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A4GGA2

- PSBD_PHAVU

UniProt

A4GGA2 - PSBD_PHAVU

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Protein

Photosystem II D2 protein

Gene

psbD

Organism
Phaseolus vulgaris (Kidney bean) (French bean)
Status
Reviewed - Annotation score: 3 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. D2 is needed for assembly of a stable PSII complex.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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi118 – 1181Magnesium (chlorophyll-a ChlzD2, axial ligand; peripheral); via tele nitrogenUniRule annotation
Binding sitei130 – 1301Pheophytin D2UniRule annotation
Binding sitei143 – 1431Pheophytin D2UniRule annotation
Metal bindingi198 – 1981Magnesium (chlorophyll-a PD2 axial ligand); via tele nitrogenUniRule annotation
Metal bindingi215 – 2151Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation
Binding sitei215 – 2151Plastoquinone Q(A)UniRule annotation
Binding sitei262 – 2621Plastoquinone Q(A); via amide nitrogenUniRule annotation
Metal bindingi269 – 2691Iron; shared with heterodimeric partner; via tele nitrogenUniRule annotation

GO - Molecular functioni

  1. electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity Source: InterPro
  2. iron ion binding Source: UniProtKB-HAMAP
  3. oxidoreductase activity Source: UniProtKB-KW

GO - Biological processi

  1. photosynthetic electron transport in photosystem II Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Photosynthesis, Transport

Keywords - Ligandi

Chlorophyll, 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
OrganismiPhaseolus vulgaris (Kidney bean) (French bean)
Taxonomic identifieri3885 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsfabidsFabalesFabaceaePapilionoideaePhaseoleaePhaseolus

Subcellular locationi

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

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei41 – 6121HelicalUniRule annotationAdd
BLAST
Transmembranei125 – 14117HelicalUniRule annotationAdd
BLAST
Transmembranei153 – 16614HelicalUniRule annotationAdd
BLAST
Transmembranei208 – 22821HelicalUniRule annotationAdd
BLAST
Transmembranei279 – 29517HelicalUniRule annotationAdd
BLAST

GO - Cellular componenti

  1. chloroplast thylakoid membrane Source: UniProtKB-HAMAP
  2. integral component of membrane Source: UniProtKB-KW
  3. photosystem II Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Membrane, Photosystem II, Plastid, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 353353Photosystem II D2 proteinPRO_0000359685Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylthreonineUniRule annotation
Modified residuei2 – 21PhosphothreonineUniRule annotation

Keywords - PTMi

Acetylation, Phosphoprotein

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

Structurei

3D structure databases

ProteinModelPortaliA4GGA2.
SMRiA4GGA2. Positions 1-351.
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

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.

A4GGA2-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTIALGKFTK DEKDLFDIMD DWLRRDRFVF VGWSGLLLFP CAYFALGGWF
60 70 80 90 100
TGTTFVTSWY THGLASSYLE GCNFLTAAVS TPANSLSHSL LLLWGPEAQG
110 120 130 140 150
DFTRWCQLGG LWTFVALHGA FGLIGFMLRQ 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):39,580
Last modified:April 17, 2007 - v1
Checksum:i86DEFBD8E6445718
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ886273 Genomic DNA. Translation: ABH88083.1.
EU196765 Genomic DNA. Translation: ABW22785.1.
RefSeqiYP_001122803.1. NC_009259.1.

Genome annotation databases

GeneIDi4961781.
KEGGipvu:PhvuCp19.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ886273 Genomic DNA. Translation: ABH88083.1 .
EU196765 Genomic DNA. Translation: ABW22785.1 .
RefSeqi YP_001122803.1. NC_009259.1.

3D structure databases

ProteinModelPortali A4GGA2.
SMRi A4GGA2. Positions 1-351.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 4961781.
KEGGi pvu:PhvuCp19.

Phylogenomic databases

KOi K02706.

Family and domain databases

Gene3Di 1.20.85.10. 2 hits.
HAMAPi MF_01383. PSII_PsbD_D2.
InterProi IPR000484. Photo_RC_L/M.
IPR005868. PSII_PsbD/D2.
[Graphical view ]
Pfami PF00124. Photo_RC. 1 hit.
[Graphical view ]
PRINTSi PR00256. REACTNCENTRE.
SUPFAMi SSF81483. SSF81483. 1 hit.
TIGRFAMsi TIGR01152. psbD. 1 hit.
PROSITEi PS00244. REACTION_CENTER. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts."
    Guo X., Castillo-Ramirez S., Gonzalez V., Bustos P., Fernandez-Vazquez J.L., Santamaria R.I., Arellano J., Cevallos M.A., Davila G.
    BMC Genomics 8:228-228(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Negro Jamapa.
  2. "Complete nucleotide sequence of the plastid genome of the common bean, Phaseolus vulgaris."
    Moore M.J., Triplett E.W., Broughton W.J., Soltis P.S., Soltis D.E.
    Submitted (OCT-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Entry informationi

Entry nameiPSBD_PHAVU
AccessioniPrimary (citable) accession number: A4GGA2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 20, 2009
Last sequence update: April 17, 2007
Last modified: November 26, 2014
This is version 47 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3