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Protein

Bacteriophytochrome

Gene

bphP

Organism
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.

Catalytic activityi

ATP + protein L-histidine = ADP + protein N-phospho-L-histidine.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei24 – 241Tetrapyrrole chromophore (covalent; via 1 link)Curated

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Photoreceptor protein, Receptor, Transferase

Keywords - Biological processi

Sensory transduction

Keywords - Ligandi

ATP-binding, Chromophore, Nucleotide-binding

Enzyme and pathway databases

BioCyciDRAD243230:GH46-2741-MONOMER.
BRENDAi2.7.13.3. 1856.

Names & Taxonomyi

Protein namesi
Recommended name:
Bacteriophytochrome (EC:2.7.13.3)
Alternative name(s):
Phytochrome-like protein
Gene namesi
Name:bphP
Ordered Locus Names:DR_A0050
OrganismiDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Taxonomic identifieri243230 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciDeinococcalesDeinococcaceaeDeinococcus
Proteomesi
  • UP000002524 Componenti: Chromosome II

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi259 – 2591M → A: Binds PCB (in vitro), but difference spectrum is altered. 1 Publication
Mutagenesisi259 – 2591M → C: Binds PCB (in vitro), but difference spectrum is altered. 1 Publication
Mutagenesisi260 – 2601H → A: 100-fold reduction of chromophore-binding activity. 1 Publication
Mutagenesisi289 – 2891C → A: Binds PCB (in vitro), but has aberrant spectral properties. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 755755BacteriophytochromePRO_0000171999Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei532 – 5321Phosphohistidine; by autocatalysisPROSITE-ProRule annotation

Post-translational modificationi

Contains one covalently linked tetrapyrrole chromophore. Lacks the cysteine conserved in plant phytochromes (at the position of Met-259) that binds chromophore. An engineered sequence used for X-ray crystallography forms a thioether link to biliverdin through Cys-24. The natural sequence can bind phycocyanobilin and phytochromobilin in vitro, but the identity of the natural chromophore is unknown.

Keywords - PTMi

Phosphoprotein

Proteomic databases

PRIDEiQ9RZA4.

Interactioni

Protein-protein interaction databases

DIPiDIP-59338N.
STRINGi243230.DR_A0050.

Structurei

Secondary structure

755
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1 – 33Combined sources
Helixi12 – 143Combined sources
Turni21 – 233Combined sources
Helixi24 – 263Combined sources
Beta strandi33 – 353Combined sources
Beta strandi39 – 457Combined sources
Turni46 – 483Combined sources
Beta strandi50 – 556Combined sources
Helixi58 – 625Combined sources
Helixi66 – 694Combined sources
Beta strandi70 – 734Combined sources
Helixi74 – 774Combined sources
Helixi81 – 888Combined sources
Beta strandi99 – 1035Combined sources
Beta strandi107 – 1093Combined sources
Beta strandi110 – 1189Combined sources
Beta strandi121 – 1299Combined sources
Helixi131 – 1333Combined sources
Helixi139 – 14911Combined sources
Helixi153 – 16816Combined sources
Beta strandi171 – 1788Combined sources
Beta strandi184 – 1918Combined sources
Beta strandi193 – 1953Combined sources
Helixi205 – 2073Combined sources
Helixi210 – 2189Combined sources
Beta strandi221 – 2255Combined sources
Beta strandi232 – 2387Combined sources
Turni240 – 2423Combined sources
Beta strandi243 – 2453Combined sources
Helixi258 – 2669Combined sources
Beta strandi270 – 27910Combined sources
Beta strandi282 – 29312Combined sources
Helixi299 – 32022Combined sources
Beta strandi344 – 3463Combined sources
Helixi348 – 3525Combined sources
Turni355 – 3573Combined sources
Helixi359 – 3624Combined sources
Beta strandi366 – 3727Combined sources
Beta strandi375 – 3817Combined sources
Helixi385 – 39713Combined sources
Beta strandi400 – 4067Combined sources
Helixi408 – 4114Combined sources
Helixi413 – 4186Combined sources
Turni419 – 4213Combined sources
Beta strandi423 – 4297Combined sources
Turni433 – 4353Combined sources
Beta strandi436 – 4427Combined sources
Beta strandi447 – 4537Combined sources
Turni456 – 4616Combined sources
Beta strandi462 – 4643Combined sources
Beta strandi470 – 4767Combined sources
Helixi485 – 50117Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZTUX-ray2.50A1-321[»]
2O9BX-ray2.15A1-321[»]
2O9CX-ray1.45A1-321[»]
3S7NX-ray2.45A1-321[»]
3S7OX-ray1.24A1-321[»]
3S7PX-ray1.72A1-321[»]
3S7QX-ray1.75A1-321[»]
4CQHX-ray1.14A1-317[»]
4IJGX-ray1.70A7-321[»]
4O01X-ray3.24A/B/C/D1-502[»]
4O0PX-ray3.80A/B1-502[»]
4O8GX-ray1.65A1-321[»]
4Q0HX-ray1.16A1-321[»]
4Q0IX-ray1.74A1-321[»]
4Q0JX-ray2.75A1-502[»]
4Y3IX-ray1.69A4-321[»]
4Y5FX-ray1.70A4-321[»]
4Z1WX-ray1.30A1-321[»]
4ZRRX-ray1.50A1-321[»]
5AJGX-ray1.11A1-321[»]
5C5KX-ray3.31A/B/C/D1-502[»]
ProteinModelPortaliQ9RZA4.
SMRiQ9RZA4. Positions 4-321.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9RZA4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini26 – 9469PASAdd
BLAST
Domaini152 – 316165GAFAdd
BLAST
Domaini529 – 747219Histidine kinasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni95 – 504410Chromophore binding domainAdd
BLAST

Sequence similaritiesi

In the N-terminal section; belongs to the phytochrome family.Curated
Contains 1 GAF domain.Curated
Contains 1 histidine kinase domain.PROSITE-ProRule annotation
Contains 1 PAS (PER-ARNT-SIM) domain.Curated

Phylogenomic databases

eggNOGiCOG4251. LUCA.
HOGENOMiHOG000030537.
InParanoidiQ9RZA4.
OMAiWIRLISD.
OrthoDBiEOG6G4VQG.

Family and domain databases

Gene3Di3.30.450.40. 1 hit.
3.30.565.10. 1 hit.
InterProiIPR003018. GAF.
IPR029016. GAF_dom-like.
IPR003594. HATPase_C.
IPR005467. His_kinase_dom.
IPR003661. HisK_dim/P.
IPR000014. PAS.
IPR013654. PAS_2.
IPR016132. Phyto_chromo_attachment.
IPR013515. Phytochrome_cen-reg.
IPR004358. Sig_transdc_His_kin-like_C.
[Graphical view]
PfamiPF01590. GAF. 1 hit.
PF02518. HATPase_c. 1 hit.
PF08446. PAS_2. 1 hit.
PF00360. PHY. 1 hit.
[Graphical view]
PRINTSiPR00344. BCTRLSENSOR.
SMARTiSM00065. GAF. 1 hit.
SM00387. HATPase_c. 1 hit.
[Graphical view]
SUPFAMiSSF47384. SSF47384. 1 hit.
SSF55781. SSF55781. 2 hits.
SSF55785. SSF55785. 1 hit.
SSF55874. SSF55874. 1 hit.
PROSITEiPS50109. HIS_KIN. 1 hit.
PS50046. PHYTOCHROME_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9RZA4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRDPLPFFP PLYLGGPEIT TENCEREPIH IPGSIQPHGA LLTADGHSGE
60 70 80 90 100
VLQMSLNAAT FLGQEPTVLR GQTLAALLPE QWPALQAALP PGCPDALQYR
110 120 130 140 150
ATLDWPAAGH LSLTVHRVGE LLILEFEPTE AWDSTGPHAL RNAMFALESA
160 170 180 190 200
PNLRALAEVA TQTVRELTGF DRVMLYKFAP DATGEVIAEA RREGLHAFLG
210 220 230 240 250
HRFPASDIPA QARALYTRHL LRLTADTRAA AVPLDPVLNP QTNAPTPLGG
260 270 280 290 300
AVLRATSPMH MQYLRNMGVG SSLSVSVVVG GQLWGLIACH HQTPYVLPPD
310 320 330 340 350
LRTTLEYLGR LLSLQVQVKE AADVAAFRQS LREHHARVAL AAAHSLSPHD
360 370 380 390 400
TLSDPALDLL GLMRAGGLIL RFEGRWQTLG EVPPAPAVDA LLAWLETQPG
410 420 430 440 450
ALVQTDALGQ LWPAGADLAP SAAGLLAISV GEGWSECLVW LRPELRLEVA
460 470 480 490 500
WGGATPDQAK DDLGPRHSFD TYLEEKRGYA EPWHPGEIEE AQDLRDTLTG
510 520 530 540 550
ALGERLSVIR DLNRALTQSN AEWRQYGFVI SHHMQEPVRL ISQFAELLTR
560 570 580 590 600
QPRAQDGSPD SPQTERITGF LLRETSRLRS LTQDLHTYTA LLSAPPPVRR
610 620 630 640 650
PTPLGRVVDD VLQDLEPRIA DTGASIEVAP ELPVIAADAG LLRDLLLHLI
660 670 680 690 700
GNALTFGGPE PRIAVRTERQ GAGWSIAVSD QGAGIAPEYQ ERIFLLFQRL
710 720 730 740 750
GSLDEALGNG LGLPLCRKIA ELHGGTLTVE SAPGEGSTFR CWLPDAGPLP

GAADA
Length:755
Mass (Da):81,585
Last modified:May 1, 2000 - v1
Checksum:iA631E471B208F187
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE001825 Genomic DNA. Translation: AAF12261.1.
PIRiD75598.
RefSeqiNP_285374.1. NC_001264.1.
WP_010889310.1. NC_001264.1.

Genome annotation databases

EnsemblBacteriaiAAF12261; AAF12261; DR_A0050.
GeneIDi1798221.
KEGGidra:DR_A0050.
PATRICi21633128. VBIDeiRad64572_2934.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE001825 Genomic DNA. Translation: AAF12261.1.
PIRiD75598.
RefSeqiNP_285374.1. NC_001264.1.
WP_010889310.1. NC_001264.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZTUX-ray2.50A1-321[»]
2O9BX-ray2.15A1-321[»]
2O9CX-ray1.45A1-321[»]
3S7NX-ray2.45A1-321[»]
3S7OX-ray1.24A1-321[»]
3S7PX-ray1.72A1-321[»]
3S7QX-ray1.75A1-321[»]
4CQHX-ray1.14A1-317[»]
4IJGX-ray1.70A7-321[»]
4O01X-ray3.24A/B/C/D1-502[»]
4O0PX-ray3.80A/B1-502[»]
4O8GX-ray1.65A1-321[»]
4Q0HX-ray1.16A1-321[»]
4Q0IX-ray1.74A1-321[»]
4Q0JX-ray2.75A1-502[»]
4Y3IX-ray1.69A4-321[»]
4Y5FX-ray1.70A4-321[»]
4Z1WX-ray1.30A1-321[»]
4ZRRX-ray1.50A1-321[»]
5AJGX-ray1.11A1-321[»]
5C5KX-ray3.31A/B/C/D1-502[»]
ProteinModelPortaliQ9RZA4.
SMRiQ9RZA4. Positions 4-321.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59338N.
STRINGi243230.DR_A0050.

Proteomic databases

PRIDEiQ9RZA4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF12261; AAF12261; DR_A0050.
GeneIDi1798221.
KEGGidra:DR_A0050.
PATRICi21633128. VBIDeiRad64572_2934.

Phylogenomic databases

eggNOGiCOG4251. LUCA.
HOGENOMiHOG000030537.
InParanoidiQ9RZA4.
OMAiWIRLISD.
OrthoDBiEOG6G4VQG.

Enzyme and pathway databases

BioCyciDRAD243230:GH46-2741-MONOMER.
BRENDAi2.7.13.3. 1856.

Miscellaneous databases

EvolutionaryTraceiQ9RZA4.

Family and domain databases

Gene3Di3.30.450.40. 1 hit.
3.30.565.10. 1 hit.
InterProiIPR003018. GAF.
IPR029016. GAF_dom-like.
IPR003594. HATPase_C.
IPR005467. His_kinase_dom.
IPR003661. HisK_dim/P.
IPR000014. PAS.
IPR013654. PAS_2.
IPR016132. Phyto_chromo_attachment.
IPR013515. Phytochrome_cen-reg.
IPR004358. Sig_transdc_His_kin-like_C.
[Graphical view]
PfamiPF01590. GAF. 1 hit.
PF02518. HATPase_c. 1 hit.
PF08446. PAS_2. 1 hit.
PF00360. PHY. 1 hit.
[Graphical view]
PRINTSiPR00344. BCTRLSENSOR.
SMARTiSM00065. GAF. 1 hit.
SM00387. HATPase_c. 1 hit.
[Graphical view]
SUPFAMiSSF47384. SSF47384. 1 hit.
SSF55781. SSF55781. 2 hits.
SSF55785. SSF55785. 1 hit.
SSF55874. SSF55874. 1 hit.
PROSITEiPS50109. HIS_KIN. 1 hit.
PS50046. PHYTOCHROME_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  2. "Bacteriophytochromes: phytochrome-like photoreceptors from nonphotosynthetic eubacteria."
    Davis S.J., Vener A.V., Vierstra R.D.
    Science 286:2517-2520(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, MUTAGENESIS OF MET-259; HIS-260 AND CYS-289.
  3. "A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome."
    Wagner J.R., Brunzelle J.S., Forest K.T., Vierstra R.D.
    Nature 438:325-331(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-321.

Entry informationi

Entry nameiBPHY_DEIRA
AccessioniPrimary (citable) accession number: Q9RZA4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: May 1, 2000
Last modified: June 8, 2016
This is version 132 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.