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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)DescriptionActionsGraphical viewLength
Metal bindingi118Magnesium (chlorophyll-a ChlzD1 axial ligand); via tele nitrogenUniRule annotation1
Binding sitei126Pheophytin D1UniRule annotation1
Sitei161Tyrosine radical intermediateUniRule annotation1
Metal bindingi170Calcium-manganese-oxide [Ca-4Mn-5O]; calciumUniRule annotation1
Metal bindingi170Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4UniRule annotation1
Metal bindingi189Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1UniRule annotation1
Sitei190Stabilizes free radical intermediateUniRule annotation1
Metal bindingi198Magnesium (chlorophyll-a PD1 axial ligand); via tele nitrogenUniRule annotation1
Metal bindingi215Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation1
Binding sitei215Quinone (B)UniRule annotation1
Metal bindingi272Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation1
Metal bindingi332Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1; via tele nitrogenUniRule annotation1
Metal bindingi333Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 3UniRule annotation1
Metal bindingi333Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4UniRule annotation1
Metal bindingi342Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1UniRule annotation1
Metal bindingi342Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2UniRule annotation1
Metal bindingi344Calcium-manganese-oxide [Ca-4Mn-5O]; calcium; via carboxylateUniRule annotation1
Metal bindingi344Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2; via carboxylateUniRule annotation1

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)DescriptionActionsGraphical viewLength
Transmembranei29 – 46HelicalUniRule annotationAdd BLAST18
Transmembranei118 – 133HelicalUniRule annotationAdd BLAST16
Transmembranei142 – 156HelicalUniRule annotationAdd BLAST15
Transmembranei197 – 218HelicalUniRule annotationAdd BLAST22
Transmembranei274 – 288HelicalUniRule annotationAdd BLAST15

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Membrane, Photosystem II, Plastid, Thylakoid

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL2366481.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000302462 – 344Photosystem II protein D1UniRule annotationAdd BLAST343
PropeptideiPRO_0000030247345 – 353UniRule annotation9

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylthreonineUniRule annotation1 Publication1
Modified residuei2PhosphothreonineUniRule annotation1 Publication1

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)DescriptionActionsGraphical viewLength
Sitei344 – 345Cleavage; by CTPAUniRule annotation2

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

Protein-protein interaction databases

DIPiDIP-62007N.

Structurei

3D structure databases

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

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni264 – 265Quinone (B)UniRule annotation2

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]
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DOPmodel-A1-353[»]
3JCUelectron microscopy3.20A/a1-344[»]
ProteinModelPortaliP69560.
SMRiP69560.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-62007N.

Chemistry databases

ChEMBLiCHEMBL2366481.

PTM databases

iPTMnetiP69560.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi2715607.

Miscellaneous databases

PMAP-CutDBP69560.
PROiP69560.

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

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: November 30, 2016
This is version 85 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.