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Protein

Probable diguanylate cyclase YcdT

Gene

ycdT

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

Functioni

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.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 bindingi318 – 3181MagnesiumBy similarity
Sitei323 – 3231Transition state stabilizerSequence analysis
Binding sitei326 – 3261SubstrateBy similarity
Binding sitei335 – 3351SubstrateBy similarity
Active sitei361 – 3611Proton acceptorSequence analysis
Metal bindingi361 – 3611MagnesiumBy similarity

GO - Molecular functioni

  • diguanylate cyclase activity Source: EcoCyc
  • GTP binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • negative regulation of cellular component movement Source: EcoCyc
  • single-species submerged biofilm formation Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciEcoCyc:G6532-MONOMER.
ECOL316407:JW5143-MONOMER.
MetaCyc:G6532-MONOMER.
UniPathwayiUPA00599.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable diguanylate cyclase YcdT (EC:2.7.7.65)
Short name:
DGC
Gene namesi
Name:ycdT
Ordered Locus Names:b1025, JW5143
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13866. ycdT.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 77CytoplasmicSequence analysis
Transmembranei8 – 2821HelicalSequence analysisAdd
BLAST
Topological domaini29 – 4517PeriplasmicSequence analysisAdd
BLAST
Transmembranei46 – 6621HelicalSequence analysisAdd
BLAST
Topological domaini67 – 748CytoplasmicSequence analysis
Transmembranei75 – 9521HelicalSequence analysisAdd
BLAST
Topological domaini96 – 11116PeriplasmicSequence analysisAdd
BLAST
Transmembranei112 – 13221HelicalSequence analysisAdd
BLAST
Topological domaini133 – 14816CytoplasmicSequence analysisAdd
BLAST
Transmembranei149 – 16921HelicalSequence analysisAdd
BLAST
Topological domaini170 – 19526PeriplasmicSequence analysisAdd
BLAST
Transmembranei196 – 21621HelicalSequence analysisAdd
BLAST
Topological domaini217 – 2193CytoplasmicSequence analysis
Transmembranei220 – 24021HelicalSequence analysisAdd
BLAST
Topological domaini241 – 25414PeriplasmicSequence analysisAdd
BLAST
Transmembranei255 – 27521HelicalSequence analysisAdd
BLAST
Topological domaini276 – 452177CytoplasmicSequence analysisAdd
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

A slight increase in motility. No visible effect on curli production.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi359 – 3602GG → AA: Cells overexpressing this mutant are no longer swimming suppressed. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 452452Probable diguanylate cyclase YcdTPRO_0000168806Add
BLAST

Proteomic databases

PaxDbiP75908.
PRIDEiP75908.

Expressioni

Inductioni

CsrA binds to the mRNA and reduces its levels. Expressed at low levels at both 28 and 37 degrees Celsius.1 Publication

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

BioGridi4263227. 7 interactions.
STRINGi511145.b1025.

Structurei

3D structure databases

ProteinModelPortaliP75908.
SMRiP75908. Positions 285-442.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini310 – 445136GGDEFPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 GGDEF domain.PROSITE-ProRule annotation

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105BZU. Bacteria.
ENOG410XNMH. LUCA.
HOGENOMiHOG000118907.
InParanoidiP75908.
OMAiWNGVSVI.
PhylomeDBiP75908.

Family and domain databases

CDDicd01949. GGDEF. 1 hit.
InterProiIPR000160. GGDEF_dom.
IPR033424. MASE4.
IPR029787. Nucleotide_cyclase.
[Graphical view]
PfamiPF00990. GGDEF. 1 hit.
PF17158. MASE4. 1 hit.
[Graphical view]
SMARTiSM00267. GGDEF. 1 hit.
[Graphical view]
SUPFAMiSSF55073. SSF55073. 1 hit.
TIGRFAMsiTIGR00254. GGDEF. 1 hit.
PROSITEiPS50887. GGDEF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P75908-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKDYLRISS TVLVSLLFGL ALVLVNSWFN QPGVEEVVPR STYLMVMIAL
60 70 80 90 100
FFIDTVAFIF MQLYFIYDRR QFSNCVLSLA FLSCLIYFVI TVIIIQQIIE
110 120 130 140 150
ERLTSSVVQN DIAIYYLFRQ MSLCILIFLA LVNKVSENTK QRNLFSKKMT
160 170 180 190 200
LCISLFFVFG GPIVAHILSS HYESYNLHIA ELTNENGQVV WKASYVTIMI
210 220 230 240 250
FMWLTLLSVN LYFNGLRYDI WNGVTVIAFC AVLYNISLLF MSRYSVSTWY
260 270 280 290 300
ISRTIEVVSK LTVMVIFMCH IFSALRVTKN IAHRDPLTNI FNRNYFFNEL
310 320 330 340 350
TVQSASAQKT PYCVMIMDID HFKKVNDTWG HPVGDQVIKT VVNIIGKSIR
360 370 380 390 400
PDDLLARVGG EEFGVLLTDI DTERAKALAE RIRENVERLT GDNPEYAIPQ
410 420 430 440 450
KVTISIGAVV TQENALNPNE IYRLADNALY EAKETGRNKV VVRDVVNFCE

SP
Length:452
Mass (Da):51,783
Last modified:February 1, 1997 - v1
Checksum:iB6FB9E7EB894D701
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti130 – 1301A → V in strain: K12 / W3110 / ATCC 27325 / DSM 5911.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74110.1.
AP009048 Genomic DNA. Translation: BAA35810.2.
PIRiG64844.
RefSeqiNP_415544.1. NC_000913.3.
WP_000409873.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74110; AAC74110; b1025.
BAA35810; BAA35810; BAA35810.
GeneIDi945593.
KEGGiecj:JW5143.
eco:b1025.
PATRICi32117283. VBIEscCol129921_1065.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74110.1.
AP009048 Genomic DNA. Translation: BAA35810.2.
PIRiG64844.
RefSeqiNP_415544.1. NC_000913.3.
WP_000409873.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP75908.
SMRiP75908. Positions 285-442.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263227. 7 interactions.
STRINGi511145.b1025.

Proteomic databases

PaxDbiP75908.
PRIDEiP75908.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74110; AAC74110; b1025.
BAA35810; BAA35810; BAA35810.
GeneIDi945593.
KEGGiecj:JW5143.
eco:b1025.
PATRICi32117283. VBIEscCol129921_1065.

Organism-specific databases

EchoBASEiEB3626.
EcoGeneiEG13866. ycdT.

Phylogenomic databases

eggNOGiENOG4105BZU. Bacteria.
ENOG410XNMH. LUCA.
HOGENOMiHOG000118907.
InParanoidiP75908.
OMAiWNGVSVI.
PhylomeDBiP75908.

Enzyme and pathway databases

UniPathwayiUPA00599.
BioCyciEcoCyc:G6532-MONOMER.
ECOL316407:JW5143-MONOMER.
MetaCyc:G6532-MONOMER.

Miscellaneous databases

PROiP75908.

Family and domain databases

CDDicd01949. GGDEF. 1 hit.
InterProiIPR000160. GGDEF_dom.
IPR033424. MASE4.
IPR029787. Nucleotide_cyclase.
[Graphical view]
PfamiPF00990. GGDEF. 1 hit.
PF17158. MASE4. 1 hit.
[Graphical view]
SMARTiSM00267. GGDEF. 1 hit.
[Graphical view]
SUPFAMiSSF55073. SSF55073. 1 hit.
TIGRFAMsiTIGR00254. GGDEF. 1 hit.
PROSITEiPS50887. GGDEF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYCDT_ECOLI
AccessioniPrimary (citable) accession number: P75908
Secondary accession number(s): Q9R7P4, Q9R7P6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: February 1, 1997
Last modified: September 7, 2016
This is version 119 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

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.