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Protein

Probable diguanylate cyclase YfiN

Gene

yfiN

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria.1 Publication

Catalytic activityi

2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate.

Cofactori

Mg2+By similarityNote: Binds 1 Mg2+ ion per monomer.By similarity

Pathwayi: 3',5'-cyclic di-GMP biosynthesis

This protein is involved in the pathway 3',5'-cyclic di-GMP biosynthesis, which is part of Purine metabolism.
View all proteins of this organism that are known to be involved in the pathway 3',5'-cyclic di-GMP biosynthesis and in Purine metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi286 – 2861MagnesiumBy similarity
Sitei291 – 2911Transition state stabilizerSequence analysis
Binding sitei294 – 2941SubstrateBy similarity
Binding sitei303 – 3031SubstrateBy similarity
Active sitei329 – 3291Proton acceptorSequence analysis
Metal bindingi329 – 3291MagnesiumBy similarity

GO - Molecular functioni

GO - Biological processi

  • negative regulation of bacterial-type flagellum-dependent cell motility Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Ligandi

GTP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG12880-MONOMER.
ECOL316407:JW2585-MONOMER.
UniPathwayiUPA00599.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable diguanylate cyclase YfiN (EC:2.7.7.65)
Short name:
DGC
Gene namesi
Name:yfiN
Ordered Locus Names:b2604, JW2585
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12880. yfiN.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 2424Cytoplasmic1 PublicationAdd
BLAST
Transmembranei25 – 4521HelicalSequence analysisAdd
BLAST
Topological domaini46 – 527Periplasmic1 Publication
Transmembranei53 – 7321HelicalSequence analysisAdd
BLAST
Topological domaini74 – 11239Cytoplasmic1 PublicationAdd
BLAST
Transmembranei113 – 13321HelicalSequence analysisAdd
BLAST
Topological domaini134 – 15421Periplasmic1 PublicationAdd
BLAST
Transmembranei155 – 17521HelicalSequence analysisAdd
BLAST
Topological domaini176 – 408233Cytoplasmic1 PublicationAdd
BLAST

GO - Cellular componenti

  • integral component of membrane Source: UniProtKB-KW
  • plasma membrane Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

Disruption partially suppresses the reduced motility of a yhjH disruption; concomitant disruption of dosC, yegE, yedQ and yfiN completely restores motility, suggesting these 4 genes, together with the c-di-GMP phosphodiesterase YhjH, form a network that regulates cell motility by altering levels of c-di-GMP.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 408408Probable diguanylate cyclase YfiNPRO_0000169270Add
BLAST

Proteomic databases

PaxDbiP46139.
PRIDEiP46139.

Expressioni

Inductioni

Expressed at low levels at both 28 and 37 degrees Celsius during transition into stationary phase.1 Publication

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

BioGridi4263361. 11 interactions.
STRINGi511145.b2604.

Structurei

3D structure databases

ProteinModelPortaliP46139.
SMRiP46139. Positions 212-401.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini183 – 23654HAMPPROSITE-ProRule annotationAdd
BLAST
Domaini278 – 408131GGDEFPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 GGDEF domain.PROSITE-ProRule annotation
Contains 1 HAMP domain.PROSITE-ProRule annotation

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4108KHX. Bacteria.
COG2199. LUCA.
HOGENOMiHOG000217416.
InParanoidiP46139.
OMAiGNDFNAL.
OrthoDBiEOG6FZ482.

Family and domain databases

InterProiIPR033417. CHASE8.
IPR000160. GGDEF_dom.
IPR003660. HAMP_dom.
IPR029787. Nucleotide_cyclase.
[Graphical view]
PfamiPF17152. CHASE8. 1 hit.
PF00990. GGDEF. 1 hit.
[Graphical view]
SMARTiSM00267. GGDEF. 1 hit.
[Graphical view]
SUPFAMiSSF55073. SSF55073. 1 hit.
TIGRFAMsiTIGR00254. GGDEF. 1 hit.
PROSITEiPS50887. GGDEF. 1 hit.
PS50885. HAMP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P46139-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMDNDNSLNK RPTFKRALRN ISMTSIFITM MLIWLLLSVT SVLTLKQYAQ
60 70 80 90 100
KNLALTAATM TYSLEAAVVF ADGPAATETL AALGQQGQFS TAEVRDKQQN
110 120 130 140 150
ILASWHYTRK DPGDTFSNFI SHWLFPAPII QPIRHNGETI GEVRLTARDS
160 170 180 190 200
SISHFIWFSL AVLTGCILLA SGIAITLTRH LHNGLVEALK NITDVVHDVR
210 220 230 240 250
SNRNFSRRVS EERIAEFHRF ALDFNSLLDE MEEWQLRLQA KNAQLLRTAL
260 270 280 290 300
HDPLTGLANR AAFRSGINTL MNNSDARKTS ALLFLDGDNF KYINDTWGHA
310 320 330 340 350
TGDRVLIEIA KRLAEFGGLR HKAYRLGGDE FAMVLYDVQS ESEVQQICSA
360 370 380 390 400
LTQIFNLPFD LHNGHQTTMT LSIGYAMTIE HASAEKLQEL ADHNMYQAKH

QRAEKLVR
Length:408
Mass (Da):45,989
Last modified:November 1, 1997 - v2
Checksum:i720B6539EF43DB16
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75653.1.
AP009048 Genomic DNA. Translation: BAA16489.2.
X01818 Genomic DNA. No translation available.
PIRiG65038.
RefSeqiNP_417095.1. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAC75653; AAC75653; b2604.
BAA16489; BAA16489; BAA16489.
GeneIDi947091.
KEGGiecj:JW2585.
eco:b2604.
PATRICi32120607. VBIEscCol129921_2702.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75653.1.
AP009048 Genomic DNA. Translation: BAA16489.2.
X01818 Genomic DNA. No translation available.
PIRiG65038.
RefSeqiNP_417095.1. NC_000913.3.

3D structure databases

ProteinModelPortaliP46139.
SMRiP46139. Positions 212-401.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263361. 11 interactions.
STRINGi511145.b2604.

Proteomic databases

PaxDbiP46139.
PRIDEiP46139.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75653; AAC75653; b2604.
BAA16489; BAA16489; BAA16489.
GeneIDi947091.
KEGGiecj:JW2585.
eco:b2604.
PATRICi32120607. VBIEscCol129921_2702.

Organism-specific databases

EchoBASEiEB2718.
EcoGeneiEG12880. yfiN.

Phylogenomic databases

eggNOGiENOG4108KHX. Bacteria.
COG2199. LUCA.
HOGENOMiHOG000217416.
InParanoidiP46139.
OMAiGNDFNAL.
OrthoDBiEOG6FZ482.

Enzyme and pathway databases

UniPathwayiUPA00599.
BioCyciEcoCyc:EG12880-MONOMER.
ECOL316407:JW2585-MONOMER.

Miscellaneous databases

PROiP46139.

Family and domain databases

InterProiIPR033417. CHASE8.
IPR000160. GGDEF_dom.
IPR003660. HAMP_dom.
IPR029787. Nucleotide_cyclase.
[Graphical view]
PfamiPF17152. CHASE8. 1 hit.
PF00990. GGDEF. 1 hit.
[Graphical view]
SMARTiSM00267. GGDEF. 1 hit.
[Graphical view]
SUPFAMiSSF55073. SSF55073. 1 hit.
TIGRFAMsiTIGR00254. GGDEF. 1 hit.
PROSITEiPS50887. GGDEF. 1 hit.
PS50885. HAMP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
    Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
    , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
    DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "The nucleotide sequence of an Escherichia coli operon containing genes for the tRNA(m1G)methyltransferase, the ribosomal proteins S16 and L19 and a 21-K polypeptide."
    Bystroem A.S., Hjalmarsson K.J., Wikstroem P.M., Bjoerk G.R.
    EMBO J. 2:899-905(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 330-408.
  5. "Detection of new genes in a bacterial genome using Markov models for three gene classes."
    Borodovsky M., McIninch J., Koonin E.V., Rudd K.E., Medigue C., Danchin A.
    Nucleic Acids Res. 23:3554-3562(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  6. "Global topology analysis of the Escherichia coli inner membrane proteome."
    Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G.
    Science 308:1321-1323(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: TOPOLOGY [LARGE SCALE ANALYSIS].
    Strain: K12 / MG1655 / ATCC 47076.
  7. "Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli."
    Sommerfeldt N., Possling A., Becker G., Pesavento C., Tschowri N., Hengge R.
    Microbiology 155:1318-1331(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  8. "Second messenger-mediated adjustment of bacterial swimming velocity."
    Boehm A., Kaiser M., Li H., Spangler C., Kasper C.A., Ackermann M., Kaever V., Sourjik V., Roth V., Jenal U.
    Cell 141:107-116(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: ROLE IN MOTILITY, DISRUPTION PHENOTYPE.
    Strain: K12 / MG1655 / ATCC 47076.

Entry informationi

Entry nameiYFIN_ECOLI
AccessioniPrimary (citable) accession number: P46139
Secondary accession number(s): P76598, P77005
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1997
Last modified: May 11, 2016
This is version 131 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.