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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)DescriptionActionsGraphical viewLength
Metal bindingi118Magnesium (chlorophyll-a ChlzD1 axial ligand); via tele nitrogenUniRule annotation1 Publication1
Binding sitei126Pheophytin D1UniRule annotation3 Publications1
Binding sitei130Pheophytin D11 Publication2 Publications1
Binding sitei147Pheophytin D13 Publications1
Sitei161Tyrosine radical intermediate2 PublicationsUniRule annotation1 Publication1
Metal bindingi170Calcium-manganese-oxide [Ca-4Mn-5O]; calcium1 PublicationUniRule annotation2 Publications1
Metal bindingi170Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 12 PublicationsUniRule annotation2 Publications1
Metal bindingi189Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 21 PublicationUniRule annotation2 Publications1
Sitei190Stabilizes free radical intermediateUniRule annotation1
Metal bindingi198Magnesium (chlorophyll-a PD1 axial ligand); via tele nitrogenUniRule annotation2 Publications1
Binding sitei214Pheophytin D12 Publications1
Metal bindingi215Iron; shared with heterodimeric partner; via tele nitrogen1 PublicationUniRule annotation2 Publications1
Binding sitei215Quinone (B)1 PublicationUniRule annotation2 Publications1
Metal bindingi272Iron; shared with heterodimeric partner; via tele nitrogen1 PublicationUniRule annotation2 Publications1
Metal bindingi332Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2; via tele nitrogen1 PublicationUniRule annotation2 Publications1
Metal bindingi333Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 11 PublicationUniRule annotation2 Publications1
Metal bindingi333Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 31 PublicationUniRule annotation2 Publications1
Metal bindingi342Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 21 PublicationUniRule annotation2 Publications1
Metal bindingi342Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 41 PublicationUniRule annotation2 Publications1
Metal bindingi344Calcium-manganese-oxide [Ca-4Mn-5O]; calcium; via carboxylate1 PublicationUniRule annotation2 Publications1
Metal bindingi344Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4; via carboxylate2 PublicationsUniRule annotation2 Publications1

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 lineageiBacteriaCyanobacteriaSynechococcalesSynechococcaceaeThermosynechococcus

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 28Cytoplasmic1 PublicationAdd BLAST28
Transmembranei29 – 46HelicalUniRule annotation1 PublicationAdd BLAST18
Topological domaini47 – 117Lumenal1 PublicationAdd BLAST71
Transmembranei118 – 133HelicalUniRule annotation1 PublicationAdd BLAST16
Topological domaini134 – 141Cytoplasmic1 Publication8
Transmembranei142 – 156HelicalUniRule annotation1 PublicationAdd BLAST15
Topological domaini157 – 196Lumenal1 PublicationAdd BLAST40
Transmembranei197 – 218HelicalUniRule annotation1 PublicationAdd BLAST22
Topological domaini219 – 273Cytoplasmic1 PublicationAdd BLAST55
Transmembranei274 – 288HelicalUniRule annotation1 PublicationAdd BLAST15
Topological domaini289 – 360Lumenal1 PublicationAdd BLAST72

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane, Photosystem II, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000904911 – 344Photosystem II protein D1UniRule annotationAdd BLAST344
PropeptideiPRO_0000316426345 – 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.2 PublicationsUniRule annotation1 Publication

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 annotation4 Publications

Protein-protein interaction databases

DIPiDIP-48859N.

Structurei

Secondary structure

1360
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi13 – 21Combined sources9
Beta strandi26 – 28Combined sources3
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 – 136Combined sources27
Helixi143 – 158Combined sources16
Helixi160 – 165Combined sources6
Helixi168 – 170Combined sources3
Helixi176 – 190Combined sources15
Helixi192 – 194Combined sources3
Helixi196 – 221Combined sources26
Helixi233 – 236Combined sources4
Helixi248 – 258Combined sources11
Helixi261 – 263Combined sources3
Helixi268 – 293Combined sources26
Turni294 – 296Combined sources3
Beta strandi297 – 299Combined sources3
Beta strandi309 – 311Combined sources3
Helixi317 – 331Combined sources15
Turni332 – 336Combined sources5

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP51765.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni264 – 265Quinone (B)1 PublicationUniRule annotation2 Publications2

Sequence similaritiesi

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

Keywords - Domaini

Transmembrane, Transmembrane helix

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.

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48859N.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP51765.

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 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: November 30, 2016
This is version 102 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.