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Protein

Photosystem II protein D1

Gene

psbA

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

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.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. D1 provides most of the ligands for the Mn4-Ca-O5 cluster of the oxygen-evolving complex (OEC). 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 ChlzD1 axial ligand); via tele nitrogenUniRule annotation1
Binding sitei126Pheophytin D1UniRule annotation1
Sitei161Tyrosine radical intermediateUniRule annotation1
Metal bindingi170Calcium-manganese-oxide [Ca-4Mn-5O]; calciumUniRule annotation1
Metal bindingi170Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4UniRule annotation1
Metal bindingi189Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1UniRule annotation1
Sitei190Stabilizes free radical intermediateUniRule annotation1
Metal bindingi198Magnesium (chlorophyll-a PD1 axial ligand); via tele nitrogenUniRule annotation1
Metal bindingi215Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation1
Binding sitei215Quinone (B)UniRule annotation1
Metal bindingi272Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation1
Metal bindingi332Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1; via tele nitrogenUniRule annotation1
Metal bindingi333Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 3UniRule annotation1
Metal bindingi333Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 4UniRule annotation1
Metal bindingi342Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 1UniRule annotation1
Metal bindingi342Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2UniRule annotation1
Metal bindingi344Calcium-manganese-oxide [Ca-4Mn-5O]; calcium; via carboxylateUniRule annotation1
Metal bindingi344Calcium-manganese-oxide [Ca-4Mn-5O]; manganese 2; via carboxylateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Herbicide resistance, Photosynthesis, Transport

Keywords - Ligandi

Calcium, Chlorophyll, Chromophore, Iron, Magnesium, Manganese, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Photosystem II protein D1UniRule annotation (EC:1.10.3.9UniRule annotation)
Short name:
PSII D1 proteinUniRule annotation
Alternative name(s):
Photosystem II Q(B) proteinUniRule annotation
Gene namesi
Name:psbAUniRule annotation
ORF Names:Nip001
Encoded oniPlastid; Chloroplast
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryza
Proteomesi
  • UP000059680 Componenti: Chloroplast

Subcellular locationi

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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei29 – 46HelicalUniRule annotationAdd BLAST18
Transmembranei118 – 133HelicalUniRule annotationAdd BLAST16
Transmembranei142 – 156HelicalUniRule annotationAdd BLAST15
Transmembranei197 – 218HelicalUniRule annotationAdd BLAST22
Transmembranei274 – 288HelicalUniRule annotationAdd BLAST15

GO - Cellular componenti

  • chloroplast thylakoid membrane Source: GO_Central
  • integral component of membrane Source: UniProtKB-KW
  • photosystem II Source: GO_Central
  • plastid Source: Gramene
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Membrane, Photosystem II, Plastid, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedUniRule annotation
ChainiPRO_00002900382 – 344Photosystem II protein D1UniRule annotationAdd BLAST343
PropeptideiPRO_0000316471345 – 353UniRule annotation9

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylthreonineUniRule annotation1
Modified residuei2PhosphothreonineUniRule annotation1

Post-translational modificationi

Tyr-161 forms a radical intermediate that is referred to as redox-active TyrZ, YZ or Y-Z.UniRule annotation
C-terminally processed by CTPA; processing is essential to allow assembly of the oxygen-evolving complex and thus photosynthetic growth.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei344 – 345Cleavage; by CTPAUniRule annotation2

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiP0C434.

Expressioni

Gene expression databases

GenevisibleiP0C434. OS.

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

STRINGi39947.LOC_Osp1g00110.1.

Structurei

3D structure databases

ProteinModelPortaliP0C434.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni264 – 265Quinone (B)UniRule annotation2

Sequence similaritiesi

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

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IHF0. Eukaryota.
ENOG410XPX5. LUCA.
InParanoidiP0C434.
KOiK02703.
OrthoDBiEOG09360DM3.

Family and domain databases

CDDicd09289. Photosystem-II_D1. 1 hit.
Gene3Di1.20.85.10. 1 hit.
HAMAPiMF_01379. PSII_PsbA_D1. 1 hit.
InterProiIPR000484. Photo_RC_L/M.
IPR005867. PSII_D1.
[Graphical view]
PfamiPF00124. Photo_RC. 1 hit.
[Graphical view]
PRINTSiPR00256. REACTNCENTRE.
SUPFAMiSSF81483. SSF81483. 1 hit.
TIGRFAMsiTIGR01151. psbA. 1 hit.
PROSITEiPS00244. REACTION_CENTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P0C434-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTAILERRES TSLWGRFCNW ITSTENRLYI GWFGVLMIPT LLTATSVFII
60 70 80 90 100
AFIAAPPVDI DGIREPVSGS LLYGNNIISG AIIPTSAAIG LHFYPIWEAA
110 120 130 140 150
SVDEWLYNGG PYELIVLHFL LGVACYMGRE WELSFRLGMR PWIAVAYSAP
160 170 180 190 200
VAAATAVFLI YPIGQGSFSD GMPLGISGTF NFMIVFQAEH NILMHPFHML
210 220 230 240 250
GVAGVFGGSL FSAMHGSLVT SSLIRETTEN ESANEGYRFG QEEETYNIVA
260 270 280 290 300
AHGYFGRLIF QYASFNNSRS LHFFLAAWPV VGIWFTALGI STMAFNLNGF
310 320 330 340 350
NFNQSVVDSQ GRVINTWADI INRANLGMEV MHERNAHNFP LDLAALEVPS

LNG
Length:353
Mass (Da):38,963
Last modified:June 12, 2007 - v1
Checksum:i0A72FB4531E571CF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M36191 Genomic DNA. Translation: AAA84591.1.
X15901 Genomic DNA. Translation: CAA34007.1.
AY522330 Genomic DNA. Translation: AAS46104.1.
BX569685 Genomic DNA. Translation: CAE05900.1.
AP004662 Genomic DNA. Translation: BAD09798.1.
AP005483 Genomic DNA. Translation: BAD10401.1.
PIRiJQ0200. FMRZ32.
RefSeqiNP_039360.1. NC_001320.1.

Genome annotation databases

GeneIDi3131409.
KEGGiosa:3131409.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M36191 Genomic DNA. Translation: AAA84591.1.
X15901 Genomic DNA. Translation: CAA34007.1.
AY522330 Genomic DNA. Translation: AAS46104.1.
BX569685 Genomic DNA. Translation: CAE05900.1.
AP004662 Genomic DNA. Translation: BAD09798.1.
AP005483 Genomic DNA. Translation: BAD10401.1.
PIRiJQ0200. FMRZ32.
RefSeqiNP_039360.1. NC_001320.1.

3D structure databases

ProteinModelPortaliP0C434.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Osp1g00110.1.

Proteomic databases

PaxDbiP0C434.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi3131409.
KEGGiosa:3131409.

Phylogenomic databases

eggNOGiENOG410IHF0. Eukaryota.
ENOG410XPX5. LUCA.
InParanoidiP0C434.
KOiK02703.
OrthoDBiEOG09360DM3.

Gene expression databases

GenevisibleiP0C434. OS.

Family and domain databases

CDDicd09289. Photosystem-II_D1. 1 hit.
Gene3Di1.20.85.10. 1 hit.
HAMAPiMF_01379. PSII_PsbA_D1. 1 hit.
InterProiIPR000484. Photo_RC_L/M.
IPR005867. PSII_D1.
[Graphical view]
PfamiPF00124. Photo_RC. 1 hit.
[Graphical view]
PRINTSiPR00256. REACTNCENTRE.
SUPFAMiSSF81483. SSF81483. 1 hit.
TIGRFAMsiTIGR01151. psbA. 1 hit.
PROSITEiPS00244. REACTION_CENTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPSBA_ORYSJ
AccessioniPrimary (citable) accession number: P0C434
Secondary accession number(s): P12094, Q6QY90, Q7DNA9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 12, 2007
Last sequence update: June 12, 2007
Last modified: November 30, 2016
This is version 77 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

2 of the reaction center chlorophylls (ChlD1 and ChlD2) are entirely coordinated by water.UniRule annotation
Herbicides such as atrazine, BNT, diuron or ioxynil bind in the Q(B) binding site and block subsequent electron transfer.UniRule annotation

Caution

A stretch of the chloroplast genome is duplicated within chromosomes 4 and 8 resulting in the duplication of the gene. The expression of these duplicated genes (Os04g0236400 and Os08g0455300) has not been demonstrated.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  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.