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Protein

Photosystem II protein D1

Gene

psbA

Organism
Spinacia oleracea (Spinach)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

This is one of the two reaction center proteins of photosystem II.
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 annotation

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 annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi118 – 1181Magnesium (chlorophyll-a ChlzD1 axial ligand); via tele nitrogenUniRule annotation
Binding sitei126 – 1261Pheophytin D1UniRule annotation
Sitei161 – 1611Tyrosine radical intermediateUniRule annotation
Metal bindingi170 – 1701Calcium-manganese-oxide [Ca-4Mn-5O]; calciumUniRule annotation
Metal bindingi170 – 1701Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4UniRule annotation
Metal bindingi189 – 1891Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1UniRule annotation
Sitei190 – 1901Stabilizes free radical intermediateUniRule annotation
Metal bindingi198 – 1981Magnesium (chlorophyll-a PD1 axial ligand); via tele nitrogenUniRule annotation
Metal bindingi215 – 2151Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation
Binding sitei215 – 2151Quinone (B)UniRule annotation
Metal bindingi272 – 2721Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation
Metal bindingi332 – 3321Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1; via tele nitrogenUniRule annotation
Metal bindingi333 – 3331Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 3UniRule annotation
Metal bindingi333 – 3331Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4UniRule annotation
Metal bindingi342 – 3421Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1UniRule annotation
Metal bindingi342 – 3421Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2UniRule annotation
Metal bindingi344 – 3441Calcium-manganese-oxide [Ca-4Mn-5O]; calcium; via carboxylateUniRule annotation
Metal bindingi344 – 3441Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2; via carboxylateUniRule annotation

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):
32 kDa thylakoid membrane protein1 Publication
Photosystem II Q(B) proteinUniRule annotation
Gene namesi
Name:psbAUniRule annotation
Encoded oniPlastid; Chloroplast
OrganismiSpinacia oleracea (Spinach)
Taxonomic identifieri3562 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeCaryophyllalesChenopodiaceaeChenopodioideaeAnserineaeSpinacia

Subcellular locationi

  • Plastidchloroplast thylakoid membrane UniRule annotation; Multi-pass membrane protein UniRule annotation

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei29 – 4618HelicalUniRule annotationAdd
BLAST
Transmembranei118 – 13316HelicalUniRule annotationAdd
BLAST
Transmembranei142 – 15615HelicalUniRule annotationAdd
BLAST
Transmembranei197 – 21822HelicalUniRule annotationAdd
BLAST
Transmembranei274 – 28815HelicalUniRule annotationAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Membrane, Photosystem II, Plastid, Thylakoid

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL2366481.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 344343Photosystem II protein D1UniRule annotationPRO_0000030246Add
BLAST
Propeptidei345 – 3539UniRule annotationPRO_0000030247

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylthreonineUniRule annotation1 Publication
Modified residuei2 – 21PhosphothreonineUniRule annotation1 Publication

Post-translational modificationi

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

Sites

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

Keywords - PTMi

Acetylation, Phosphoprotein

PTM databases

iPTMnetiP69560.

Miscellaneous databases

PMAP-CutDBP69560.

Interactioni

Subunit structurei

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 of the oxygen-evolving complex and a large number of cofactors. It forms dimeric complexes.UniRule annotation

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DOPmodel-A1-353[»]
3JCUelectron microscopy3.20A/a1-344[»]
ProteinModelPortaliP69560.
SMRiP69560. Positions 10-344.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni264 – 2652Quinone (B)UniRule annotation

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]
PRINTSiPR00256. REACTNCENTRE.
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.

P69560-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTAILERRES ESLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII
60 70 80 90 100
AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAIG LHFYPIWEAA
110 120 130 140 150
SVDEWLYNGG PYELIVLHFL LGVACYMGRE WELSFRLGMR PWIAVAYSAP
160 170 180 190 200
VAAATAVFLI YPIGQGSFSD GMPLGISGTF NFMIVFQAEH NILMHPFHML
210 220 230 240 250
GVAGVFGGSL FSAMHGSLVT SSLIRETTEN ESANEGYRFG QEEETYNIVA
260 270 280 290 300
AHGYFGRLIF QYASFNNSRS LHFFLAAWPV VGIWFTALGI STMAFNLNGF
310 320 330 340 350
NFNQSVVDSQ GRVINTWADI INRANLGMEV MHERNAHNFP LDLAAIEAPS

TNG
Length:353
Mass (Da):38,951
Last modified:January 23, 2007 - v2
Checksum:iBAD3F384DAB4D602
GO

Mass spectrometryi

Molecular mass is 38022.1±3.8 Da from positions 2 - 344. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ400848 Genomic DNA. Translation: CAB88705.1.
PIRiA38055. FMSP32.
RefSeqiNP_054912.1. NC_002202.1.

Genome annotation databases

GeneIDi2715607.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ400848 Genomic DNA. Translation: CAB88705.1.
PIRiA38055. FMSP32.
RefSeqiNP_054912.1. NC_002202.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DOPmodel-A1-353[»]
3JCUelectron microscopy3.20A/a1-344[»]
ProteinModelPortaliP69560.
SMRiP69560. Positions 10-344.
ModBaseiSearch...
MobiDBiSearch...

Chemistry

ChEMBLiCHEMBL2366481.

PTM databases

iPTMnetiP69560.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi2715607.

Miscellaneous databases

PMAP-CutDBP69560.
PROiP69560.

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]
PRINTSiPR00256. REACTNCENTRE.
SUPFAMiSSF81483. SSF81483. 1 hit.
TIGRFAMsiTIGR01151. psbA. 1 hit.
PROSITEiPS00244. REACTION_CENTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the gene for the M-r 32,000 thylakoid membrane protein from Spinacia oleracea and Nicotiana debneyi predicts a totally conserved primary translation product of M-r 38,950."
    Zurawski G., Bohnert H.J., Whitfeld P.R., Bottomley W.
    Proc. Natl. Acad. Sci. U.S.A. 79:7699-7703(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization."
    Schmitz-Linneweber C., Maier R.M., Alcaraz J.-P., Cottet A., Herrmann R.G., Mache R.
    Plant Mol. Biol. 45:307-315(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Geant d'hiver and cv. Monatol.
  3. "Tandem mass spectrometry reveals that three photosystem II proteins of spinach chloroplasts contain N-acetyl-O-phosphothreonine at their NH2 termini."
    Michel H., Hunt D.F., Shabanowitz J., Bennett J.
    J. Biol. Chem. 263:1123-1130(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-8, ACETYLATION AT THR-2, PHOSPHORYLATION AT THR-2.
  4. "COOH-terminal residues of D1 and the 44 kDa CPa-2 at spinach photosystem II core complex."
    Takahashi M., Shiraishi T., Asada K.
    FEBS Lett. 240:6-8(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEOLYTIC PROCESSING.
  5. "Electrospray-ionization mass spectrometry of intact intrinsic membrane proteins."
    Whitelegge J.P., Gundersen C.B., Faull K.F.
    Protein Sci. 7:1423-1430(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: MASS SPECTROMETRY.
  6. "A model for the photosystem II reaction center core including the structure of the primary donor P680."
    Svensson B., Etchebest C., Tuffery P., van Kan P., Smith J., Styring S.
    Biochemistry 35:14486-14502(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING.

Entry informationi

Entry nameiPSBA_SPIOL
AccessioniPrimary (citable) accession number: P69560
Secondary accession number(s): P02955
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: July 6, 2016
This is version 81 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water.UniRule annotation
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, Direct protein sequencing

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.