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Protein

Photosystem II D2 protein

Gene

psbD1

more
Organism
Thermosynechococcus elongatus (strain BP-1)
Status
Reviewed-Annotation score: Annotation score: 5 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 annotation3 Publications

Catalytic activityi

2 H2O + 2 plastoquinone + 4 light = O2 + 2 plastoquinol.UniRule annotation2 Publications

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 (PubMed:19219048, PubMed:21367867). PSII binds additional chlorophylls, carotenoids and specific lipids.UniRule annotation8 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi117Magnesium (chlorophyll-a ChlzD2, axial ligand; peripheral); via tele nitrogen6 PublicationsUniRule annotation2 Publications1
Binding sitei129Pheophytin D22 PublicationsUniRule annotation1 Publication1
Binding sitei142Pheophytin D23 PublicationsUniRule annotation2 Publications1
Metal bindingi197Magnesium (chlorophyll-a PD2 axial ligand); via tele nitrogen7 PublicationsUniRule annotation2 Publications1
Metal bindingi214Iron; shared with heterodimeric partner; via tele nitrogen7 PublicationsUniRule annotation2 Publications1
Binding sitei214Plastoquinone Q(A)7 PublicationsUniRule annotation2 Publications1
Binding sitei261Plastoquinone Q(A); via amide nitrogen7 PublicationsUniRule annotation2 Publications1
Metal bindingi268Iron; shared with heterodimeric partner; via tele nitrogen8 PublicationsUniRule annotation2 Publications1

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

BRENDAi1.10.3.9. 7763.

Names & Taxonomyi

Protein namesi
Recommended name:
Photosystem II D2 proteinUniRule annotation (EC:1.10.3.9UniRule annotation2 Publications)
Short name:
PSII D2 proteinUniRule annotation
Alternative name(s):
Photosystem II Q(A) proteinUniRule annotation
Gene namesi
Name:psbD1UniRule annotation
Ordered Locus Names:tlr0455
AND
Name:psbD2UniRule annotation
Ordered Locus Names:tlr1630
OrganismiThermosynechococcus elongatus (strain BP-1)
Taxonomic identifieri197221 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaSynechococcalesSynechococcaceaeThermosynechococcus
Proteomesi
  • UP000000440 Componenti: Chromosome

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 32Cytoplasmic1 PublicationAdd BLAST32
Transmembranei33 – 49Helical1 PublicationAdd BLAST17
Topological domaini50 – 112Lumenal1 PublicationAdd BLAST63
Transmembranei113 – 127Helical1 PublicationAdd BLAST15
Topological domaini128 – 143Cytoplasmic1 PublicationAdd BLAST16
Transmembranei144 – 156Helical1 PublicationAdd BLAST13
Topological domaini157 – 194Lumenal1 PublicationAdd BLAST38
Transmembranei195 – 213Helical1 PublicationAdd BLAST19
Topological domaini214 – 270Cytoplasmic1 PublicationAdd BLAST57
Transmembranei271 – 285Helical1 PublicationAdd BLAST15
Topological domaini286 – 352Lumenal1 PublicationAdd BLAST67

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane, Photosystem II, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003596031 – 352Photosystem II D2 proteinAdd BLAST352

Proteomic databases

PRIDEiQ8CM25.

Interactioni

Subunit structurei

Cyanobacterial 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 PsbO, PsbU, PsbV and a large number of cofactors. It forms dimeric complexes.UniRule annotation10 Publications

Protein-protein interaction databases

DIPiDIP-48490N.
STRINGi197221.tlr1630.

Structurei

Secondary structure

1352
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi14 – 22Combined sources9
Beta strandi26 – 28Combined sources3
Turni31 – 33Combined sources3
Helixi34 – 51Combined sources18
Turni52 – 54Combined sources3
Turni58 – 61Combined sources4
Helixi67 – 69Combined sources3
Turni73 – 75Combined sources3
Helixi83 – 85Combined sources3
Turni95 – 99Combined sources5
Helixi101 – 107Combined sources7
Helixi109 – 136Combined sources28
Helixi141 – 145Combined sources5
Helixi147 – 157Combined sources11
Helixi159 – 163Combined sources5
Beta strandi164 – 166Combined sources3
Helixi167 – 169Combined sources3
Helixi175 – 187Combined sources13
Helixi191 – 193Combined sources3
Helixi195 – 219Combined sources25
Beta strandi221 – 223Combined sources3
Beta strandi224 – 226Combined sources3
Beta strandi227 – 230Combined sources4
Helixi231 – 233Combined sources3
Helixi246 – 256Combined sources11
Helixi264 – 289Combined sources26
Turni290 – 292Combined sources3
Helixi299 – 307Combined sources9
Helixi314 – 333Combined sources20
Helixi335 – 337Combined sources3
Helixi343 – 345Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1S5LX-ray3.50D/d1-352[»]
1W5CX-ray3.20D/J1-352[»]
2AXTX-ray3.00D/d1-352[»]
3KZIX-ray3.60D1-352[»]
4FBYX-ray6.56D/Q1-352[»]
4IXQX-ray5.70D/d1-352[»]
4IXRX-ray5.90D/d1-352[»]
4PBUX-ray5.00D/d11-352[»]
4PJ0X-ray2.44D/d1-352[»]
4RVYX-ray5.50D/d11-352[»]
4TNHX-ray4.90D/d1-352[»]
4TNIX-ray4.60D/d1-352[»]
4TNJX-ray4.50D/d1-352[»]
4TNKX-ray5.20D/d1-352[»]
4V62X-ray2.90AD/BD1-352[»]
4V82X-ray3.20AD/BD1-352[»]
5E7CX-ray4.50D/d11-352[»]
ProteinModelPortaliQ8CM25.
SMRiQ8CM25.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8CM25.

Family & Domainsi

Sequence similaritiesi

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

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105D6H. Bacteria.
ENOG410XRUT. LUCA.
HOGENOMiHOG000233052.
KOiK02706.
OMAiDFVRWCQ.
OrthoDBiPOG091H1437.

Family and domain databases

CDDicd09288. Photosystem-II_D2. 1 hit.
Gene3Di1.20.85.10. 2 hits.
HAMAPiMF_01383. PSII_PsbD_D2. 1 hit.
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.

Q8CM25-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTIAIGRAPA ERGWFDILDD WLKRDRFVFV GWSGILLFPC AYLALGGWLT
60 70 80 90 100
GTTFVTSWYT HGLASSYLEG CNFLTVAVST PANSMGHSLL LLWGPEAQGD
110 120 130 140 150
FTRWCQLGGL WTFIALHGAF GLIGFMLRQF EIARLVGVRP YNAIAFSAPI
160 170 180 190 200
AVFVSVFLIY PLGQSSWFFA PSFGVAAIFR FLLFFQGFHN WTLNPFHMMG
210 220 230 240 250
VAGVLGGALL CAIHGATVEN TLFQDGEGAS TFRAFNPTQA EETYSMVTAN
260 270 280 290 300
RFWSQIFGIA FSNKRWLHFF MLFVPVTGLW MSAIGVVGLA LNLRSYDFIS
310 320 330 340 350
QEIRAAEDPE FETFYTKNLL LNEGIRAWMA PQDQPHENFV FPEEVLPRGN

AL
Length:352
Mass (Da):39,361
Last modified:March 1, 2003 - v1
Checksum:iC5D91543CD148FD4
GO

Mass spectrometryi

Molecular mass is 39290±79 Da from positions 1 - 352. Determined by MALDI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000039 Genomic DNA. Translation: BAC08007.1.
BA000039 Genomic DNA. Translation: BAC09182.1.
RefSeqiNP_681245.1. NC_004113.1.
NP_682420.1. NC_004113.1.
WP_011056308.1. NC_004113.1.

Genome annotation databases

EnsemblBacteriaiBAC08007; BAC08007; BAC08007.
BAC09182; BAC09182; BAC09182.
GeneIDi1011901.
1012700.
KEGGitel:tlr0455.
tel:tlr1630.
PATRICi23926154. VBITheElo119873_0480.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000039 Genomic DNA. Translation: BAC08007.1.
BA000039 Genomic DNA. Translation: BAC09182.1.
RefSeqiNP_681245.1. NC_004113.1.
NP_682420.1. NC_004113.1.
WP_011056308.1. NC_004113.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1S5LX-ray3.50D/d1-352[»]
1W5CX-ray3.20D/J1-352[»]
2AXTX-ray3.00D/d1-352[»]
3KZIX-ray3.60D1-352[»]
4FBYX-ray6.56D/Q1-352[»]
4IXQX-ray5.70D/d1-352[»]
4IXRX-ray5.90D/d1-352[»]
4PBUX-ray5.00D/d11-352[»]
4PJ0X-ray2.44D/d1-352[»]
4RVYX-ray5.50D/d11-352[»]
4TNHX-ray4.90D/d1-352[»]
4TNIX-ray4.60D/d1-352[»]
4TNJX-ray4.50D/d1-352[»]
4TNKX-ray5.20D/d1-352[»]
4V62X-ray2.90AD/BD1-352[»]
4V82X-ray3.20AD/BD1-352[»]
5E7CX-ray4.50D/d11-352[»]
ProteinModelPortaliQ8CM25.
SMRiQ8CM25.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48490N.
STRINGi197221.tlr1630.

Proteomic databases

PRIDEiQ8CM25.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC08007; BAC08007; BAC08007.
BAC09182; BAC09182; BAC09182.
GeneIDi1011901.
1012700.
KEGGitel:tlr0455.
tel:tlr1630.
PATRICi23926154. VBITheElo119873_0480.

Phylogenomic databases

eggNOGiENOG4105D6H. Bacteria.
ENOG410XRUT. LUCA.
HOGENOMiHOG000233052.
KOiK02706.
OMAiDFVRWCQ.
OrthoDBiPOG091H1437.

Enzyme and pathway databases

BRENDAi1.10.3.9. 7763.

Miscellaneous databases

EvolutionaryTraceiQ8CM25.

Family and domain databases

CDDicd09288. Photosystem-II_D2. 1 hit.
Gene3Di1.20.85.10. 2 hits.
HAMAPiMF_01383. PSII_PsbD_D2. 1 hit.
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...

Entry informationi

Entry nameiPSBD_THEEB
AccessioniPrimary (citable) accession number: Q8CM25
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 20, 2009
Last sequence update: March 1, 2003
Last modified: November 2, 2016
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water.UniRule annotation2 Publications

Caution

According to (Ref. 2, PubMed:22665786, PubMed:23413188, PubMed:25006873) there are no direct protein ligands to pheophytin D2, whereas (PubMed:14764885, PubMed:16355230, PubMed:19219048, PubMed:20558739, PubMed:21367867, PubMed:25043005) show 1 or 2 direct ligands.8 Publications2 Publications

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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.