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Protein

Phytochrome-like protein cph2

Gene

cph2

Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei129 – 1291Tetrapyrrole chromophore 1 (covalent; via 1 link)Curated
Binding sitei1022 – 10221Tetrapyrrole chromophore 2 (covalent; via 1 link)Sequence Analysis

GO - Molecular functioni

  • red or far-red light photoreceptor activity Source: UniProtKB

GO - Biological processi

  • detection of visible light Source: InterPro
  • protein-chromophore linkage Source: UniProtKB
  • red, far-red light phototransduction Source: UniProtKB
  • regulation of transcription, DNA-templated Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Photoreceptor protein, Receptor

Keywords - Biological processi

Sensory transduction

Keywords - Ligandi

Chromophore

Names & Taxonomyi

Protein namesi
Recommended name:
Phytochrome-like protein cph2
Alternative name(s):
Bacteriophytochrome cph2
Gene namesi
Name:cph2
Ordered Locus Names:sll0821
OrganismiSynechocystis sp. (strain PCC 6803 / Kazusa)
Taxonomic identifieri1111708 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechocystis
ProteomesiUP000001425 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi129 – 1291C → S: Holoprotein exhibits no photochromic activity. 1 Publication
Mutagenesisi130 – 1301H → F: Chromophore ligating activity (in vitro) is 30-40% lower than wild-type. 1 Publication
Mutagenesisi130 – 1301H → Q: Chromophore ligating activity (in vitro) is about 10% more efficient than wild-type. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12761276Phytochrome-like protein cph2PRO_0000172002Add
BLAST

Post-translational modificationi

Contains two covalently linked tetrapyrrole chromophores.

Interactioni

Protein-protein interaction databases

DIPiDIP-48801N.
IntActiQ55434. 11 interactions.

Structurei

Secondary structure

1
1276
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 1812Combined sources
Helixi24 – 3916Combined sources
Beta strandi42 – 498Combined sources
Beta strandi55 – 628Combined sources
Turni64 – 663Combined sources
Helixi77 – 793Combined sources
Helixi82 – 898Combined sources
Beta strandi93 – 986Combined sources
Helixi99 – 1013Combined sources
Beta strandi103 – 1108Combined sources
Helixi128 – 1369Combined sources
Beta strandi140 – 14910Combined sources
Beta strandi152 – 16312Combined sources
Helixi169 – 21547Combined sources
Helixi219 – 23214Combined sources
Beta strandi236 – 2427Combined sources
Beta strandi252 – 2576Combined sources
Helixi263 – 2664Combined sources
Helixi269 – 2757Combined sources
Beta strandi313 – 3164Combined sources
Helixi317 – 3204Combined sources
Turni331 – 3333Combined sources
Helixi334 – 3363Combined sources
Beta strandi338 – 34710Combined sources
Beta strandi352 – 36110Combined sources
Beta strandi363 – 3719Combined sources
Beta strandi388 – 3958Combined sources
Helixi401 – 41818Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BWIX-ray2.60A/B2-424[»]
ProteinModelPortaliQ55434.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini23 – 186164GAF 1Add
BLAST
Domaini461 – 598138GGDEF 1PROSITE-ProRule annotationAdd
BLAST
Domaini607 – 861255EALPROSITE-ProRule annotationAdd
BLAST
Domaini939 – 1080142GAF 2Add
BLAST
Domaini1130 – 1266137GGDEF 2PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 197197Bilin lyase domain 1Add
BLAST
Regioni939 – 1075137Bilin lyase domain 2Add
BLAST

Domaini

Both bilin lyase domains bind with the bilin tetrapyrrole chromophore precursor. The domain 1 shows red, far-red light photoreversibility. The domain 2 is photochemically inactive.

Sequence similaritiesi

Belongs to the phytochrome family.Curated
Contains 1 EAL domain.PROSITE-ProRule annotation
Contains 2 GAF domains.Curated
Contains 2 GGDEF domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG2203.
InParanoidiQ55434.
OMAiAIHQGEL.
OrthoDBiEOG6G4VQG.

Family and domain databases

Gene3Di3.20.20.450. 1 hit.
3.30.450.40. 4 hits.
InterProiIPR001633. EAL_dom.
IPR003018. GAF.
IPR029016. GAF_dom-like.
IPR000160. GGDEF_dom.
IPR029787. Nucleotide_cyclase.
IPR016132. Phyto_chromo_attachment.
IPR001294. Phytochrome.
IPR013515. Phytochrome_cen-reg.
[Graphical view]
PfamiPF00563. EAL. 1 hit.
PF01590. GAF. 2 hits.
PF00990. GGDEF. 2 hits.
PF00360. PHY. 1 hit.
[Graphical view]
PRINTSiPR01033. PHYTOCHROME.
SMARTiSM00052. EAL. 1 hit.
SM00065. GAF. 3 hits.
SM00267. GGDEF. 2 hits.
[Graphical view]
SUPFAMiSSF141868. SSF141868. 1 hit.
SSF55073. SSF55073. 2 hits.
SSF55781. SSF55781. 4 hits.
TIGRFAMsiTIGR00254. GGDEF. 2 hits.
PROSITEiPS50883. EAL. 1 hit.
PS50887. GGDEF. 2 hits.
PS50046. PHYTOCHROME_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q55434-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNPNRSLEDF LRNVINKFHR ALTLRETLQV IVEEARIFLG VDRVKIYKFA
60 70 80 90 100
SDGSGEVLAE AVNRAALPSL LGLHFPVEDI PPQAREELGN QRKMIAVDVA
110 120 130 140 150
HRRKKSHELS GRISPTEHSN GHYTTVDSCH IQYLLAMGVL SSLTVPVMQD
160 170 180 190 200
QQLWGIMAVH HSKPRRFTEQ EWETMALLSK EVSLAITQSQ LSRQVHQQQV
210 220 230 240 250
QEALVQRLET TVAQYGDRPE TWQYALETVG QAVEADGAVL YIAPDLTGSV
260 270 280 290 300
AQHYQWNLRF DWGNWLETSL WQELMRGQPS AAMEPMAAVQ STWEKPRPFT
310 320 330 340 350
SVAPLPPTNC VPHGYTLGEL EQRSDWIAPP ESLSAENFQS FLIVPLAADQ
360 370 380 390 400
QWVGSLILLR KEKSLVKHWA GKRGIDRRNI LPRLSFEAWE ETQKLVPTWN
410 420 430 440 450
RSERKLAQVA STQLYMAITQ QFVTRLITQQ TAYDPLTQLP NWIIFNRQLT
460 470 480 490 500
LALLDALYEG KMVGVLVIAM DRFKRINESF GHKTGDGLLQ EVADRLNQKL
510 520 530 540 550
SPLAAYSPLL SRWHGDGFTI LLTQISDNQE MIPLCERLLS TFQEPFFLQG
560 570 580 590 600
QPIYLTASMG ISTAPYDGET AESLLKFAEI ALTRAKCQGK NTYQFYRPQD
610 620 630 640 650
SAPMLDRLTL ESDLRQALTN QEFVLYFQPQ VALDTGKLLG VEALVRWQHP
660 670 680 690 700
RLGQVAPDVF IPLAEELGLI NHLGQWVLET ACATHQHFFR ETGRRLRMAV
710 720 730 740 750
NISARQFQDE KWLNSVLECL KRTGMPPEDL ELEITESLMM EDIKGTVVLL
760 770 780 790 800
HRLREEGVQV AIDDFGTGYS SLSILKQLPI HRLKIDKSFV NDLLNEGADT
810 820 830 840 850
AIIQYVIDLA NGLNLETVAE GIESEAQLQR LQKMGCHLGQ GYFLTRPLPA
860 870 880 890 900
EAMMTYLYYP QILDFGPTPP LPKVALPETE TEAGQGNVGD RPLPNSLNRE
910 920 930 940 950
NPWTEKLHDY VLLKERLQQR NVKEKLVLKI ANKIRASLNI NDILYSTVTE
960 970 980 990 1000
VRQFLNTDRV VLFKFNSQWS GQVVTESHND FCRSIINDEI DDPCFKGHYL
1010 1020 1030 1040 1050
RLYREGRVRA VSDIEKADLA DCHKELLRHY QVKANLVVPV VFNENLWGLL
1060 1070 1080 1090 1100
IAHECKTPRY WQEEDLQLLM ELATQVAIAI HQGELYEQLE TANIRLQQIS
1110 1120 1130 1140 1150
SLDALTQVGN RYLFDSTLER EWQRLQRIRE PLALLLCDVD FFKGFNDNYG
1160 1170 1180 1190 1200
HPAGDRCLKK IADAMAKVAK RPTDLVARYG GEEFAIILSE TSLEGAINVT
1210 1220 1230 1240 1250
EALQVEVANL AIPHTVSGTG HVTLSIGIAV YTPERHINPN ALVKAADLAL
1260 1270
YEAKAKGRNQ WLAYEGSQLP HVDGEV
Length:1,276
Mass (Da):144,687
Last modified:November 1, 1996 - v1
Checksum:i318CF3A73962D99E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000022 Genomic DNA. Translation: BAA10536.1.
PIRiS75801.

Genome annotation databases

EnsemblBacteriaiBAA10536; BAA10536; BAA10536.
KEGGisyy:SYNGTS_2574.
syz:MYO_125990.
PATRICi23842638. VBISynSp132158_2858.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000022 Genomic DNA. Translation: BAA10536.1.
PIRiS75801.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BWIX-ray2.60A/B2-424[»]
ProteinModelPortaliQ55434.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48801N.
IntActiQ55434. 11 interactions.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA10536; BAA10536; BAA10536.
KEGGisyy:SYNGTS_2574.
syz:MYO_125990.
PATRICi23842638. VBISynSp132158_2858.

Phylogenomic databases

eggNOGiCOG2203.
InParanoidiQ55434.
OMAiAIHQGEL.
OrthoDBiEOG6G4VQG.

Family and domain databases

Gene3Di3.20.20.450. 1 hit.
3.30.450.40. 4 hits.
InterProiIPR001633. EAL_dom.
IPR003018. GAF.
IPR029016. GAF_dom-like.
IPR000160. GGDEF_dom.
IPR029787. Nucleotide_cyclase.
IPR016132. Phyto_chromo_attachment.
IPR001294. Phytochrome.
IPR013515. Phytochrome_cen-reg.
[Graphical view]
PfamiPF00563. EAL. 1 hit.
PF01590. GAF. 2 hits.
PF00990. GGDEF. 2 hits.
PF00360. PHY. 1 hit.
[Graphical view]
PRINTSiPR01033. PHYTOCHROME.
SMARTiSM00052. EAL. 1 hit.
SM00065. GAF. 3 hits.
SM00267. GGDEF. 2 hits.
[Graphical view]
SUPFAMiSSF141868. SSF141868. 1 hit.
SSF55073. SSF55073. 2 hits.
SSF55781. SSF55781. 4 hits.
TIGRFAMsiTIGR00254. GGDEF. 2 hits.
PROSITEiPS50883. EAL. 1 hit.
PS50887. GGDEF. 2 hits.
PS50046. PHYTOCHROME_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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.
    , Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., 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 second photochromic bacteriophytochrome from Synechocystis sp. PCC 6803: spectral analysis and down-regulation by light."
    Park C.-M., Kim J.-I., Yang S.-S., Kang J.-G., Kang J.-H., Shim J.-Y., Chung Y.-H., Park Y.-M., Song P.-S.
    Biochemistry 39:10840-10847(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHROMOPHORE 1 BINDING, MUTAGENESIS OF CYS-129 AND HIS-130.
  4. "Defining the bilin lyase domain: lessons from the extended phytochrome superfamily."
    Wu S.-H., Lagarias J.C.
    Biochemistry 39:13487-13495(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION OF TWO BILIN LYASE DOMAINS.

Entry informationi

Entry nameiPHY2_SYNY3
AccessioniPrimary (citable) accession number: Q55434
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: November 1, 1996
Last modified: July 22, 2015
This is version 120 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
  3. Synechocystis PCC 6803
    Synechocystis (strain PCC 6803): entries and gene names

External Data

Dasty 3

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 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.