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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi117 – 1171Magnesium (chlorophyll-a ChlzD2, axial ligand; peripheral); via tele nitrogen6 PublicationsUniRule annotation2 Publications
Binding sitei129 – 1291Pheophytin D22 PublicationsUniRule annotation1 Publication
Binding sitei142 – 1421Pheophytin D23 PublicationsUniRule annotation2 Publications
Metal bindingi197 – 1971Magnesium (chlorophyll-a PD2 axial ligand); via tele nitrogen7 PublicationsUniRule annotation2 Publications
Metal bindingi214 – 2141Iron; shared with heterodimeric partner; via tele nitrogen7 PublicationsUniRule annotation2 Publications
Binding sitei214 – 2141Plastoquinone Q(A)7 PublicationsUniRule annotation2 Publications
Binding sitei261 – 2611Plastoquinone Q(A); via amide nitrogen7 PublicationsUniRule annotation2 Publications
Metal bindingi268 – 2681Iron; shared with heterodimeric partner; via tele nitrogen8 PublicationsUniRule annotation2 Publications

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 lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesThermosynechococcus
Proteomesi
  • UP000000440 Componenti: Chromosome

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 3232Cytoplasmic1 PublicationAdd
BLAST
Transmembranei33 – 4917Helical1 PublicationAdd
BLAST
Topological domaini50 – 11263Lumenal1 PublicationAdd
BLAST
Transmembranei113 – 12715Helical1 PublicationAdd
BLAST
Topological domaini128 – 14316Cytoplasmic1 PublicationAdd
BLAST
Transmembranei144 – 15613Helical1 PublicationAdd
BLAST
Topological domaini157 – 19438Lumenal1 PublicationAdd
BLAST
Transmembranei195 – 21319Helical1 PublicationAdd
BLAST
Topological domaini214 – 27057Cytoplasmic1 PublicationAdd
BLAST
Transmembranei271 – 28515Helical1 PublicationAdd
BLAST
Topological domaini286 – 35267Lumenal1 PublicationAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane, Photosystem II, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 352352Photosystem II D2 proteinPRO_0000359603Add
BLAST

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

1
352
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi14 – 229Combined sources
Beta strandi26 – 283Combined sources
Turni31 – 333Combined sources
Helixi34 – 5118Combined sources
Turni52 – 543Combined sources
Turni58 – 614Combined sources
Helixi67 – 693Combined sources
Turni73 – 753Combined sources
Helixi83 – 853Combined sources
Turni95 – 995Combined sources
Helixi101 – 1077Combined sources
Helixi109 – 13628Combined sources
Helixi141 – 1455Combined sources
Helixi147 – 15711Combined sources
Helixi159 – 1635Combined sources
Beta strandi164 – 1663Combined sources
Helixi167 – 1693Combined sources
Helixi175 – 18713Combined sources
Helixi191 – 1933Combined sources
Helixi195 – 21925Combined sources
Beta strandi221 – 2233Combined sources
Beta strandi224 – 2263Combined sources
Beta strandi227 – 2304Combined sources
Helixi231 – 2333Combined sources
Helixi246 – 25611Combined sources
Helixi264 – 28926Combined sources
Turni290 – 2923Combined sources
Helixi299 – 3079Combined sources
Helixi314 – 33320Combined sources
Helixi335 – 3373Combined sources
Helixi343 – 3453Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-350.
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.
OrthoDBiEOG6DG2PK.

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.

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
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. Positions 1-350.
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.
OrthoDBiEOG6DG2PK.

Enzyme and pathway databases

BRENDAi1.10.3.9. 7763.

Miscellaneous databases

EvolutionaryTraceiQ8CM25.

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: BP-1.
  2. "Crystal structure of cyanobacterial photosystem II at 3.2 A resolution: a closer look at the Mn-cluster."
    Biesiadka J., Loll B., Kern J., Irrgang K.-D., Zouni A.
    Phys. Chem. Chem. Phys. 6:4733-4736(2004)
    Cited for: X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS) IN PHOTOSYSTEM II WITH IRON, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
  3. "Architecture of the photosynthetic oxygen-evolving center."
    Ferreira K.N., Iverson T.M., Maghlaoui K., Barber J., Iwata S.
    Science 303:1831-1838(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.50 ANGSTROMS) IN PHOTOSYSTEM II WITH IRON, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
  4. "Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II."
    Loll B., Kern J., Saenger W., Zouni A., Biesiadka J.
    Nature 438:1040-1044(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) IN PHOTOSYSTEM II WITH IRON, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.
  5. "Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride."
    Guskov A., Kern J., Gabdulkhakov A., Broser M., Zouni A., Saenger W.
    Nat. Struct. Mol. Biol. 16:334-342(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) IN PHOTOSYSTEM II WITH IRON, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION, MASS SPECTROMETRY.
    Strain: BP-1.
  6. "Crystal structure of monomeric photosystem II from Thermosynechococcus elongatus at 3.6 A resolution."
    Broser M., Gabdulkhakov A., Kern J., Guskov A., Muh F., Saenger W., Zouni A.
    J. Biol. Chem. 285:26255-26262(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.60 ANGSTROMS) IN PHOTOSYSTEM II WITH IRON, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.
  7. "Structural basis of cyanobacterial photosystem II inhibition by the herbicide terbutryn."
    Broser M., Glockner C., Gabdulkhakov A., Guskov A., Buchta J., Kern J., Muh F., Dau H., Saenger W., Zouni A.
    J. Biol. Chem. 286:15964-15972(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS) IN PHOTOSYSTEM II WITH IRON, FUNCTION, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
  8. Cited for: X-RAY CRYSTALLOGRAPHY (6.56 ANGSTROMS) IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.
  9. Cited for: X-RAY CRYSTALLOGRAPHY (5.70 ANGSTROMS) IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.
  10. "Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser."
    Kupitz C., Basu S., Grotjohann I., Fromme R., Zatsepin N.A., Rendek K.N., Hunter M.S., Shoeman R.L., White T.A., Wang D., James D., Yang J.H., Cobb D.E., Reeder B., Sierra R.G., Liu H., Barty A., Aquila A.L.
    , Deponte D., Kirian R.A., Bari S., Bergkamp J.J., Beyerlein K.R., Bogan M.J., Caleman C., Chao T.C., Conrad C.E., Davis K.M., Fleckenstein H., Galli L., Hau-Riege S.P., Kassemeyer S., Laksmono H., Liang M., Lomb L., Marchesini S., Martin A.V., Messerschmidt M., Milathianaki D., Nass K., Ros A., Roy-Chowdhury S., Schmidt K., Seibert M., Steinbrener J., Stellato F., Yan L., Yoon C., Moore T.A., Moore A.L., Pushkar Y., Williams G.J., Boutet S., Doak R.B., Weierstall U., Frank M., Chapman H.N., Spence J.C., Fromme P.
    Nature 513:261-265(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (5.00 ANGSTROMS) OF 11-352 IN PHOTOSYSTEM II, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.
  11. Cited for: X-RAY CRYSTALLOGRAPHY (4.50 ANGSTROMS) IN PHOTOSYSTEM II, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BP-1.

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: April 13, 2016
This is version 96 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.