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Protein

Photosystem II D2 protein

Gene

psbD

Organism
Spinacia oleracea (Spinach)
Status
Reviewed-Annotation score: -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

Miscellaneous

2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water.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 bindingi118Magnesium (chlorophyll-a ChlzD2, axial ligand; peripheral); via tele nitrogenUniRule annotation1
Binding sitei130Pheophytin D2UniRule annotation1
Binding sitei143Pheophytin D2UniRule annotation1
Metal bindingi198Magnesium (chlorophyll-a PD2 axial ligand); via tele nitrogenUniRule annotation1
Metal bindingi215Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation1
Binding sitei215Plastoquinone Q(A)UniRule annotation1
Binding sitei262Plastoquinone Q(A); via amide nitrogenUniRule annotation1
Metal bindingi269Iron; 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
OrganismiSpinacia oleracea (Spinach)
Taxonomic identifieri3562 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeCaryophyllalesChenopodiaceaeChenopodioideaeAnserineaeSpinacia
Proteomesi
  • UP000054095 Componenti: Chloroplast

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei41 – 61HelicalUniRule annotationAdd BLAST21
Transmembranei125 – 141HelicalUniRule annotationAdd BLAST17
Transmembranei153 – 166HelicalUniRule annotationAdd BLAST14
Transmembranei208 – 228HelicalUniRule annotationAdd BLAST21
Transmembranei279 – 295HelicalUniRule annotationAdd BLAST17

Keywords - Cellular componenti

Chloroplast, Membrane, Photosystem II, Plastid, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000905212 – 353Photosystem II D2 proteinAdd BLAST352

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylthreonine1 Publication1
Modified residuei2Phosphothreonine1 Publication1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PRIDEiP06005

PTM databases

iPTMnetiP06005

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

DIPiDIP-62010N
IntActiP06005, 1 interactor

Structurei

Secondary structure

1353
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi15 – 23Combined sources9
Beta strandi27 – 29Combined sources3
Helixi32 – 54Combined sources23
Turni59 – 62Combined sources4
Turni68 – 71Combined sources4
Turni74 – 76Combined sources3
Helixi84 – 86Combined sources3
Turni96 – 98Combined sources3
Helixi102 – 107Combined sources6
Helixi110 – 136Combined sources27
Helixi143 – 158Combined sources16
Helixi160 – 164Combined sources5
Beta strandi165 – 167Combined sources3
Helixi168 – 170Combined sources3
Helixi176 – 190Combined sources15
Turni192 – 194Combined sources3
Helixi196 – 221Combined sources26
Turni233 – 235Combined sources3
Helixi247 – 256Combined sources10
Helixi265 – 290Combined sources26
Turni291 – 293Combined sources3
Helixi300 – 308Combined sources9
Helixi315 – 334Combined sources20
Helixi336 – 338Combined sources3
Helixi344 – 346Combined sources3

3D structure databases

ProteinModelPortaliP06005
SMRiP06005
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

KOiK02706

Family and domain databases

CDDicd09288 Photosystem-II_D2, 1 hit
Gene3Di1.20.85.10, 1 hit
HAMAPiMF_01383 PSII_PsbD_D2, 1 hit
InterProiView protein in InterPro
IPR036854 Photo_II_D1/D2_sf
IPR000484 Photo_RC_L/M
IPR005868 PSII_PsbD/D2
PANTHERiPTHR33149 PTHR33149, 1 hit
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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P06005-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTIAVGKFTK DEKDLFDSMD DWLRRDRFVF VGWSGLLLFP CAYFALGGWF
60 70 80 90 100
TGTTFVTSWY THGLASSYLE GCNFLTAAVS TPANSLAHSL LLLWGPEAQG
110 120 130 140 150
DFTRWCQLGG LWAFVALHGA FALIGFMLRQ FELARSVQLR PYNAIAFSGP
160 170 180 190 200
IAVFVSVFLI YPLGQSGWFF APSFGVAAIF RFILFFQGFH NWTLNPFHMM
210 220 230 240 250
GVAGVLGAAL LCAIHGATVE NTLFEDGDGA NTFRAFNPTQ AEETYSMVTA
260 270 280 290 300
NRFWSQIFGV AFSNKRWLHF FMLFVPVTGL WMSALGVVGL ALNLRAYDFV
310 320 330 340 350
SQEIRAAEDP EFETFYTKNI LLNEGIRAWM AAQDQPHENL IFPEEVLPRG

NAL
Length:353
Mass (Da):39,507
Last modified:January 23, 2007 - v3
Checksum:i288090F22B659EA0
GO

Mass spectrometryi

Molecular mass is 39418.8±3.9 Da from positions 2 - 353. Determined by ESI. Non-phosphorylated.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M36833 Genomic DNA Translation: AAA84630.1
AJ400848 Genomic DNA Translation: CAB88721.1
PIRiA23038 F2SPD2
RefSeqiNP_054928.1, NC_002202.1

Genome annotation databases

GeneIDi2715610
KEGGisoe:2715610

Similar proteinsi

Entry informationi

Entry nameiPSBD_SPIOL
AccessioniPrimary (citable) accession number: P06005
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: January 23, 2007
Last modified: February 28, 2018
This is version 141 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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