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Protein

Photosystem II D2 protein

Gene

psbD

Organism
Thermosynechococcus vulcanus (Synechococcus vulcanus)
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 (PubMed:19433803, PubMed:23426624). D2 is needed for assembly of a stable PSII complex.UniRule annotation2 Publications

Miscellaneous

2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water.UniRule annotation1 Publication

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 annotation4 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi107Magnesium (chlorophyll-a ChlzD2, axial ligand; peripheral); via tele nitrogenUniRule annotation1 Publication1
Binding sitei119Pheophytin D2UniRule annotation2 Publications1
Binding sitei132Pheophytin D21 PublicationUniRule annotation2 Publications1
Metal bindingi187Magnesium (chlorophyll-a PD2 axial ligand); via tele nitrogenUniRule annotation2 Publications1
Metal bindingi204Iron; shared with heterodimeric partner; via tele nitrogen1 PublicationUniRule annotation2 Publications1
Binding sitei204Plastoquinone Q(A)1 PublicationUniRule annotation2 Publications1
Binding sitei251Plastoquinone Q(A); via amide nitrogenUniRule annotation2 Publications1
Metal bindingi258Iron; shared with heterodimeric partner; via tele nitrogen1 PublicationUniRule annotation2 Publications1

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
OrganismiThermosynechococcus vulcanus (Synechococcus vulcanus)
Taxonomic identifieri32053 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaSynechococcalesSynechococcaceaeThermosynechococcus

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 29Cytoplasmic1 PublicationAdd BLAST29
Transmembranei30 – 50HelicalUniRule annotation1 PublicationAdd BLAST21
Topological domaini51 – 113Lumenal1 PublicationAdd BLAST63
Transmembranei114 – 130HelicalUniRule annotation1 PublicationAdd BLAST17
Topological domaini131 – 141Cytoplasmic1 PublicationAdd BLAST11
Transmembranei142 – 155HelicalUniRule annotation1 PublicationAdd BLAST14
Topological domaini156 – 196Lumenal1 PublicationAdd BLAST41
Transmembranei197 – 217HelicalUniRule annotation1 PublicationAdd BLAST21
Topological domaini218 – 267Cytoplasmic1 PublicationAdd BLAST50
Transmembranei268 – 284HelicalUniRule annotation1 PublicationAdd BLAST17
Topological domaini285 – 342Lumenal1 PublicationAdd BLAST58

GO - Cellular componenti

Keywords - Cellular componenti

Membrane, Photosystem II, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004226021 – 342Photosystem II D2 proteinAdd BLAST342

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 annotation4 Publications

Protein-protein interaction databases

DIPiDIP-61466N
IntActiD0VWR8, 1 interactor

Structurei

Secondary structure

1342
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 12Combined sources9
Helixi21 – 44Combined sources24
Helixi48 – 51Combined sources4
Helixi57 – 59Combined sources3
Turni63 – 65Combined sources3
Helixi73 – 75Combined sources3
Turni85 – 89Combined sources5
Helixi91 – 96Combined sources6
Helixi99 – 126Combined sources28
Helixi131 – 147Combined sources17
Helixi149 – 153Combined sources5
Beta strandi154 – 156Combined sources3
Helixi157 – 159Combined sources3
Helixi165 – 179Combined sources15
Helixi181 – 183Combined sources3
Helixi185 – 210Combined sources26
Beta strandi211 – 213Combined sources3
Beta strandi216 – 219Combined sources4
Helixi221 – 224Combined sources4
Helixi236 – 247Combined sources12
Helixi254 – 280Combined sources27
Helixi289 – 297Combined sources9
Helixi304 – 323Combined sources20
Helixi325 – 327Combined sources3
Helixi333 – 335Combined sources3

3D structure databases

SMRiD0VWR8
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiD0VWR8

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, 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: Fragment.

D0VWR8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
ERGWFDILDD WLKRDRFVFV GWSGILLFPC AYLALGGWLT GTTFVTSWYT
60 70 80 90 100
HGLASSYLEG CNFLTVAVST PANSMGHSLL LLWGPEAQGD FTRWCQLGGL
110 120 130 140 150
WTFIALHGAF GLIGFMLRQF EIARLVGVRP YNAIAFSAPI AVFVSVFLIY
160 170 180 190 200
PLGQSSWFFA PSFGVAAIFR FLLFFQGFHN WTLNPFHMMG VAGVLGGALL
210 220 230 240 250
CAIHGATVEN TLFQDGEGAS TFRAFNPTQA EETYSMVTAN RFWSQIFGIA
260 270 280 290 300
FSNKRWLHFF MLFVPVTGLW MSAIGVVGLA LNLRSYDFIS QEIRAAEDPE
310 320 330 340
FETFYTKNLL LNEGIRAWMA PQDQPHENFV FPEEVLPRGN AL
Length:342
Mass (Da):38,379
Last modified:May 29, 2013 - v2
Checksum:i3CD88A6D811BB788
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Non-terminal residuei11

Similar proteinsi

Entry informationi

Entry nameiPSBD_THEVL
AccessioniPrimary (citable) accession number: D0VWR8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 29, 2013
Last sequence update: May 29, 2013
Last modified: February 28, 2018
This is version 47 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

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