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Protein

Photosystem II D2 protein

Gene

psbD

Organism
Chlamydomonas reinhardtii (Chlamydomonas smithii)
Status
Reviewed-Annotation score: Annotation score: 3 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. D2 is needed for assembly of a stable PSII complex.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. 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 bindingi117 – 1171Magnesium (chlorophyll-a ChlzD2, axial ligand; peripheral); via tele nitrogenUniRule annotation
Binding sitei129 – 1291Pheophytin D2UniRule annotation
Binding sitei142 – 1421Pheophytin D2UniRule annotation
Metal bindingi197 – 1971Magnesium (chlorophyll-a PD2 axial ligand); via tele nitrogenUniRule annotation
Metal bindingi214 – 2141Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation
Binding sitei214 – 2141Plastoquinone Q(A)UniRule annotation
Binding sitei261 – 2611Plastoquinone Q(A); via amide nitrogenUniRule annotation
Metal bindingi268 – 2681Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Photosynthesis, Transport

Keywords - Ligandi

Chlorophyll, Chromophore, Iron, Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciCHLAMY:CHRECP064-MONOMER.
MetaCyc:CHRECP064-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Photosystem II D2 proteinUniRule annotation (EC:1.10.3.9UniRule annotation)
Short name:
PSII D2 proteinUniRule annotation
Alternative name(s):
Photosystem Q(A) proteinUniRule annotation
Gene namesi
Name:psbDUniRule annotation
Encoded oniPlastid; Chloroplast
OrganismiChlamydomonas reinhardtii (Chlamydomonas smithii)
Taxonomic identifieri3055 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeChlorophytaChlorophyceaeChlamydomonadalesChlamydomonadaceaeChlamydomonas
ProteomesiUP000006906 Componenti: Chloroplast

Subcellular locationi

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

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei40 – 6021HelicalUniRule annotationAdd
BLAST
Transmembranei124 – 14017HelicalUniRule annotationAdd
BLAST
Transmembranei152 – 16514HelicalUniRule annotationAdd
BLAST
Transmembranei207 – 22721HelicalUniRule annotationAdd
BLAST
Transmembranei278 – 29417HelicalUniRule annotationAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Membrane, Photosystem II, Plastid, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 352352Photosystem II D2 proteinPRO_0000090500Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PRIDEiP06007.

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

STRINGi3055.DAA00964.

Structurei

3D structure databases

ProteinModelPortaliP06007.
SMRiP06007. Positions 1-350.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

InParanoidiP06007.
KOiK02706.

Family and domain databases

Gene3Di1.20.85.10. 2 hits.
HAMAPiMF_01383. PSII_PsbD_D2.
InterProiIPR000484. Photo_RC_L/M.
IPR005868. PSII_PsbD/D2.
[Graphical view]
PfamiPF00124. Photo_RC. 1 hit.
[Graphical view]
PRINTSiPR00256. REACTNCENTRE.
SUPFAMiSSF81483. SSF81483. 1 hit.
TIGRFAMsiTIGR01152. psbD. 1 hit.
PROSITEiPS00244. REACTION_CENTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P06007-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTIAIGTYQE KRTWFDDADD WLRQDRFVFV GWSGLLLFPC AYFALGGWLT
60 70 80 90 100
GTTFVTSWYT HGLATSYLEG CNFLTAAVST PANSMAHSLL FVWGPEAQGD
110 120 130 140 150
FTRWCQLGGL WAFVALHGAF GLIGFMLRQF EIARSVNLRP YNAIAFSAPI
160 170 180 190 200
AVFVSVFLIY PLGQSGWFFA PSFGVAAIFR FILFFQGFHN WTLNPFHMMG
210 220 230 240 250
VAGVLGAALL CAIHGATVEN TLFEDGDGAN TFRAFNPTQA EETYSMVTAN
260 270 280 290 300
RFWSQIFGVA FSNKRWLHFF MLLVPVTGLW MSAIGVVGLA LNLRAYDFVS
310 320 330 340 350
QEIRAAEDPE FETFYTKNIL LNEGIRAWMA AQDQPHERLV FPEEVLPRGN

AL
Length:352
Mass (Da):39,447
Last modified:August 13, 1987 - v1
Checksum:i81046BC2D36A2C61
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04147 Genomic DNA. Translation: CAA27766.1.
FJ423446 Genomic DNA. Translation: ACJ50151.1.
BK000554 Genomic DNA. Translation: DAA00964.1.
PIRiA25466.
RefSeqiNP_958420.1. NC_005353.1.

Genome annotation databases

EnsemblPlantsiDAA00964; DAA00964; DAA00964.
GeneIDi2716961.
KEGGicre:ChreCp064.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04147 Genomic DNA. Translation: CAA27766.1.
FJ423446 Genomic DNA. Translation: ACJ50151.1.
BK000554 Genomic DNA. Translation: DAA00964.1.
PIRiA25466.
RefSeqiNP_958420.1. NC_005353.1.

3D structure databases

ProteinModelPortaliP06007.
SMRiP06007. Positions 1-350.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3055.DAA00964.

Proteomic databases

PRIDEiP06007.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiDAA00964; DAA00964; DAA00964.
GeneIDi2716961.
KEGGicre:ChreCp064.

Phylogenomic databases

InParanoidiP06007.
KOiK02706.

Enzyme and pathway databases

BioCyciCHLAMY:CHRECP064-MONOMER.
MetaCyc:CHRECP064-MONOMER.

Family and domain databases

Gene3Di1.20.85.10. 2 hits.
HAMAPiMF_01383. PSII_PsbD_D2.
InterProiIPR000484. Photo_RC_L/M.
IPR005868. PSII_PsbD/D2.
[Graphical view]
PfamiPF00124. Photo_RC. 1 hit.
[Graphical view]
PRINTSiPR00256. REACTNCENTRE.
SUPFAMiSSF81483. SSF81483. 1 hit.
TIGRFAMsiTIGR01152. psbD. 1 hit.
PROSITEiPS00244. REACTION_CENTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Lack of the D2 protein in a Chlamydomonas reinhardtii psbD mutant affects photosystem II stability and D1 expression."
    Erickson J.M., Rahire M., Malnoe P., Girard-Bascou J., Pierre Y., Bennoun P., Rochaix J.-D.
    EMBO J. 5:1745-1754(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis."
    Smith D.R., Lee R.W.
    BMC Evol. Biol. 9:120-120(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CC-503.
  3. "The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats."
    Maul J.E., Lilly J.W., Cui L., dePamphilis C.W., Miller W., Harris E.H., Stern D.B.
    Plant Cell 14:2659-2679(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION, COMPLETE PLASTID GENOME.

Entry informationi

Entry nameiPSBD_CHLRE
AccessioniPrimary (citable) accession number: P06007
Secondary accession number(s): B7U1K4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: June 24, 2015
This is version 119 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

Keywords - Technical termi

Complete proteome, Reference proteome

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.