Diguanylate cyclase YdeH - Escherichia coli (strain K12)

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P31129 (YDEH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 100. History...

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

Documents (4) |

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:
Diguanylate cyclase YdeH
Short name=DGC
EC=2.7.7.65

Gene names

Name:	ydeH
Synonyms:	ydeG
Ordered Locus Names:	b1535, JW1528

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	296 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	A diguanylate cyclase, overexpression leads to a strong repression of swimming; swimming returnes to normal when residues 206-207 are both mutated to Ala. Overexpression also leads to a reduction in flagellar abundance and a 20-fold increase in c-di-GMP levels in vivo. Required for aminoglycoside-mediated induction of biofilm formation, it also plays a lesser role in biofilm production in response to other classes of translation inhibitors. The c-di-GMP produced by this enzyme up-regulates poly-GlcNAc production as well as the biofilm synthesis protein PgaD, although c-di-GMP is probably not the main inducing principle. Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria. Ref.7
Catalytic activity	2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate. Ref.5
Cofactor	Binds 1 Mg²⁺ per monomer By similarity.
Enzyme regulation	Subject to product inhibition by c-di-GMP at a KI of 44 µM. Ref.7
Pathway	Purine metabolism; 3',5'-cyclic di-GMP biosynthesis.
Subunit structure	Homodimer. Ref.7
Induction	CsrA binds to the mRNA and reduces its levels. Expressed at low levels at both 28 and 37 degrees Celsius. Repressed by RpoS. Ref.5 Ref.6 Ref.7
Disruption phenotype	A slight increase in motility. No visible effect on curli production (Ref.5). Decreased biofilm formation, very little associated poly-GlcNAc production, and a complete loss of aminogylcoside-mediated induction of biofilm formation (Ref.7). Ref.5 Ref.7
Sequence similarities	Contains 1 GGDEF domain.
Biophysicochemical properties	Kinetic parameters: K_M=17 µM for GTP Ref.7
Sequence caution	The sequence M96235 differs from that shown. Reason: Frameshift at position 176.

Ontologies

Keywords
Ligand	GTP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell adhesion involved in single-species biofilm formation Inferred from mutant phenotype Ref.7. Source: EcoCyc 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 negative regulation of flagellum assembly Inferred from mutant phenotype Ref.5. Source: EcoCyc
Molecular_function	GTP binding Inferred from electronic annotation. Source: UniProtKB-KW diguanylate cyclase activity Inferred from direct assay Ref.5 Ref.7. 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 – 296

296

Diguanylate cyclase YdeH

PRO_0000168946

Regions

Domain

157 – 289

133

GGDEF

Sites

Active site

208

Proton acceptor Potential

Metal binding

165

Magnesium By similarity

Metal binding

208

Magnesium By similarity

Binding site

173

Substrate By similarity

Binding site

182

Substrate By similarity

Site

170

Transition state stabilizer Potential

Experimental info

Mutagenesis

206 – 207

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

Mutagenesis

208

E → Q: Significantly decreased biofilm formation. Ref.5 Ref.7

Secondary structure

296

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P31129 [UniParc].

Last modified July 15, 1998. Version 2.
Checksum: 7B6884E6B8A6D8D8
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FASTA

296

33,863

        10         20         30         40         50         60 
MIKKTTEIDA ILLNLNKAID AHYQWLVSMF HSVVARDASK PEITDNHSYG LCQFGRWIDH 

        70         80         90        100        110        120 
LGPLDNDELP YVRLMDSAHQ HMHNCGRELM LAIVENHWQD AHFDAFQEGL LSFTAALTDY 

       130        140        150        160        170        180 
KIYLLTIRSN MDVLTGLPGR RVLDESFDHQ LRNAEPLNLY LMLLDIDRFK LVNDTYGHLI 

       190        200        210        220        230        240 
GDVVLRTLAT YLASWTRDYE TVYRYGGEEF IIIVKAANDE EACRAGVRIC QLVDNHAITH 

       250        260        270        280        290 
SEGHINITVT AGVSRAFPEE PLDVVIGRAD RAMYEGKQTG RNRCMFIDEQ NVINRV

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genetic and functional analysis of the multiple antibiotic resistance (mar) locus in Escherichia coli." Cohen S.P., Haechler H., Levy S.B. J. Bacteriol. 175:1484-1492(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"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.
[3]	"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.
[4]	"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.
[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, MUTAGENESIS OF 206-GLY-GLY-207, 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, RPOS-REPRESSION. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"Second messenger signalling governs Escherichia coli biofilm induction upon ribosomal stress." Boehm A., Steiner S., Zaehringer F., Casanova A., Hamburger F., Ritz D., Keck W., Ackermann M., Schirmer T., Jenal U. Mol. Microbiol. 72:1500-1516(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN BIOFILM FORMATION, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT, MUTAGENESIS OF GLU-208, DISRUPTION PHENOTYPE. Strain: K12 / AB400.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M96235 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAC74608.1.
AP009048 Genomic DNA. Translation: BAA18882.2.

PIR

B64908.

RefSeq

NP_416052.1. NC_000913.2.
YP_489798.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3T9O	X-ray	2.20	A/B	2-126	[»]
3TVK	X-ray	1.80	A	127-296	[»]

ProteinModelPortal

P31129.

SMR

P31129. Positions 7-296.

ModBase

Search...

Protein-protein interaction databases

IntAct

P31129. 6 interactions.

STRING

511145.b1535.

Proteomic databases

PaxDb

P31129.

PRIDE

P31129.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74608; AAC74608; b1535.
BAA18882; BAA18882; BAA18882.

GeneID

12930120.
946075.

KEGG

ecj:Y75_p1510.
eco:b1535.

PATRIC

32118370. VBIEscCol129921_1605.

Organism-specific databases

EchoBASE

EB1596.

EcoGene

EG11643. ydeH.

Phylogenomic databases

eggNOG

COG2199.

HOGENOM

HOG000120785.

OMA

NCTILIN.

ProtClustDB

PRK09894.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11643-MONOMER.
ECOL316407:JW1528-MONOMER.
MetaCyc:EG11643-MONOMER.

UniPathway

UPA00599.

Gene expression databases

Genevestigator

P31129.

Family and domain databases

InterPro

IPR001054. A/G_cyclase.
IPR000160. GGDEF_dom.
IPR025991. MCPsignal_assoc_dom.
[Graphical view]

Pfam

PF00990. GGDEF. 1 hit.
PF13682. MCPsignal_assoc. 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

YDEH_ECOLI

Accession

Primary (citable) accession number: P31129
Secondary accession number(s): P76152, P77452

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	July 15, 1998
Last modified:	May 1, 2013
This is version 100 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

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

Secondary structure

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