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Protein

Photosystem II D2 protein

Gene

psbD

Organism
Cyanidium caldarium (Red alga)
Status
Reviewed-Annotation score: Annotation score: 3 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. 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)DescriptionActionsGraphical viewLength
Metal bindingi116Magnesium (chlorophyll-a ChlzD2, axial ligand; peripheral); via tele nitrogenUniRule annotation1
Binding sitei128Pheophytin D2UniRule annotation1
Binding sitei141Pheophytin D2UniRule annotation1
Metal bindingi196Magnesium (chlorophyll-a PD2 axial ligand); via tele nitrogenUniRule annotation1
Metal bindingi213Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation1
Binding sitei213Plastoquinone Q(A)UniRule annotation1
Binding sitei260Plastoquinone Q(A); via amide nitrogenUniRule annotation1
Metal bindingi267Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionOxidoreductase
Biological processElectron transport, Photosynthesis, Transport
LigandChlorophyll, Chromophore, Iron, Magnesium, Metal-binding

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
OrganismiCyanidium caldarium (Red alga)
Taxonomic identifieri2771 [NCBI]
Taxonomic lineageiEukaryotaRhodophytaBangiophyceaeCyanidialesCyanidiaceaeCyanidium

Subcellular locationi

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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei39 – 59HelicalUniRule annotationAdd BLAST21
Transmembranei123 – 139HelicalUniRule annotationAdd BLAST17
Transmembranei151 – 164HelicalUniRule annotationAdd BLAST14
Transmembranei206 – 226HelicalUniRule annotationAdd BLAST21
Transmembranei277 – 293HelicalUniRule annotationAdd BLAST17

GO - Cellular componenti

Keywords - Cellular componenti

Chloroplast, Membrane, Photosystem II, Plastid, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000905011 – 351Photosystem II D2 proteinAdd BLAST351

Proteomic databases

PRIDEiQ9TM47.

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4YUUX-ray2.77D1/D2/d1/d21-351[»]
ProteinModelPortaliQ9TM47.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Keywords - Domaini

Transmembrane, Transmembrane helix

Family and domain databases

CDDicd09288. Photosystem-II_D2. 1 hit.
Gene3Di1.20.85.10. 2 hits.
HAMAPiMF_01383. PSII_PsbD_D2. 1 hit.
InterProiView protein in InterPro
IPR000484. Photo_RC_L/M.
IPR005868. PSII_PsbD/D2.
PfamiView protein in Pfam
PF00124. Photo_RC. 1 hit.
PRINTSiPR00256. REACTNCENTRE.
SUPFAMiSSF81483. SSF81483. 1 hit.
TIGRFAMsiTIGR01152. psbD. 1 hit.
PROSITEiView protein in PROSITE
PS00244. REACTION_CENTER. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9TM47-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTIAIGREQE RGWFDLLDDW LKRDRFVFIG WSGILLFPCA YLALGAWFTG
60 70 80 90 100
TTFVSSWYTH GLASSYLEGC NFLTAAVSSP ANSMGHSLLF LWGPEAQGDF
110 120 130 140 150
TRWCQIGGLW TFTALHGSFG LIGFCLRQFE IARLVGLRPY NAIAFSGPIA
160 170 180 190 200
VFVSVFLLYP LGQASWFFAP SFGVAAIFRF LLFLQGFHNW TLNPFHMMGV
210 220 230 240 250
AGILGGALLC AIHGATVENT LFEDGEASDT FRAFTPTQSE ETYSMVTANR
260 270 280 290 300
FWSQIFGVAF ANKRWLHFFL LFVPVTGLWV SSIGIVGLAL NLRAYDFVSQ
310 320 330 340 350
EIRAAEDPEF ETFYTKNILL NEGIRAWMAA QDQPHENFVF PEEVLPRGNA

L
Length:351
Mass (Da):39,315
Last modified:May 1, 2000 - v1
Checksum:iB26260FD183216B2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF022186 Genomic DNA. Translation: AAF13026.1.
RefSeqiNP_045019.1. NC_001840.1.

Genome annotation databases

GeneIDi800240.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF022186 Genomic DNA. Translation: AAF13026.1.
RefSeqiNP_045019.1. NC_001840.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4YUUX-ray2.77D1/D2/d1/d21-351[»]
ProteinModelPortaliQ9TM47.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ9TM47.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi800240.

Family and domain databases

CDDicd09288. Photosystem-II_D2. 1 hit.
Gene3Di1.20.85.10. 2 hits.
HAMAPiMF_01383. PSII_PsbD_D2. 1 hit.
InterProiView protein in InterPro
IPR000484. Photo_RC_L/M.
IPR005868. PSII_PsbD/D2.
PfamiView protein in Pfam
PF00124. Photo_RC. 1 hit.
PRINTSiPR00256. REACTNCENTRE.
SUPFAMiSSF81483. SSF81483. 1 hit.
TIGRFAMsiTIGR01152. psbD. 1 hit.
PROSITEiView protein in PROSITE
PS00244. REACTION_CENTER. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPSBD_CYACA
AccessioniPrimary (citable) accession number: Q9TM47
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: May 1, 2000
Last modified: March 15, 2017
This is version 90 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Miscellaneous

2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water.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.