.20.85.10. 1 hit.
HAMAPiMF_01379. PSII_PsbA_D1. 1 hit.
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...

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: November 30, 2016
This is version 97 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.