BPHY_DEIRA
ID BPHY_DEIRA Reviewed; 755 AA.
AC Q9RZA4;
DT 11-JAN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=Bacteriophytochrome;
DE EC=2.7.13.3;
DE AltName: Full=Phytochrome-like protein;
GN Name=bphP; OrderedLocusNames=DR_A0050;
OS Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG
OS 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422).
OC Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae;
OC Deinococcus.
OX NCBI_TaxID=243230;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=10567266; DOI=10.1126/science.286.5444.1571;
RA White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D.,
RA Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L.,
RA Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M.,
RA Vamathevan J.J., Lam P., McDonald L.A., Utterback T.R., Zalewski C.,
RA Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D.,
RA Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C.,
RA Fraser C.M.;
RT "Genome sequence of the radioresistant bacterium Deinococcus radiodurans
RT R1.";
RL Science 286:1571-1577(1999).
RN [2]
RP CHARACTERIZATION, AND MUTAGENESIS OF MET-259; HIS-260 AND CYS-289.
RX PubMed=10617469; DOI=10.1126/science.286.5449.2517;
RA Davis S.J., Vener A.V., Vierstra R.D.;
RT "Bacteriophytochromes: phytochrome-like photoreceptors from
RT nonphotosynthetic eubacteria.";
RL Science 286:2517-2520(1999).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-321.
RX PubMed=16292304; DOI=10.1038/nature04118;
RA Wagner J.R., Brunzelle J.S., Forest K.T., Vierstra R.D.;
RT "A light-sensing knot revealed by the structure of the chromophore-binding
RT domain of phytochrome.";
RL Nature 438:325-331(2005).
CC -!- FUNCTION: Photoreceptor which exists in two forms that are reversibly
CC interconvertible by light: the R form that absorbs maximally in the red
CC region of the spectrum and the FR form that absorbs maximally in the
CC far-red region. Has also a slight blue shift for the far-red maximum.
CC Could also absorb green light. May participate in regulating pigment
CC synthesis like the carotenoid deinoxanthin which could protect the
CC bacterium from intense visible light.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + protein L-histidine = ADP + protein N-phospho-L-
CC histidine.; EC=2.7.13.3;
CC -!- INTERACTION:
CC Q9RZA4; Q9RZA4: bphP; NbExp=7; IntAct=EBI-15858311, EBI-15858311;
CC -!- PTM: Contains one covalently linked tetrapyrrole chromophore. Lacks the
CC cysteine conserved in plant phytochromes (at the position of Met-259)
CC that binds chromophore. An engineered sequence used for X-ray
CC crystallography forms a thioether link to biliverdin through Cys-24.
CC The natural sequence can bind phycocyanobilin and phytochromobilin in
CC vitro, but the identity of the natural chromophore is unknown.
CC -!- SIMILARITY: In the N-terminal section; belongs to the phytochrome
CC family. {ECO:0000305}.
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DR EMBL; AE001825; AAF12261.1; -; Genomic_DNA.
DR PIR; D75598; D75598.
DR RefSeq; NP_285374.1; NC_001264.1.
DR RefSeq; WP_010889310.1; NZ_CP015082.1.
DR PDB; 1ZTU; X-ray; 2.50 A; A=1-321.
DR PDB; 2O9B; X-ray; 2.15 A; A=1-321.
DR PDB; 2O9C; X-ray; 1.45 A; A=1-321.
DR PDB; 3S7N; X-ray; 2.45 A; A=1-321.
DR PDB; 3S7O; X-ray; 1.24 A; A=1-321.
DR PDB; 3S7P; X-ray; 1.72 A; A=1-321.
DR PDB; 3S7Q; X-ray; 1.75 A; A=1-321.
DR PDB; 4CQH; X-ray; 1.14 A; A=1-317.
DR PDB; 4IJG; X-ray; 1.70 A; A=7-321.
DR PDB; 4O01; X-ray; 3.24 A; A/B/C/D=1-502.
DR PDB; 4O0P; X-ray; 3.80 A; A/B=1-502.
DR PDB; 4O8G; X-ray; 1.65 A; A=1-321.
DR PDB; 4Q0H; X-ray; 1.16 A; A=1-321.
DR PDB; 4Q0I; X-ray; 1.74 A; A=1-321.
DR PDB; 4Q0J; X-ray; 2.75 A; A=1-502.
DR PDB; 4Y3I; X-ray; 1.69 A; A=4-321.
DR PDB; 4Y5F; X-ray; 1.70 A; A=4-321.
DR PDB; 4Z1W; X-ray; 1.30 A; A=1-321.
DR PDB; 4ZRR; X-ray; 1.50 A; A=1-321.
DR PDB; 5AJG; X-ray; 1.11 A; A=1-321.
DR PDB; 5C5K; X-ray; 3.31 A; A/B/C/D=1-502.
DR PDB; 5K5B; X-ray; 1.35 A; A=1-321.
DR PDB; 5L8M; X-ray; 2.10 A; A=1-321.
DR PDB; 5LBR; X-ray; 2.20 A; A=1-321.
DR PDB; 5MG0; X-ray; 1.65 A; A=1-321.
DR PDB; 5MG1; X-ray; 3.30 A; A=1-502.
DR PDB; 5NFX; X-ray; 1.34 A; A=1-321.
DR PDB; 5NM3; X-ray; 3.30 A; A/B/C/D=1-502.
DR PDB; 5NWN; X-ray; 3.60 A; A/B/C/D=1-502.
DR PDB; 6FHT; X-ray; 2.35 A; A/B=3-510.
DR PDB; 6FTD; X-ray; 1.40 A; A/B=1-321.
DR PDB; 6T3L; X-ray; 2.07 A; A/B=1-321.
DR PDB; 6T3U; X-ray; 2.21 A; A/B=1-321.
DR PDBsum; 1ZTU; -.
DR PDBsum; 2O9B; -.
DR PDBsum; 2O9C; -.
DR PDBsum; 3S7N; -.
DR PDBsum; 3S7O; -.
DR PDBsum; 3S7P; -.
DR PDBsum; 3S7Q; -.
DR PDBsum; 4CQH; -.
DR PDBsum; 4IJG; -.
DR PDBsum; 4O01; -.
DR PDBsum; 4O0P; -.
DR PDBsum; 4O8G; -.
DR PDBsum; 4Q0H; -.
DR PDBsum; 4Q0I; -.
DR PDBsum; 4Q0J; -.
DR PDBsum; 4Y3I; -.
DR PDBsum; 4Y5F; -.
DR PDBsum; 4Z1W; -.
DR PDBsum; 4ZRR; -.
DR PDBsum; 5AJG; -.
DR PDBsum; 5C5K; -.
DR PDBsum; 5K5B; -.
DR PDBsum; 5L8M; -.
DR PDBsum; 5LBR; -.
DR PDBsum; 5MG0; -.
DR PDBsum; 5MG1; -.
DR PDBsum; 5NFX; -.
DR PDBsum; 5NM3; -.
DR PDBsum; 5NWN; -.
DR PDBsum; 6FHT; -.
DR PDBsum; 6FTD; -.
DR PDBsum; 6T3L; -.
DR PDBsum; 6T3U; -.
DR AlphaFoldDB; Q9RZA4; -.
DR SMR; Q9RZA4; -.
DR DIP; DIP-59338N; -.
DR STRING; 243230.DR_A0050; -.
DR PRIDE; Q9RZA4; -.
DR EnsemblBacteria; AAF12261; AAF12261; DR_A0050.
DR KEGG; dra:DR_A0050; -.
DR PATRIC; fig|243230.17.peg.2934; -.
DR eggNOG; COG4251; Bacteria.
DR HOGENOM; CLU_000445_50_1_0; -.
DR InParanoid; Q9RZA4; -.
DR OMA; ECHRGRI; -.
DR OrthoDB; 1635706at2; -.
DR BRENDA; 2.7.13.3; 1856.
DR EvolutionaryTrace; Q9RZA4; -.
DR Proteomes; UP000002524; Chromosome II.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0000156; F:phosphorelay response regulator activity; IBA:GO_Central.
DR GO; GO:0000155; F:phosphorelay sensor kinase activity; IEA:InterPro.
DR GO; GO:0009881; F:photoreceptor activity; IEA:UniProtKB-KW.
DR GO; GO:0030295; F:protein kinase activator activity; IBA:GO_Central.
DR GO; GO:0009584; P:detection of visible light; IEA:InterPro.
DR GO; GO:0007234; P:osmosensory signaling via phosphorelay pathway; IBA:GO_Central.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:InterPro.
DR Gene3D; 3.30.450.270; -; 1.
DR Gene3D; 3.30.450.40; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR InterPro; IPR003018; GAF.
DR InterPro; IPR029016; GAF-like_dom_sf.
DR InterPro; IPR003594; HATPase_C.
DR InterPro; IPR036890; HATPase_C_sf.
DR InterPro; IPR005467; His_kinase_dom.
DR InterPro; IPR036097; HisK_dim/P_sf.
DR InterPro; IPR035965; PAS-like_dom_sf.
DR InterPro; IPR013654; PAS_2.
DR InterPro; IPR016132; Phyto_chromo_attachment.
DR InterPro; IPR013515; Phytochrome_cen-reg.
DR InterPro; IPR043150; Phytochrome_PHY.
DR InterPro; IPR004358; Sig_transdc_His_kin-like_C.
DR Pfam; PF01590; GAF; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR Pfam; PF08446; PAS_2; 1.
DR Pfam; PF00360; PHY; 1.
DR PRINTS; PR00344; BCTRLSENSOR.
DR SMART; SM00065; GAF; 1.
DR SMART; SM00387; HATPase_c; 1.
DR SUPFAM; SSF47384; SSF47384; 1.
DR SUPFAM; SSF55785; SSF55785; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR PROSITE; PS50109; HIS_KIN; 1.
DR PROSITE; PS50046; PHYTOCHROME_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Chromophore; Kinase; Nucleotide-binding;
KW Phosphoprotein; Photoreceptor protein; Receptor; Reference proteome;
KW Sensory transduction; Transferase.
FT CHAIN 1..755
FT /note="Bacteriophytochrome"
FT /id="PRO_0000171999"
FT DOMAIN 26..94
FT /note="PAS"
FT DOMAIN 152..316
FT /note="GAF"
FT DOMAIN 529..747
FT /note="Histidine kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00107"
FT REGION 95..504
FT /note="Chromophore binding domain"
FT BINDING 24
FT /ligand="a tetrapyrrole"
FT /ligand_id="ChEBI:CHEBI:26932"
FT /note="covalent, via 1 link"
FT /evidence="ECO:0000305"
FT MOD_RES 532
FT /note="Phosphohistidine; by autocatalysis"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00107"
FT MUTAGEN 259
FT /note="M->A: Binds PCB (in vitro), but difference spectrum
FT is altered."
FT /evidence="ECO:0000269|PubMed:10617469"
FT MUTAGEN 259
FT /note="M->C: Binds PCB (in vitro), but difference spectrum
FT is altered."
FT /evidence="ECO:0000269|PubMed:10617469"
FT MUTAGEN 260
FT /note="H->A: 100-fold reduction of chromophore-binding
FT activity."
FT /evidence="ECO:0000269|PubMed:10617469"
FT MUTAGEN 289
FT /note="C->A: Binds PCB (in vitro), but has aberrant
FT spectral properties."
FT /evidence="ECO:0000269|PubMed:10617469"
FT STRAND 1..3
FT /evidence="ECO:0007829|PDB:4Q0H"
FT HELIX 12..14
FT /evidence="ECO:0007829|PDB:5AJG"
FT TURN 21..23
FT /evidence="ECO:0007829|PDB:4Q0H"
FT HELIX 24..26
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 33..35
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 39..45
FT /evidence="ECO:0007829|PDB:5AJG"
FT TURN 46..48
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 50..55
FT /evidence="ECO:0007829|PDB:5AJG"
FT HELIX 58..62
FT /evidence="ECO:0007829|PDB:5AJG"
FT HELIX 66..69
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 70..73
FT /evidence="ECO:0007829|PDB:1ZTU"
FT HELIX 74..77
FT /evidence="ECO:0007829|PDB:5AJG"
FT HELIX 81..88
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 99..103
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 107..109
FT /evidence="ECO:0007829|PDB:4Z1W"
FT STRAND 110..118
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 121..129
FT /evidence="ECO:0007829|PDB:5AJG"
FT HELIX 131..133
FT /evidence="ECO:0007829|PDB:2O9C"
FT HELIX 139..149
FT /evidence="ECO:0007829|PDB:5AJG"
FT HELIX 153..168
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 171..178
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 184..191
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 193..195
FT /evidence="ECO:0007829|PDB:4O01"
FT HELIX 205..207
FT /evidence="ECO:0007829|PDB:5AJG"
FT HELIX 210..218
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 221..225
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 232..238
FT /evidence="ECO:0007829|PDB:5AJG"
FT TURN 240..242
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 243..245
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 252..254
FT /evidence="ECO:0007829|PDB:6T3U"
FT HELIX 258..266
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 270..279
FT /evidence="ECO:0007829|PDB:5AJG"
FT STRAND 282..293
FT /evidence="ECO:0007829|PDB:5AJG"
FT HELIX 299..320
FT /evidence="ECO:0007829|PDB:5AJG"
FT HELIX 332..344
FT /evidence="ECO:0007829|PDB:6FHT"
FT HELIX 348..352
FT /evidence="ECO:0007829|PDB:6FHT"
FT TURN 355..357
FT /evidence="ECO:0007829|PDB:6FHT"
FT HELIX 359..363
FT /evidence="ECO:0007829|PDB:6FHT"
FT STRAND 366..372
FT /evidence="ECO:0007829|PDB:6FHT"
FT STRAND 375..381
FT /evidence="ECO:0007829|PDB:6FHT"
FT HELIX 385..395
FT /evidence="ECO:0007829|PDB:6FHT"
FT STRAND 400..406
FT /evidence="ECO:0007829|PDB:6FHT"
FT HELIX 408..411
FT /evidence="ECO:0007829|PDB:6FHT"
FT HELIX 415..418
FT /evidence="ECO:0007829|PDB:6FHT"
FT TURN 419..421
FT /evidence="ECO:0007829|PDB:4Q0J"
FT STRAND 423..442
FT /evidence="ECO:0007829|PDB:6FHT"
FT STRAND 447..453
FT /evidence="ECO:0007829|PDB:6FHT"
FT HELIX 456..458
FT /evidence="ECO:0007829|PDB:6FHT"
FT STRAND 461..464
FT /evidence="ECO:0007829|PDB:6FHT"
FT STRAND 470..476
FT /evidence="ECO:0007829|PDB:6FHT"
FT HELIX 485..500
FT /evidence="ECO:0007829|PDB:6FHT"
FT HELIX 502..510
FT /evidence="ECO:0007829|PDB:6FHT"
SQ SEQUENCE 755 AA; 81585 MW; A631E471B208F187 CRC64;
MSRDPLPFFP PLYLGGPEIT TENCEREPIH IPGSIQPHGA LLTADGHSGE VLQMSLNAAT
FLGQEPTVLR GQTLAALLPE QWPALQAALP PGCPDALQYR ATLDWPAAGH LSLTVHRVGE
LLILEFEPTE AWDSTGPHAL RNAMFALESA PNLRALAEVA TQTVRELTGF DRVMLYKFAP
DATGEVIAEA RREGLHAFLG HRFPASDIPA QARALYTRHL LRLTADTRAA AVPLDPVLNP
QTNAPTPLGG AVLRATSPMH MQYLRNMGVG SSLSVSVVVG GQLWGLIACH HQTPYVLPPD
LRTTLEYLGR LLSLQVQVKE AADVAAFRQS LREHHARVAL AAAHSLSPHD TLSDPALDLL
GLMRAGGLIL RFEGRWQTLG EVPPAPAVDA LLAWLETQPG ALVQTDALGQ LWPAGADLAP
SAAGLLAISV GEGWSECLVW LRPELRLEVA WGGATPDQAK DDLGPRHSFD TYLEEKRGYA
EPWHPGEIEE AQDLRDTLTG ALGERLSVIR DLNRALTQSN AEWRQYGFVI SHHMQEPVRL
ISQFAELLTR QPRAQDGSPD SPQTERITGF LLRETSRLRS LTQDLHTYTA LLSAPPPVRR
PTPLGRVVDD VLQDLEPRIA DTGASIEVAP ELPVIAADAG LLRDLLLHLI GNALTFGGPE
PRIAVRTERQ GAGWSIAVSD QGAGIAPEYQ ERIFLLFQRL GSLDEALGNG LGLPLCRKIA
ELHGGTLTVE SAPGEGSTFR CWLPDAGPLP GAADA
