Reviewed, UniProtKB/Swiss-Prot Q9RZA4 (BPHY_DEIRA)

Names and origin

Protein names

Recommended name:
    Bacteriophytochrome
    EC=2.7.13.3
Alternative name(s):
    Phytochrome-like protein

Gene names

Name:	bphP
Ordered Locus Names:	DR_A0050

Organism

Deinococcus radiodurans [Complete proteome] [HAMAP]

Taxonomic identifier

1299 [NCBI]

Taxonomic lineage

Bacteria › Deinococcus-Thermus › Deinococci › Deinococcales › Deinococcaceae › Deinococcus

Protein attributes

Sequence length	755 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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 activity	ATP + protein L-histidine = ADP + protein N-phospho-L-histidine.
Post-translational modification	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.
Sequence similarities	In the N-terminal section; belongs to the phytochrome family. Contains 1 GAF domain. Contains 1 histidine kinase domain. Contains 1 PAS (PER-ARNT-SIM) domain.

Ontologies

Keywords
Biological process	Sensory transduction
Ligand	ATP-binding Chromophore Nucleotide-binding
Molecular function	Kinase Photoreceptor protein Receptor Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	peptidyl-histidine phosphorylation Inferred from electronic annotation. Source: InterPro protein-chromophore linkage Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro response to stimulus Inferred from electronic annotation. Source: UniProtKB-KW sensory perception Inferred from electronic annotation. Source: InterPro signal transduction Inferred from electronic annotation. Source: InterPro
Cellular component	membrane Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW G-protein coupled photoreceptor activity Inferred from electronic annotation. Source: InterPro two-component sensor activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 755

755

Bacteriophytochrome

PRO_0000171999

Regions

Domain

26 – 94

69

PAS

Domain

152 – 316

165

GAF

Domain

529 – 747

219

Histidine kinase

Region

95 – 504

410

Chromophore binding domain

Sites

Binding site

24

1

Tetrapyrrole chromophore (covalent; via 1 link) Probable

Amino acid modifications

Modified residue

532

1

Phosphohistidine; by autocatalysis By similarity

Experimental info

Mutagenesis

259

1

M → A: Binds PCB (in vitro), but difference spectrum is altered. Ref.2

Mutagenesis

259

1

M → C: Binds PCB (in vitro), but difference spectrum is altered. Ref.2

Mutagenesis

260

1

H → A: 100-fold reduction of chromophore-binding activity. Ref.2

Mutagenesis

289

1

C → A: Binds PCB (in vitro), but has aberrant spectral properties. Ref.2

Secondary structure

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755

Helix Strand Turn

Details...

Helix

12 – 14

3

Turn

21 – 23

3

Helix

24 – 26

3

Beta strand

33 – 35

3

Beta strand

39 – 45

7

Turn

46 – 48

3

Beta strand

50 – 55

6

Helix

58 – 62

5

Helix

66 – 69

4

Helix

74 – 77

4

Turn

79 – 81

3

Helix

82 – 88

7

Beta strand

99 – 103

5

Beta strand

106 – 118

13

Beta strand

121 – 129

9

Helix

131 – 133

3

Helix

138 – 149

12

Helix

153 – 168

16

Beta strand

171 – 178

8

Beta strand

184 – 191

8

Helix

205 – 207

3

Helix

210 – 218

9

Beta strand

221 – 225

5

Beta strand

232 – 238

7

Turn

240 – 242

3

Beta strand

243 – 245

3

Helix

258 – 266

9

Beta strand

270 – 279

10

Beta strand

282 – 293

12

Helix

299 – 320

22

Sequences

	Sequence		Length	Mass (Da)
	Q9RZA4-1 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: A631E471B208F187	FASTA	755	81,585
	10 20 30 40 50 60 MSRDPLPFFP PLYLGGPEIT TENCEREPIH IPGSIQPHGA LLTADGHSGE VLQMSLNAAT 70 80 90 100 110 120 FLGQEPTVLR GQTLAALLPE QWPALQAALP PGCPDALQYR ATLDWPAAGH LSLTVHRVGE 130 140 150 160 170 180 LLILEFEPTE AWDSTGPHAL RNAMFALESA PNLRALAEVA TQTVRELTGF DRVMLYKFAP 190 200 210 220 230 240 DATGEVIAEA RREGLHAFLG HRFPASDIPA QARALYTRHL LRLTADTRAA AVPLDPVLNP 250 260 270 280 290 300 QTNAPTPLGG AVLRATSPMH MQYLRNMGVG SSLSVSVVVG GQLWGLIACH HQTPYVLPPD 310 320 330 340 350 360 LRTTLEYLGR LLSLQVQVKE AADVAAFRQS LREHHARVAL AAAHSLSPHD TLSDPALDLL 370 380 390 400 410 420 GLMRAGGLIL RFEGRWQTLG EVPPAPAVDA LLAWLETQPG ALVQTDALGQ LWPAGADLAP 430 440 450 460 470 480 SAAGLLAISV GEGWSECLVW LRPELRLEVA WGGATPDQAK DDLGPRHSFD TYLEEKRGYA 490 500 510 520 530 540 EPWHPGEIEE AQDLRDTLTG ALGERLSVIR DLNRALTQSN AEWRQYGFVI SHHMQEPVRL 550 560 570 580 590 600 ISQFAELLTR QPRAQDGSPD SPQTERITGF LLRETSRLRS LTQDLHTYTA LLSAPPPVRR 610 620 630 640 650 660 PTPLGRVVDD VLQDLEPRIA DTGASIEVAP ELPVIAADAG LLRDLLLHLI GNALTFGGPE 670 680 690 700 710 720 PRIAVRTERQ GAGWSIAVSD QGAGIAPEYQ ERIFLLFQRL GSLDEALGNG LGLPLCRKIA 730 740 750 ELHGGTLTVE SAPGEGSTFR CWLPDAGPLP GAADA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1." White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D., Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L., Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M., Vamathevan J.J., Lam P. , McDonald L.A., Utterback T.R., Zalewski C., Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D., Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C., Fraser C.M. Science 286:1571-1577(1999) [PubMed: 10567266] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 13939 / DSM 20539 / IFO 15346 / LMG 4051 / NCIB 9279 / R1.
[2]	"Bacteriophytochromes: phytochrome-like photoreceptors from nonphotosynthetic eubacteria." Davis S.J., Vener A.V., Vierstra R.D. Science 286:2517-2520(1999) [PubMed: 10617469] [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: 16292304] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-321.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE001825 Genomic DNA. Translation: AAF12261.1.

PIR

D75598.

RefSeq

NP_285374.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZTU	X-ray	2.50	A	1-321	[»]
2O9B	X-ray	2.15	A	1-321	[»]
2O9C	X-ray	1.45	A	1-321	[»]

SMR

Q9RZA4. Positions 518-746.

ModBase

Search...

Genome annotation databases

GeneID

1798221.

GenomeReviews

Gene locus DR_A0050 in contig AE001825_GR.

KEGG

dra:DR_A0050.

NMPDR

fig|243230.1.peg.2864.

TIGR

DR_A0050.

Phylogenomic databases

HOGENOM

HBG639461.

OMA

REMGDER.

Enzyme and pathway databases

BioCyc

DRAD243230:DR_A0050-MONOMER.

BRENDA

2.7.13.3. 96172.

Family and domain databases

InterPro

IPR003594. ATPase-like_ATP-bd.
IPR003018. GAF.
IPR000014. PAS.
IPR013654. PAS_2.
IPR016132. Phyto_chromo_attachment.
IPR013515. Phytochrome_cen-reg.
IPR004358. Sig_transdc_His_kin-like_C.
IPR003661. Sig_transdc_His_kin_sub1_dim/P.
IPR005467. Sig_transdc_His_kinase_core.
IPR009082. Sig_transdc_His_kinase_dimeric.
[Graphical view]

Gene3D

G3DSA:3.30.565.10. ATP_bd_ATPase. 1 hit.

Pfam

PF01590. GAF. 1 hit.
PF02518. HATPase_c. 1 hit.
PF08446. PAS_2. 1 hit.
PF00360. Phytochrome. 1 hit.
[Graphical view]

PRINTS

PR00344. BCTRLSENSOR.

SMART

SM00065. GAF. 1 hit.
SM00387. HATPase_c. 1 hit.
SM00388. HisKA. 1 hit.
SM00091. PAS. 1 hit.
[Graphical view]

PROSITE

PS50109. HIS_KIN. 1 hit.
PS50112. PAS. False negative.
PS00245. PHYTOCHROME_1. False negative.
PS50046. PHYTOCHROME_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

BPHY_DEIRA

Accession

Primary (citable) accession number: Q9RZA4

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 11, 2001
Last sequence update:	May 1, 2000
Last modified:	January 19, 2010
This is version 85 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)