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Protein

Photosystem II protein D1

Gene

psbA

Organism
Coffea arabica (Arabian coffee)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

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 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
Sitei344 – 3452Cleavage; by CTPAUniRule 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

  1. chlorophyll binding Source: UniProtKB-HAMAP
  2. electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity Source: InterPro
  3. iron ion binding Source: UniProtKB-HAMAP
  4. oxygen evolving activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. photosynthetic electron transport in photosystem II Source: InterPro
  2. protein-chromophore linkage Source: UniProtKB-KW
  3. response to herbicide Source: UniProtKB-KW
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
Encoded oniPlastid; Chloroplast
OrganismiCoffea arabica (Arabian coffee)
Taxonomic identifieri13443 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeasteridslamiidsGentianalesRubiaceaeIxoroideaeCoffeeaeCoffea

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

  1. chloroplast thylakoid membrane Source: UniProtKB-SubCell
  2. integral component of membrane Source: UniProtKB-KW
  3. photosystem II Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Membrane, Photosystem II, Plastid, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedUniRule annotation
Chaini2 – 344343Photosystem II protein D1UniRule annotationPRO_0000339974Add
BLAST
Propeptidei345 – 3539UniRule annotationPRO_0000339975

Amino acid modifications

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

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

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PRIDEiA0A315.

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

ProteinModelPortaliA0A315.
SMRiA0A315. 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.

A0A315-1 [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 ESANAGYRFG QEEETYNIVA
260 270 280 290 300
AHGYFGRLIF QYASFNNSRS LHFFLAAWPV VGIWFTSLGI STMAFNLNGF
310 320 330 340 350
NFNQSVVDSQ GRVINTWADI INRANLGMEV MHERNAHNFP LDLAAIDAPS

VNG
Length:353
Mass (Da):38,893
Last modified:November 14, 2006 - v1
Checksum:iFED3E89CBEACACCE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF044213 Genomic DNA. Translation: ABJ89659.1.
RefSeqiYP_817462.1. NC_008535.1.

Genome annotation databases

GeneIDi4421839.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF044213 Genomic DNA. Translation: ABJ89659.1.
RefSeqiYP_817462.1. NC_008535.1.

3D structure databases

ProteinModelPortaliA0A315.
SMRiA0A315. Positions 10-344.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiA0A315.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi4421839.

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

  1. "The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms."
    Samson N., Bausher M.G., Lee S.-B., Jansen R.K., Daniell H.
    Plant Biotechnol. J. 5:339-353(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Entry informationi

Entry nameiPSBA_COFAR
AccessioniPrimary (citable) accession number: A0A315
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: November 14, 2006
Last modified: March 4, 2015
This is version 50 of the entry and version 1 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.