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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)DescriptionActionsGraphical viewLength
Binding sitei24Tetrapyrrole chromophore (covalent; via 1 link)Curated1

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

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)DescriptionActionsGraphical viewLength
Mutagenesisi259M → A: Binds PCB (in vitro), but difference spectrum is altered. 1 Publication1
Mutagenesisi259M → C: Binds PCB (in vitro), but difference spectrum is altered. 1 Publication1
Mutagenesisi260H → A: 100-fold reduction of chromophore-binding activity. 1 Publication1
Mutagenesisi289C → A: Binds PCB (in vitro), but has aberrant spectral properties. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001719991 – 755BacteriophytochromeAdd BLAST755

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei532Phosphohistidine; by autocatalysisPROSITE-ProRule annotation1

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

Interactioni

Protein-protein interaction databases

DIPiDIP-59338N.
STRINGi243230.DR_A0050.

Structurei

Secondary structure

1755
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 3Combined sources3
Helixi12 – 14Combined sources3
Turni21 – 23Combined sources3
Helixi24 – 26Combined sources3
Beta strandi33 – 35Combined sources3
Beta strandi39 – 45Combined sources7
Turni46 – 48Combined sources3
Beta strandi50 – 55Combined sources6
Helixi58 – 62Combined sources5
Helixi66 – 69Combined sources4
Beta strandi70 – 73Combined sources4
Helixi74 – 77Combined sources4
Helixi81 – 88Combined sources8
Beta strandi99 – 103Combined sources5
Beta strandi107 – 109Combined sources3
Beta strandi110 – 118Combined sources9
Beta strandi121 – 129Combined sources9
Helixi131 – 133Combined sources3
Helixi139 – 149Combined sources11
Helixi153 – 168Combined sources16
Beta strandi171 – 178Combined sources8
Beta strandi184 – 191Combined sources8
Beta strandi193 – 195Combined sources3
Helixi205 – 207Combined sources3
Helixi210 – 218Combined sources9
Beta strandi221 – 225Combined sources5
Beta strandi232 – 238Combined sources7
Turni240 – 242Combined sources3
Beta strandi243 – 245Combined sources3
Helixi258 – 266Combined sources9
Beta strandi270 – 279Combined sources10
Beta strandi282 – 293Combined sources12
Helixi299 – 320Combined sources22
Beta strandi344 – 346Combined sources3
Helixi348 – 352Combined sources5
Turni355 – 357Combined sources3
Helixi359 – 362Combined sources4
Beta strandi366 – 372Combined sources7
Beta strandi375 – 381Combined sources7
Helixi385 – 397Combined sources13
Beta strandi400 – 406Combined sources7
Helixi408 – 411Combined sources4
Helixi413 – 418Combined sources6
Turni419 – 421Combined sources3
Beta strandi423 – 429Combined sources7
Turni433 – 435Combined sources3
Beta strandi436 – 442Combined sources7
Beta strandi447 – 453Combined sources7
Turni456 – 461Combined sources6
Beta strandi462 – 464Combined sources3
Beta strandi470 – 476Combined sources7
Helixi485 – 501Combined sources17

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9RZA4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini26 – 94PASAdd BLAST69
Domaini152 – 316GAFAdd BLAST165
Domaini529 – 747Histidine kinasePROSITE-ProRule annotationAdd BLAST219

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni95 – 504Chromophore binding domainAdd BLAST410

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.
OMAiEIALEFR.
OrthoDBiPOG091H0LPJ.

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. NZ_CP015082.1.

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. NZ_CP015082.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59338N.
STRINGi243230.DR_A0050.

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.
OMAiEIALEFR.
OrthoDBiPOG091H0LPJ.

Enzyme and pathway databases

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...

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: November 2, 2016
This is version 135 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.