Diguanylate cyclase DosC - Escherichia coli (strain K12)

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P0AA89 (DOSC_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 72. History...

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

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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:
Diguanylate cyclase DosC
Short name=DGC
EC=2.7.7.65

Alternative name(s):
Direct oxygen-sensing cyclase

Gene names

Name:	dosC
Synonyms:	yddV
Ordered Locus Names:	b1490, JW5241

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	460 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Globin-coupled heme-based oxygen sensor protein displaying diguanylate cyclase (DGC) activity in response to oxygen availability. Thus, catalyzes the synthesis of cyclic diguanylate (c-di-GMP) via the condensation of 2 GTP molecules. Is involved in the modulation of intracellular c-di-GMP levels, in association with DosP which catalyzes the degradation of c-di-GMP (PDE activity). Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria. DosC regulates biofilm formation through the oxygen-dependent activation of the csgBAC operon, which encodes curli structural subunits, while not affecting the expression of the regulatory operon csgDEFG. DosC, but not the other DGCs in E.coli, also promotes the production of the exopolysaccharide poly-N-acetylglucosamine (PNAG) through up-regulation of the expression of the PNAG biosynthetic pgaABCD operon, independently of CsrA. Ref.4 Ref.8 Ref.9 Ref.10 Ref.11 Overexpression leads to an increased level of c-di-GMP, which leads to changes in the cell surface, to abnormal cell division, increased biofilm formation and decreased swimming (the latter 2 in strain W3110). In a strain able to produce cellulose (strain TOB1, a fecal isolate) overexpression leads to an increase in cellulose production. Ref.4 Ref.8 Ref.9 Ref.10 Ref.11
Catalytic activity	2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate. Ref.6 Ref.8
Cofactor	Binds 1 heme group per subunit. The Fe²⁺ state binds O₂ and CO while the Fe³⁺ state can bind CN^- and imidazole. Ref.6 Binds 1 Mg²⁺ per subunit By similarity. Ref.6
Enzyme regulation	Activity depends on O(2)-binding and heme redox state: the Fe(III), Fe(II)-O₂, and Fe(II)-CO complexes of DosC are active forms, whereas Fe(II) and Fe(II)-NO complexes are inactive forms. Ref.8
Pathway	Purine metabolism; 3',5'-cyclic di-GMP biosynthesis.
Subunit structure	Forms a complex with DosP.
Induction	By RpoS in the late exponential growth phase and upon entry into stationary phase. Expression is higher at 28 than 37 degrees Celsius. In rich medium DosC and YdaM are the major RpoS-dependent GGDEF-domain containing proteins in the cell, whereas in minimal medium it is the major RpoS-dependent GGDEF-domain containing protein. Highly expressed on solid medium. A member of the dosCP operon. Ref.7 Ref.8 Ref.10
Domain	Is composed of an N-terminal sensory globin-fold domain that binds heme and oxygen, and a C-terminal GGDEF diguanylate cyclase domain. Ref.8
Disruption phenotype	Disruption results in a 2.5-fold reduction in surface adhesion, a 3.5-fold reduction in biofilm formation, a large reduction in curli production, a drastic decrease in csgB expression (400-fold reduction in aerobic growth) and in an approximately 3.5-fold reduction in pgaA transcript levels in comparison with wild-type. 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.9 Ref.10 Ref.11
Sequence similarities	Contains 1 GGDEF domain.
Biophysicochemical properties	Kinetic parameters: The Fe(III), Fe(II)-O₂, and Fe(II)-CO complexes of DosC display DGC activity with turnover numbers of 0.066, 0.022, and 0.022 min(-1), respectively. The DGC reaction catalyzed by DosC is the rate-determining step for c-di-GMP homeostasis. Binds O₂, CO, cyanide and imidazole with a dissociation constant of 14 µM, 0.095 µM, 4.7 µM and 0.055 µM, respectively. Ref.8 Redox potential: E₀ is -17 mV.
Sequence caution	The sequence BAA15155.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Ligand	GTP-binding Heme Iron 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 oxygen transport Inferred from electronic annotation. Source: InterPro regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW response to stress Inferred from expression pattern Ref.5. Source: EcoCyc transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	GTP binding Inferred from electronic annotation. Source: UniProtKB-KW diguanylate cyclase activity Inferred from direct assay Ref.4 Ref.8. Source: EcoCyc heme binding Inferred from direct assay Ref.6. Source: EcoCyc iron ion binding Inferred from electronic annotation. Source: InterPro oxygen binding Inferred from direct assay Ref.6. Source: EcoCyc 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 – 460

460

Diguanylate cyclase DosC

PRO_0000201321

Regions

Domain

325 – 458

134

GGDEF

Sites

Active site

376

Proton acceptor Potential

Metal binding

Iron (heme proximal ligand)

Metal binding

333

Magnesium By similarity

Metal binding

376

Magnesium By similarity

Binding site

341

Substrate By similarity

Binding site

350

Substrate By similarity

Site

Involved in oxygen binding and important for the stability of the Fe(II)-O(2) complex

Site

Important for oxygen binding and stability of the Fe(II)-O(2) complex

Site

Critical for restricting water access to the heme distal side to avoid rapid autoxidation

Site

338

Transition state stabilizer Potential

Experimental info

Mutagenesis

Y → A or L: Same biofilm formation activity as wild-type. Large decrease in O(2) affinity. Ref.8 Ref.11

Mutagenesis

Y → F or W: Same biofilm formation activity as wild-type. Markedly enhanced O(2) dissociation but not association rate constants. Highly enhanced autoxidation rate constant. Ref.8 Ref.11

Mutagenesis

Q → A or E: Same biofilm formation activity as wild-type. Enhanced O(2) dissociation but not association rate constants. Enhanced autoxidation rate constant. Ref.8 Ref.11

Mutagenesis

Q → L: Same biofilm formation activity as wild-type. 5-fold reduction in O(2) dissociation rate constant. Significant decrease in the autoxidation rate constant. Ref.8 Ref.11

Mutagenesis

L → G or T: Enhanced autoxidation rate constant. Markedly enhanced O(2) association rate constant. Ref.11 Ref.12

Mutagenesis

L → M or Q: Enhanced autoxidation rate constant. Decrease in O(2) association rate constant. Ref.11 Ref.12

Mutagenesis

H → A: Same biofilm formation activity as wild-type. Loss of heme-binding ability. Ref.8 Ref.11

Mutagenesis

223

H → A: Same biofilm formation activity as wild-type. Ref.8 Ref.11

Mutagenesis

365

R → A: Same biofilm formation activity as wild-type. Ref.8 Ref.11

Mutagenesis

368

D → A: Lacks biofilm formation activity, and thus is probably devoid of diguanylate cyclase activity. Ref.8 Ref.11

Mutagenesis

376 – 377

DE → AA: Loss of DGC activity. Stimulation of PNAG production and activation of pgaABCD expression are abolished. Ref.8 Ref.11

Mutagenesis

376

D → A: Lacks biofilm formation activity, and thus is probably devoid of diguanylate cyclase activity. Ref.8 Ref.11

Mutagenesis

377

E → A: Lacks biofilm formation activity, and thus is probably devoid of diguanylate cyclase activity. Ref.8 Ref.11

Sequences

Sequence

Length

Mass (Da)

Tools

P0AA89 [UniParc].

Last modified September 13, 2005. Version 1.
Checksum: 79168311553E61C3
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FASTA

460

53,178

        10         20         30         40         50         60 
MEMYFKRMKD EWTGLVEQAD PPIRAKAAEI AVAHAHYLSI EFYRIVRIDP HAEEFLSNEQ 

        70         80         90        100        110        120 
VERQLKSAME RWIINVLSAQ VDDVERLIQI QHTVAEVHAR IGIPVEIVEM GFRVLKKILY 

       130        140        150        160        170        180 
PVIFSSDYSA AEKLQVYHFS INSIDIAMEV MTRAFTFSDS SASKEDENYR IFSLLENAEE 

       190        200        210        220        230        240 
EKERQIASIL SWEIDIIYKI LLDSDLGSSL PLSQADFGLW FNHKGRHYFS GIAEVGHISR 

       250        260        270        280        290        300 
LIQDFDGIFN QTMRNTRNLN NRSLRVKFLL QIRNTVSQII TLLRELFEEV SRHEVGMDVL 

       310        320        330        340        350        360 
TKLLNRRFLP TIFKREIAHA NRTGTPLSVL IIDVDKFKEI NDTWGHNTGD EILRKVSQAF 

       370        380        390        400        410        420 
YDNVRSSDYV FRYGGDEFII VLTEASENET LRTAERIRSR VEKTKLKAAN GEDIALSLSI 

       430        440        450        460 
GAAMFNGHPD YERLIQIADE ALYIAKRRGR NRVELWKASL

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. Horiuchi T. DNA Res. 3:363-377(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]	"Genome-wide transcriptional profile of Escherichia coli in response to high levels of the second messenger 3',5'-cyclic diguanylic acid." Mendez-Ortiz M.M., Hyodo M., Hayakawa Y., Membrillo-Hernandez J. J. Biol. Chem. 281:8090-8099(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A DIGUANYLATE CYCLASE, OPERON STRUCTURE. Strain: K12 / MG1655 / ATCC 47076, K12 / W3110 / ATCC 27325 / DSM 5911 and TOB1.
[5]	"Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli." Weber H., Pesavento C., Possling A., Tischendorf G., Hengge R. Mol. Microbiol. 62:1014-1034(2006) [PubMed] [Europe PMC] [Abstract] Cited for: RPOS-DEPENDENCE. Strain: K12 / MC4100.
[6]	"An oxygen-sensing diguanylate cyclase and phosphodiesterase couple for c-di-GMP control." Tuckerman J.R., Gonzalez G., Sousa E.H., Wan X., Saito J.A., Alam M., Gilles-Gonzalez M.A. Biochemistry 48:9764-9774(2009) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, HEME COFACTOR, O(2)-BINDING, INTERACTION WITH DOSP, OPERON STRUCTURE.
[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, RPOS-DEPENDENCE. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]	"Important roles of Tyr43 at the putative heme distal side in the oxygen recognition and stability of the Fe(II)-O2 complex of YddV, a globin-coupled heme-based oxygen sensor diguanylate cyclase." Kitanishi K., Kobayashi K., Kawamura Y., Ishigami I., Ogura T., Nakajima K., Igarashi J., Tanaka A., Shimizu T. Biochemistry 49:10381-10393(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, DOMAIN, O(2)-BINDING, CO-BINDING, CYANIDE-BINDING, IMIDAZOLE-BINDING, KINETIC PARAMETERS, REDOX POTENTIAL, MUTAGENESIS OF TYR-43; GLN-60; HIS-98; HIS-223; ARG-365; ASP-368; ASP-376 AND GLU-377, ABSORPTION SPECTROSCOPY, RESONANCE RAMAN SPECTROSCOPY. Strain: K12.
[9]	"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.
[10]	"The yddV-dos operon controls biofilm formation through the regulation of genes encoding curli fibers' subunits in aerobically growing Escherichia coli." Tagliabue L., Maciag A., Antoniani D., Landini P. FEMS Immunol. Med. Microbiol. 59:477-484(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN REGULATION OF CSGBAC EXPRESSION, DISRUPTION PHENOTYPE, INDUCTION. Strain: K12 / MG1655 / ATCC 47076.
[11]	"The diguanylate cyclase YddV controls production of the exopolysaccharide poly-N-acetylglucosamine (PNAG) through regulation of the PNAG biosynthetic pgaABCD operon." Tagliabue L., Antoniani D., Maciag A., Bocci P., Raffaelli N., Landini P. Microbiology 156:2901-2911(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN REGULATION OF PGAABCD EXPRESSION, DISRUPTION PHENOTYPE, MUTAGENESIS OF 376-ASP-GLU-377. Strain: K12 / MG1655 / ATCC 47076.
[12]	"Leu65 in the heme distal side is critical for the stability of the Fe(II)-O(2) complex of YddV, a globin-coupled oxygen sensor diguanylate cyclase." Nakajima K., Kitanishi K., Kobayashi K., Kobayashi N., Igarashi J., Shimizu T. J. Inorg. Biochem. 108:163-170(2012) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF LEU-65, ABSORPTION SPECTROSCOPY. Strain: K12.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00096 Genomic DNA. Translation: AAC74563.3. AP009048 Genomic DNA. Translation: BAA15155.2. Different initiation.
PIR	E64902.
RefSeq	NP_416007.3. NC_000913.2. YP_489755.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0AA89.
SMR	P0AA89. Positions 271-455.
ModBase	Search...
Protein-protein interaction databases
STRING	511145.b1490.
Proteomic databases
PRIDE	P0AA89.
Protocols and materials databases
DNASU	945835.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC74563; AAC74563; b1490. BAA15155; BAA15155; BAA15155.
GeneID	12933168. 945835.
KEGG	ecj:Y75_p1466. eco:b1490.
PATRIC	32118274. VBIEscCol129921_1557.
Organism-specific databases
EchoBASE	EB3554.
EcoGene	EG13793. dosC.
Phylogenomic databases
eggNOG	COG2199.
HOGENOM	HOG000006777.
KO	K13069.
OMA	HDGHPDY.
ProtClustDB	CLSK880042.
Enzyme and pathway databases
BioCyc	EcoCyc:G6784-MONOMER. ECOL316407:JW5241-MONOMER. MetaCyc:G6784-MONOMER.
UniPathway	UPA00599.
Gene expression databases
Genevestigator	P0AA89.
Family and domain databases
Gene3D	1.10.490.10. 1 hit.
InterPro	IPR001054. A/G_cyclase. IPR000160. GGDEF_dom. IPR009050. Globin-like. IPR012292. Globin_dom. [Graphical view]
Pfam	PF00990. GGDEF. 1 hit. [Graphical view]
SMART	SM00267. GGDEF. 1 hit. [Graphical view]
SUPFAM	SSF55073. A/G_cyclase. 1 hit. SSF46458. Globin_like. 1 hit.
TIGRFAMs	TIGR00254. GGDEF. 1 hit.
PROSITE	PS50887. GGDEF. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DOSC_ECOLI

Accession

Primary (citable) accession number: P0AA89
Secondary accession number(s): P77793

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 13, 2005
Last sequence update:	September 13, 2005
Last modified:	May 1, 2013
This is version 72 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

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