ID BPHY_XANC8 Reviewed; 634 AA.
AC A0A0H2XCS3;
DT 07-SEP-2016, integrated into UniProtKB/Swiss-Prot.
DT 16-SEP-2015, sequence version 1.
DT 27-MAR-2024, entry version 41.
DE RecName: Full=Bacteriophytochrome {ECO:0000303|PubMed:27107635};
DE Short=BphP;
DE AltName: Full=XccBphP {ECO:0000303|PubMed:27107635};
GN Name=bphP; OrderedLocusNames=XC_4241;
OS Xanthomonas campestris pv. campestris (strain 8004).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Xanthomonas.
OX NCBI_TaxID=314565;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=8004;
RX PubMed=15899963; DOI=10.1101/gr.3378705;
RA Qian W., Jia Y., Ren S.-X., He Y.-Q., Feng J.-X., Lu L.-F., Sun Q.,
RA Ying G., Tang D.-J., Tang H., Wu W., Hao P., Wang L., Jiang B.-L., Zeng S.,
RA Gu W.-Y., Lu G., Rong L., Tian Y., Yao Z., Fu G., Chen B., Fang R.,
RA Qiang B., Chen Z., Zhao G.-P., Tang J.-L., He C.;
RT "Comparative and functional genomic analyses of the pathogenicity of
RT phytopathogen Xanthomonas campestris pv. campestris.";
RL Genome Res. 15:757-767(2005).
RN [2]
RP FUNCTION, INDUCTION, OPERON, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
RP CYS-13.
RC STRAIN=8004;
RX PubMed=27621284; DOI=10.15252/embr.201541691;
RA Bonomi H.R., Toum L., Sycz G., Sieira R., Toscani A.M., Gudesblat G.E.,
RA Leskow F.C., Goldbaum F.A., Vojnov A.A., Malamud F.;
RT "Xanthomonas campestris attenuates virulence by sensing light through a
RT bacteriophytochrome photoreceptor.";
RL EMBO Rep. 17:1565-1577(2016).
RN [3] {ECO:0007744|PDB:5AKP}
RP X-RAY CRYSTALLOGRAPHY (3.25 ANGSTROMS) OF 2-634 FORM PR IN COMPLEX WITH
RP BILIVERDIN CHROMOPHORE, FUNCTION, SUBUNIT, AND DOMAIN.
RC STRAIN=8004;
RX PubMed=27107635; DOI=10.1016/j.jmb.2016.04.012;
RA Otero L.H., Klinke S., Rinaldi J., Velazquez-Escobar F., Mroginski M.A.,
RA Lopez M.F., Malamud F., Vojnov A.A., Hildebrandt P., Goldbaum F.A.,
RA Bonomi H.R.;
RT "Structure of the full-length bacteriophytochrome from the plant pathogen
RT Xanthomonas campestris provides clues to its long-range signaling
RT mechanism.";
RL J. Mol. Biol. 428:3702-3720(2016).
CC -!- FUNCTION: Photoreceptor which exists in two forms that are reversibly
CC interconvertible by light: far-red light (733 nm) converts protein to
CC the red-absorbing (Pr) form, while red light (630 nm) partly converts
CC the protein to the far-red-absorbing (Pfr) form (PubMed:27107635).
CC Regulates virulence of X.campestris pv. campestris on its host plants,
CC perhaps by fine-tuning expression to ambient light levels and/or
CC spatial cues (PubMed:27621284). The Pr form may sense light and
CC partially inhibit virulence; in the dark (Pfr form) biofilm and
CC xanathan production rise and bacteria are more virulent
CC (PubMed:27621284). Strains overexpressing this protein have
CC significantly decreased amounts of extracellular beta-1,4-
CC endoglucanase, produce less xanthin and have decreased transcription of
CC genes involved in virulence such as endoglucanases, type 2 secretion
CC systems, xanthan production and flagellar-dependent motility
CC (PubMed:27621284). {ECO:0000269|PubMed:27107635,
CC ECO:0000269|PubMed:27621284, ECO:0000305|PubMed:27621284}.
CC -!- SUBUNIT: Forms head-to-head homodimers (PubMed:27107635).
CC {ECO:0000269|PubMed:27107635}.
CC -!- INDUCTION: Expressed in dark and light (at protein level). Part of the
CC bphO-bphP operon (PubMed:27621284). {ECO:0000269|PubMed:27621284}.
CC -!- DOMAIN: Composed of 4 domains; in the N-terminus the PAS2-GAF-PHY
CC domains form the photosensor while the C-terminal PAS9 domain is the
CC output module. Long linker helices serve as connectors within the GAF-
CC PHY and PHY-PAS9 domain pairs, forming a helical spine where the dimer
CC interface is assembled. Thus both the photosensor and PAS9 domains are
CC required for dimerization. Within the PHY domain is the mobile tongue
CC domain (residues 452-480) that probably serves as a gatekeeper to the
CC chromophore-binding pocket, in the Pr form it is a beta-sheet, in a
CC R.palustris Pfr crystal it is an alpha helix (AC B3Q7C0). In the dark
CC (Pfr) state the protein is compact and protease resistant, far-red
CC light treated protein (Pr) is quickly degraded to its domains, with
CC important cuts occurring in the hinge region (just before the PAS9
CC output domain at about residue 512) and in the tongue domain (about
CC residue 469). {ECO:0000305|PubMed:27107635}.
CC -!- PTM: Contains one covalently linked biliverdin IX-alpha chromophore;
CC present in the crystal structure as a mixture of Pr and Meta-R
CC configurations. {ECO:0000269|PubMed:27107635}.
CC -!- DISRUPTION PHENOTYPE: No growth phenotype in liquid culture, slightly
CC better growth on plates, strain loses slight sensitivity to white
CC light. In planta is more virulent, with increased growth in host
CC (A.thaliana) leaves, mutant opens leaf stomata better than wild-type,
CC has decreased leaf callose deposits, produces more xanthan than wild-
CC type and is insensitive to white light, has considerably increased
CC sliding and slightly increased swimming mobility, generates mature
CC biofilm in the light and dark. {ECO:0000269|PubMed:27621284}.
CC -!- MISCELLANEOUS: X.campestris pv. campestris colonizes plant leaves and
CC is responsible for black rot in cruciferous plants (Brassicaceae). In
CC the cruciferous model host organism A.thaliana, morning and midday
CC infections result in more hypersensitive responses than evening or
CC night infections, suggesting light plays a role in virulence.
CC {ECO:0000305|PubMed:27621284}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the phytochrome
CC family. {ECO:0000305}.
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DR EMBL; CP000050; AAY51279.1; -; Genomic_DNA.
DR RefSeq; WP_011270102.1; NC_007086.1.
DR PDB; 5AKP; X-ray; 3.25 A; A/B=2-634.
DR PDB; 5UYR; X-ray; 3.45 A; A/B=2-634.
DR PDB; 6NDO; X-ray; 3.58 A; A/B=2-634.
DR PDB; 6NDP; X-ray; 3.89 A; A/B=2-634.
DR PDB; 6PL0; X-ray; 2.96 A; A/B=2-634.
DR PDB; 7L59; X-ray; 2.68 A; A=2-634.
DR PDB; 7L5A; X-ray; 2.95 A; A=2-511.
DR PDBsum; 5AKP; -.
DR PDBsum; 5UYR; -.
DR PDBsum; 6NDO; -.
DR PDBsum; 6NDP; -.
DR PDBsum; 6PL0; -.
DR PDBsum; 7L59; -.
DR PDBsum; 7L5A; -.
DR AlphaFoldDB; A0A0H2XCS3; -.
DR SMR; A0A0H2XCS3; -.
DR KEGG; xcb:XC_4241; -.
DR HOGENOM; CLU_000445_50_5_6; -.
DR PHI-base; PHI:7645; -.
DR Proteomes; UP000000420; Chromosome.
DR GO; GO:0009881; F:photoreceptor activity; IEA:UniProtKB-KW.
DR GO; GO:0009584; P:detection of visible light; IEA:InterPro.
DR GO; GO:0006355; P:regulation of DNA-templated transcription; IEA:InterPro.
DR CDD; cd00130; PAS; 1.
DR Gene3D; 3.30.450.270; -; 1.
DR Gene3D; 3.30.450.40; -; 1.
DR Gene3D; 3.30.450.20; PAS domain; 2.
DR InterPro; IPR003018; GAF.
DR InterPro; IPR029016; GAF-like_dom_sf.
DR InterPro; IPR000014; PAS.
DR InterPro; IPR035965; PAS-like_dom_sf.
DR InterPro; IPR013654; PAS_2.
DR InterPro; IPR016132; Phyto_chromo_attachment.
DR InterPro; IPR001294; Phytochrome.
DR InterPro; IPR013515; Phytochrome_cen-reg.
DR InterPro; IPR043150; Phytochrome_PHY_sf.
DR NCBIfam; NF041576; bacphytchrmBphP; 1.
DR PANTHER; PTHR43065:SF10; PEROXIDE STRESS-ACTIVATED HISTIDINE KINASE MAK3; 1.
DR PANTHER; PTHR43065; SENSOR HISTIDINE KINASE; 1.
DR Pfam; PF01590; GAF; 1.
DR Pfam; PF08446; PAS_2; 1.
DR Pfam; PF13426; PAS_9; 1.
DR Pfam; PF00360; PHY; 1.
DR PRINTS; PR01033; PHYTOCHROME.
DR SMART; SM00065; GAF; 1.
DR SMART; SM00091; PAS; 2.
DR SUPFAM; SSF55781; GAF domain-like; 2.
DR SUPFAM; SSF55785; PYP-like sensor domain (PAS domain); 2.
DR PROSITE; PS50112; PAS; 1.
DR PROSITE; PS50046; PHYTOCHROME_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromophore; Photoreceptor protein; Receptor;
KW Sensory transduction; Virulence.
FT CHAIN 1..634
FT /note="Bacteriophytochrome"
FT /id="PRO_0000437191"
FT DOMAIN 13..118
FT /note="PAS 1"
FT /evidence="ECO:0000305|PubMed:27107635"
FT DOMAIN 151..305
FT /note="GAF"
FT /evidence="ECO:0000305|PubMed:27107635"
FT DOMAIN 515..590
FT /note="PAS 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00140"
FT REGION 13..514
FT /note="Photosensory core domain"
FT /evidence="ECO:0000305|PubMed:27107635"
FT REGION 325..508
FT /note="Phytochrome-specific (PHY)"
FT /evidence="ECO:0000305|PubMed:27107635"
FT REGION 452..480
FT /note="Tongue domain"
FT /evidence="ECO:0000305|PubMed:27107635"
FT REGION 515..634
FT /note="PAS9, output module, not required to bind biliverdin
FT IX-alpha, required for dimerization"
FT /evidence="ECO:0000305|PubMed:27107635"
FT BINDING 13
FT /ligand="biliverdin IXalpha"
FT /ligand_id="ChEBI:CHEBI:57991"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:27107635"
FT MUTAGEN 13
FT /note="C->S: Loss of photo-inducible Pr-Pfr conversion;
FT protein still binds pigment. No difference in growth in
FT host, increased callose deposits, increased xanthan
FT production, increased sliding and swimming mobility."
FT /evidence="ECO:0000269|PubMed:27621284"
FT HELIX 12..15
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 22..24
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 28..33
FT /evidence="ECO:0007829|PDB:7L59"
FT TURN 35..37
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 39..44
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 47..51
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 55..58
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 63..66
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 82..90
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 94..96
FT /evidence="ECO:0007829|PDB:6PL0"
FT STRAND 102..108
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 113..121
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 129..139
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 145..159
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 163..170
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 176..183
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 185..187
FT /evidence="ECO:0007829|PDB:5AKP"
FT STRAND 193..195
FT /evidence="ECO:0007829|PDB:5AKP"
FT HELIX 197..199
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 202..211
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 212..217
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 224..230
FT /evidence="ECO:0007829|PDB:7L59"
FT TURN 232..234
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 250..259
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 263..271
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 274..285
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 291..332
FT /evidence="ECO:0007829|PDB:7L59"
FT TURN 333..336
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 337..339
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 343..347
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 349..354
FT /evidence="ECO:0007829|PDB:7L59"
FT TURN 355..357
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 359..365
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 368..371
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 378..390
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 391..393
FT /evidence="ECO:0007829|PDB:6PL0"
FT HELIX 394..399
FT /evidence="ECO:0007829|PDB:6PL0"
FT STRAND 402..408
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 409..412
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 414..419
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 420..423
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 424..431
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 432..434
FT /evidence="ECO:0007829|PDB:6PL0"
FT STRAND 435..443
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 446..449
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 452..454
FT /evidence="ECO:0007829|PDB:7L59"
FT TURN 456..460
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 471..481
FT /evidence="ECO:0007829|PDB:7L59"
FT TURN 482..484
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 491..510
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 518..524
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 531..534
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 538..540
FT /evidence="ECO:0007829|PDB:6PL0"
FT STRAND 543..547
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 549..555
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 559..562
FT /evidence="ECO:0007829|PDB:7L59"
FT TURN 568..571
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 578..580
FT /evidence="ECO:0007829|PDB:7L59"
FT HELIX 581..587
FT /evidence="ECO:0007829|PDB:7L59"
FT TURN 588..590
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 596..598
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 608..610
FT /evidence="ECO:0007829|PDB:7L59"
FT STRAND 619..622
FT /evidence="ECO:0007829|PDB:5AKP"
FT STRAND 625..629
FT /evidence="ECO:0007829|PDB:7L59"
SQ SEQUENCE 634 AA; 70355 MW; 0E6FECCC240F6F45 CRC64;
MSTATNPLDL DVCAREPIHI PGLIQPYGVL LVIDPADGRI VQASTTAADL LGVPMAALLG
MPYTQVLTLP EAQPFAVDDQ PQHLMHAEVR FPQRATPPAS AWVAAWHLYP QQWLVEMEPR
DARLLDVTLR EAMPLLRSVE RDPGIAEAAV RVAKGLRSLI GFDRVMIYRF DEEWNGDIIA
EARKPELEAY LGLHYPASDI PAQARALYLR NRVRQIADVG YQPSPIQPTV HPQLGTPVDL
SDVSLRSVSP VHLEYLANMG VTATLVASIV VNDALWGLIS CHHYSPHFTN HAMRDVTDAV
ARTLAGRIGA LQAVARARLE SVLLTVREKL ITDFNDAEHM TVELLDDMAP DLMDVVDADG
VAIFHGNDIS RHGTTPDVAA LRRIRDHIES EHHEALREDA VGALHVDAIG EVFPELADLA
PLAAGFIFVP LMPQSRSALL WTRREQIQQI KWAGNPQLAK LEDIPNSRLS PRKSFDLWQQ
TVRGRARRWS PLHLESARSL RVLIELMERK RFQQDFTLLE ASLSRLRDGV AIIERGTANA
AHRLLFVNTA FADVCGSDVA ELIGRELQTL YASDAPRANV ELLQDALRNG RAAYVTLPLQ
VSDGAPVYRQ FHLEPLPSPS GVTAHWLLQL RDPE
//
