Probable diguanylate cyclase YcdT - Escherichia coli (strain K12)

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P75908 (YCDT_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 97. 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 YcdT
Short name=DGC
EC=2.7.7.65

Gene names

Name:	ycdT
Ordered Locus Names:	b1025, JW5143

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	452 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	A probable diguanylate cyclase, overexpression leads to a strong repression of swimming; swimming returns to normal when residues 359-360 are both mutated to Ala. Overexpression also leads to a 20-fold increase in c-di-GMP levels in vivo. Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria. Ref.5
Catalytic activity	2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate. Ref.5
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	CsrA binds to the mRNA and reduces its levels. Expressed at low levels at both 28 and 37 degrees Celsius. Ref.5 Ref.6
Disruption phenotype	A slight increase in motility. No visible effect on curli production. Ref.5
Sequence similarities	Contains 1 GGDEF 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 cellular component movement Inferred from mutant phenotype Ref.5. 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 direct assay Ref.5. Source: EcoCyc metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphorus-oxygen lyase 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 – 452

452

Probable diguanylate cyclase YcdT

PRO_0000168806

Regions

Topological domain

1 – 7

Cytoplasmic Potential

Transmembrane

8 – 28

Helical; Potential

Topological domain

29 – 45

Periplasmic Potential

Transmembrane

46 – 66

Helical; Potential

Topological domain

67 – 74

Cytoplasmic Potential

Transmembrane

75 – 95

Helical; Potential

Topological domain

96 – 111

Periplasmic Potential

Transmembrane

112 – 132

Helical; Potential

Topological domain

133 – 148

Cytoplasmic Potential

Transmembrane

149 – 169

Helical; Potential

Topological domain

170 – 195

Periplasmic Potential

Transmembrane

196 – 216

Helical; Potential

Topological domain

217 – 219

Cytoplasmic Potential

Transmembrane

220 – 240

Helical; Potential

Topological domain

241 – 254

Periplasmic Potential

Transmembrane

255 – 275

Helical; Potential

Topological domain

276 – 452

177

Cytoplasmic Potential

Domain

310 – 445

136

GGDEF

Sites

Active site

361

Proton acceptor Potential

Metal binding

318

Magnesium By similarity

Metal binding

361

Magnesium By similarity

Binding site

326

Substrate By similarity

Binding site

335

Substrate By similarity

Site

323

Transition state stabilizer Potential

Natural variations

Natural variant

130

A → V in strain: K12 / W3110 / ATCC 27325 / DSM 5911.

Experimental info

Mutagenesis

359 – 360

GG → AA: Cells overexpressing this mutant are no longer swimming suppressed. Ref.5

Sequences

Sequence

Length

Mass (Da)

Tools

P75908 [UniParc].

Last modified February 1, 1997. Version 1.
Checksum: B6FB9E7EB894D701
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FASTA

452

51,783

        10         20         30         40         50         60 
MEKDYLRISS TVLVSLLFGL ALVLVNSWFN QPGVEEVVPR STYLMVMIAL FFIDTVAFIF 

        70         80         90        100        110        120 
MQLYFIYDRR QFSNCVLSLA FLSCLIYFVI TVIIIQQIIE ERLTSSVVQN DIAIYYLFRQ 

       130        140        150        160        170        180 
MSLCILIFLA LVNKVSENTK QRNLFSKKMT LCISLFFVFG GPIVAHILSS HYESYNLHIA 

       190        200        210        220        230        240 
ELTNENGQVV WKASYVTIMI FMWLTLLSVN LYFNGLRYDI WNGVTVIAFC AVLYNISLLF 

       250        260        270        280        290        300 
MSRYSVSTWY ISRTIEVVSK LTVMVIFMCH IFSALRVTKN IAHRDPLTNI FNRNYFFNEL 

       310        320        330        340        350        360 
TVQSASAQKT PYCVMIMDID HFKKVNDTWG HPVGDQVIKT VVNIIGKSIR PDDLLARVGG 

       370        380        390        400        410        420 
EEFGVLLTDI DTERAKALAE RIRENVERLT GDNPEYAIPQ KVTISIGAVV TQENALNPNE 

       430        440        450 
IYRLADNALY EAKETGRNKV VVRDVVNFCE SP

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. Horiuchi T. DNA Res. 3:137-155(1996) [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]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"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.
[5]	"The RNA binding protein CsrA controls cyclic di-GMP metabolism by directly regulating the expression of GGDEF proteins." Jonas K., Edwards A.N., Simm R., Romeo T., Romling U., Melefors O. Mol. Microbiol. 70:236-257(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PROBABLE ENZYME ACTIVITY, FUNCTION, MUTAGENESIS OF 359-GLY-GLY-360, DISRUPTION PHENOTYPE, POST-TRANSCRIPTIONAL REGULATION BY CSRA. Strain: K12.
[6]	"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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00096 Genomic DNA. Translation: AAC74110.1. AP009048 Genomic DNA. Translation: BAA35810.2.
PIR	G64844.
RefSeq	NP_415544.1. NC_000913.2. YP_489296.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P75908.
SMR	P75908. Positions 285-442.
ModBase	Search...
Protein-protein interaction databases
STRING	511145.b1025.
Proteomic databases
PRIDE	P75908.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC74110; AAC74110; b1025. BAA35810; BAA35810; BAA35810.
GeneID	12934233. 945593.
KEGG	ecj:Y75_p0997. eco:b1025.
PATRIC	32117283. VBIEscCol129921_1065.
Organism-specific databases
EchoBASE	EB3626.
EcoGene	EG13866. ycdT.
Phylogenomic databases
eggNOG	COG2199.
HOGENOM	HOG000118907.
OMA	WIFILTT.
ProtClustDB	CLSK879933.
Enzyme and pathway databases
BioCyc	EcoCyc:G6532-MONOMER. ECOL316407:JW5143-MONOMER. MetaCyc:G6532-MONOMER.
UniPathway	UPA00599.
Gene expression databases
Genevestigator	P75908.
Family and domain databases
InterPro	IPR001054. A/G_cyclase. IPR000160. GGDEF_dom. [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. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

YCDT_ECOLI

Accession

Primary (citable) accession number: P75908
Secondary accession number(s): Q9R7P4, Q9R7P6

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	February 1, 1997
Last modified:	May 1, 2013
This is version 97 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

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

Natural variations

Experimental info

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