Phytochrome-like protein cph1 - Synechocystis sp. (strain PCC 6803 / Kazusa)

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Q55168 (PHY1_SYNY3) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 115. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Phytochrome-like protein cph1
EC=2.7.13.3

Alternative name(s):
Bacteriophytochrome cph1
Light-regulated histidine kinase 1

Gene names

Name:	cph1
Ordered Locus Names:	slr0473

Organism

Synechocystis sp. (strain PCC 6803 / Kazusa) [Reference proteome] [HAMAP]

Taxonomic identifier

1111708 [NCBI]

Taxonomic lineage

Bacteria › Cyanobacteria › Oscillatoriophycideae › Chroococcales › Synechocystis ›

Protein attributes

Sequence length	748 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Regulatory 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. Forms a two-component system with the rcp1 response regulator.
Catalytic activity	ATP + protein L-histidine = ADP + protein N-phospho-L-histidine.
Subunit structure	Homodimer.
Post-translational modification	Contains one covalently linked tetrapyrrole chromophore By similarity.
Miscellaneous	The R form exhibits both ATP-dependent autophosphorylation and phosphotransfer to rcp1 activities. Unlike the higher plants where Pfr is thought to be the active form.
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 Reference proteome
Gene Ontology (GO)
Biological_process	detection of visible light Inferred from electronic annotation. Source: InterPro phosphorelay signal transduction system Inferred from electronic annotation. Source: GOC protein autophosphorylation Inferred from direct assay Ref.4. Source: UniProtKB protein-chromophore linkage Inferred from direct assay PubMed 15641769. Source: UniProtKB regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro signal transduction by phosphorylation Inferred from electronic annotation. Source: GOC
Cellular_component	membrane Inferred from electronic annotation. Source: InterPro
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW phosphorelay sensor kinase activity Inferred from electronic annotation. Source: InterPro protein histidine kinase activity Inferred from direct assay Ref.4. Source: UniProtKB red or far-red light photoreceptor activity Inferred from direct assay PubMed 15641769. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		8	EBI-594457,EBI-594457
rcp1	Q55169	2	EBI-594457,EBI-766949

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 748

748

Phytochrome-like protein cph1

PRO_0000172001

Regions

Domain

19 – 86

PAS

Domain

152 – 320

169

GAF

Domain

535 – 748

214

Histidine kinase

Region

87 – 510

424

Chromophore binding domain

Sites

Binding site

259

Tetrapyrrole chromophore (covalent; via 1 link) By similarity

Amino acid modifications

Modified residue

538

Phosphohistidine; by autocatalysis

Experimental info

Mutagenesis

538

H → K: No autophosphorylation; no phosphotransfer to Rcp1. Ref.4

Secondary structure

748

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q55168 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: A9ECA6D8D5B3C88A
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FASTA

748

84,233

        10         20         30         40         50         60 
MATTVQLSDQ SLRQLETLAI HTAHLIQPHG LVVVLQEPDL TISQISANCT GILGRSPEDL 

        70         80         90        100        110        120 
LGRTLGEVFD SFQIDPIQSR LTAGQISSLN PSKLWARVMG DDFVIFDGVF HRNSDGLLVC 

       130        140        150        160        170        180 
ELEPAYTSDN LPFLGFYHMA NAALNRLRQQ ANLRDFYDVI VEEVRRMTGF DRVMLYRFDE 

       190        200        210        220        230        240 
NNHGDVIAED KRDDMEPYLG LHYPESDIPQ PARRLFIHNP IRVIPDVYGV AVPLTPAVNP 

       250        260        270        280        290        300 
STNRAVDLTE SILRSAYHCH LTYLKNMGVG ASLTISLIKD GHLWGLIACH HQTPKVIPFE 

       310        320        330        340        350        360 
LRKACEFFGR VVFSNISAQE DTETFDYRVQ LAEHEAVLLD KMTTAADFVE GLTNHPDRLL 

       370        380        390        400        410        420 
GLTGSQGAAI CFGEKLILVG ETPDEKAVQY LLQWLENREV QDVFFTSSLS QIYPDAVNFK 

       430        440        450        460        470        480 
SVASGLLAIP IARHNFLLWF RPEVLQTVNW GGDPNHAYEA TQEDGKIELH PRQSFDLWKE 

       490        500        510        520        530        540 
IVRLQSLPWQ SVEIQSALAL KKAIVNLILR QAEELAQLAR NLERSNADLK KFAYIASHDL 

       550        560        570        580        590        600 
QEPLNQVSNY VQLLEMRYSE ALDEDAKDFI DFAVTGVSLM QTLIDDILTY AKVDTQYAQL 

       610        620        630        640        650        660 
TFTDVQEVVD KALANLKQRI EESGAEIEVG SMPAVMADQI QLMQVFQNLI ANGIKFAGDK 

       670        680        690        700        710        720 
SPKIKIWGDR QEDAWVFAVQ DNGIGIDPQF FERIFVIFQR LHTRDEYKGT GMGLAICKKI 

       730        740 
IEGHQGQIWL ESNPGEGSTF YFSIPIGN

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome." Kaneko T., Tanaka A., Sato S., Kotani H., Sazuka T., Miyajima N., Sugiura M., Tabata S. DNA Res. 2:153-166(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 27184 / PCC 6803 / N-1.
[2]	"Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions." Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S. Tabata S. DNA Res. 3:109-136(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: PCC 6803 / Kazusa.
[3]	"A prokaryotic phytochrome." Hughes J., Lamparter T., Mittmann F., Hartmann E., Gartner W., Wilde A., Borner T. Nature 386:663-663(1997) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION.
[4]	"A cyanobacterial phytochrome two-component light sensory system." Yeh K.-C., Wu S.-H., Murphy J.T., Lagarias J.C. Science 277:1505-1508(1997) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION, MUTAGENESIS OF HIS-538.
[5]	"Chromophore-apoprotein interactions in Synechocystis sp. PCC6803 phytochrome Cph1." Park C.-M., Shim J.-Y., Yang S.-S., Kang J.-G., Kim J.-I., Luka Z., Song P.-S. Biochemistry 39:6349-6356(2000) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION.
[6]	"Prokaryotes and phytochrome. The connection to chromophores and signaling." Hughes J., Lamparter T. Plant Physiol. 121:1059-1068(1999) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BA000022 Genomic DNA. Translation: BAA10307.1.

PIR

S74389.

RefSeq

NP_442237.1. NC_000911.1.
YP_005652297.1. NC_017277.1.
YP_007452113.1. NC_020286.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2VEA	X-ray	2.21	A	1-514	[»]
3ZQ5	X-ray	1.95	A	1-514	[»]

ProteinModelPortal

Q55168.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q55168. 8 interactions.

STRING

1148.slr0473.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAA10307; BAA10307; BAA10307.

GeneID

12253516.
14617790.
952560.

KEGG

syn:slr0473.
syy:SYNGTS_2344.

PATRIC

23842112. VBISynSp132158_2597.

Phylogenomic databases

eggNOG

COG4251.

HOGENOM

HOG000030537.

K11354.

OMA

PESDIPQ.

ProtClustDB

CLSK893476.

Enzyme and pathway databases

BRENDA

2.7.13.3. 6185.

Family and domain databases

Gene3D

1.10.287.130. 1 hit.
3.30.565.10. 1 hit.

InterPro

IPR003018. GAF.
IPR003594. HATPase_ATP-bd.
IPR000014. PAS.
IPR013654. PAS_2.
IPR016132. Phyto_chromo_attachment.
IPR001294. Phytochrome.
IPR013515. Phytochrome_cen-reg.
IPR003661. Sig_transdc_His_kin_sub1_dim/P.
IPR005467. Sig_transdc_His_kinase_core.
IPR009082. Sig_transdc_His_kinase_dimeric.
[Graphical view]

Pfam

PF01590. GAF. 1 hit.
PF02518. HATPase_c. 1 hit.
PF00512. HisKA. 1 hit.
PF08446. PAS_2. 1 hit.
PF00360. PHY. 1 hit.
[Graphical view]

PRINTS

PR01033. PHYTOCHROME.

SMART

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

SUPFAM

SSF55874. ATP_bd_ATPase. 1 hit.
SSF47384. His_kin_homodim. 1 hit.

PROSITE

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

ProtoNet

Search...

Other

EvolutionaryTrace

Q55168.

Entry information

Entry name

PHY1_SYNY3

Accession

Primary (citable) accession number: Q55168

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	May 1, 2013
This is version 115 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Synechocystis PCC 6803

Synechocystis (strain PCC 6803): entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents