Probable diguanylate cyclase YfiN - Escherichia coli (strain K12)

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P46139 (YFIN_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 111. History...

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

Documents (3) |

Third-party data

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

Names and origin

Protein names

Recommended name:
Probable diguanylate cyclase YfiN
Short name=DGC
EC=2.7.7.65

Gene names

Name:	yfiN
Ordered Locus Names:	b2604, JW2585

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	408 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria. Ref.8
Catalytic activity	2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate.
Cofactor	Binds 1 Mg²⁺ per monomer By similarity.
Pathway	Purine metabolism; 3',5'-cyclic di-GMP biosynthesis.
Subunit structure	Homodimer By similarity.
Subcellular location	Cell inner membrane; Multi-pass membrane protein.
Induction	Expressed at low levels at both 28 and 37 degrees Celsius during transition into stationary phase. Ref.7
Disruption phenotype	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. Ref.8
Sequence similarities	Contains 1 GGDEF domain. Contains 1 HAMP domain.

Ontologies

Keywords
Cellular component	Cell inner membrane Cell membrane Membrane
Domain	Transmembrane Transmembrane helix
Ligand	GTP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Transferase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cyclic nucleotide biosynthetic process Inferred from electronic annotation. Source: InterPro intracellular signal transduction Inferred from electronic annotation. Source: InterPro negative regulation of flagellar cell motility Inferred from mutant phenotype PubMed 21181144. Source: EcoCyc
Cellular_component	integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	GTP binding Inferred from electronic annotation. Source: UniProtKB-KW diguanylate cyclase activity Inferred from genetic interaction Ref.8. Source: EcoCyc metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphorus-oxygen lyase activity Inferred from electronic annotation. Source: InterPro signal transducer activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 408

408

Probable diguanylate cyclase YfiN

PRO_0000169270

Regions

Topological domain

1 – 24

Cytoplasmic Probable

Transmembrane

25 – 45

Helical; Potential

Topological domain

46 – 52

Periplasmic Probable

Transmembrane

53 – 73

Helical; Potential

Topological domain

74 – 112

Cytoplasmic Probable

Transmembrane

113 – 133

Helical; Potential

Topological domain

134 – 154

Periplasmic Probable

Transmembrane

155 – 175

Helical; Potential

Topological domain

176 – 408

233

Cytoplasmic Ref.6

Domain

183 – 236

HAMP

Domain

278 – 408

131

GGDEF

Sites

Active site

329

Proton acceptor Potential

Metal binding

286

Magnesium By similarity

Metal binding

329

Magnesium By similarity

Binding site

294

Substrate By similarity

Binding site

303

Substrate By similarity

Site

291

Transition state stabilizer Potential

Sequences

Sequence

Length

Mass (Da)

Tools

P46139 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: 720B6539EF43DB16
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FASTA

408

45,989

        10         20         30         40         50         60 
MMDNDNSLNK RPTFKRALRN ISMTSIFITM MLIWLLLSVT SVLTLKQYAQ KNLALTAATM 

        70         80         90        100        110        120 
TYSLEAAVVF ADGPAATETL AALGQQGQFS TAEVRDKQQN ILASWHYTRK DPGDTFSNFI 

       130        140        150        160        170        180 
SHWLFPAPII QPIRHNGETI GEVRLTARDS SISHFIWFSL AVLTGCILLA SGIAITLTRH 

       190        200        210        220        230        240 
LHNGLVEALK NITDVVHDVR SNRNFSRRVS EERIAEFHRF ALDFNSLLDE MEEWQLRLQA 

       250        260        270        280        290        300 
KNAQLLRTAL HDPLTGLANR AAFRSGINTL MNNSDARKTS ALLFLDGDNF KYINDTWGHA 

       310        320        330        340        350        360 
TGDRVLIEIA KRLAEFGGLR HKAYRLGGDE FAMVLYDVQS ESEVQQICSA LTQIFNLPFD 

       370        380        390        400 
LHNGHQTTMT LSIGYAMTIE HASAEKLQEL ADHNMYQAKH QRAEKLVR

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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. 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]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00096 Genomic DNA. Translation: AAC75653.1. AP009048 Genomic DNA. Translation: BAA16489.2. X01818 Genomic DNA. No translation available.
PIR	G65038.
RefSeq	NP_417095.1. NC_000913.2. YP_490827.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P46139.
SMR	P46139. Positions 212-400.
ModBase	Search...
Protein-protein interaction databases
STRING	511145.b2604.
Proteomic databases
PRIDE	P46139.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC75653; AAC75653; b2604. BAA16489; BAA16489; BAA16489.
GeneID	12934367. 947091.
KEGG	ecj:Y75_p2552. eco:b2604.
PATRIC	32120607. VBIEscCol129921_2702.
Organism-specific databases
EchoBASE	EB2718.
EcoGene	EG12880. yfiN.
Phylogenomic databases
eggNOG	COG2199.
HOGENOM	HOG000217416.
OMA	RVYADHN.
ProtClustDB	PRK09966.
Enzyme and pathway databases
BioCyc	EcoCyc:EG12880-MONOMER. ECOL316407:JW2585-MONOMER.
UniPathway	UPA00599.
Gene expression databases
Genevestigator	P46139.
Family and domain databases
InterPro	IPR001054. A/G_cyclase. IPR000160. GGDEF_dom. IPR003660. HAMP_linker_domain. [Graphical view]
Pfam	PF00990. GGDEF. 1 hit. [Graphical view]
SMART	SM00267. GGDEF. 1 hit. [Graphical view]
SUPFAM	SSF55073. A/G_cyclase. 1 hit.
TIGRFAMs	TIGR00254. GGDEF. 1 hit.
PROSITE	PS50887. GGDEF. 1 hit. PS50885. HAMP. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

YFIN_ECOLI

Accession

Primary (citable) accession number: P46139
Secondary accession number(s): P76598, P77005

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1995
Last sequence update:	November 1, 1997
Last modified:	May 1, 2013
This is version 111 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

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

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents