ECMDB: Cyclic di-3',5'-guanylate (ECMDB23177) (M2MDB003567)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (6)XML

Proteins (109)

Record Information

Version

2.0

Creation Date

2012-10-10 12:20:40 -0600

Update Date

2015-06-03 17:26:05 -0600

Secondary Accession Numbers

ECMDB23177

Identification

Name:

Cyclic di-3',5'-guanylate

Description

Cyclic di-3',5'-guanylate or Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria. It is a substrate for the enzyme Cyclic di-GMP phosphodiesterase which catalyzes the reaction Cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

3',5'-cyclic di-GMP
3',5'-Cyclic diGMP
3',5'-Cyclic diguanylate
3',5'-Cyclic diguanylic acid
Bis(3',5')-cyclic diguanylate
Bis(3',5')-cyclic diguanylic acid
Bis-(3',5')-cyclic diGMP
Bis-(3'-5')-cyclic dimeric guanosine monophosphate
Bis-(3'-5')-cyclic dimeric guanosine monophosphoric acid
C-(GpGp)
CdiGMP
CGpGp
Cyclic di-3',5'-guanylic acid
Cyclic di-GMP
Cyclic diguanylate
Cyclic diguanylic acid
Cyclic dinucleotide di-GMP
Cyclic-bis(3',5')diguanylate
Cyclic-bis(3',5')diguanylic acid
Cyclic-bis(3'->5') dimeric GMP
Guanosine 3',5'-cyclic monophosphate
Guanosine 3',5'-cyclic monophosphoric acid
Guanylyl-(3'->5')-3'-guanylate, cyclic 3'->5'''-nucleotide
Guanylyl-(3'->5')-3'-guanylic acid, cyclic 3'->5'''-nucleotide

Chemical Formula:

C₂₀H₂₄N₁₀O₁₄P₂

Weight:

Average: 690.4107
Monoisotopic: 690.09486855

InChI Key:

PKFDLKSEZWEFGL-MHARETSRSA-N

InChI:

InChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1

CAS number:

Not Available

IUPAC Name:

(1S,6R,8R,9R,10S,15R,17R,18R)-3,9,12,18-tetrahydroxy-8,17-bis(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-2,4,7,11,13,16-hexaoxa-3λ⁵,12λ⁵-diphosphatricyclo[13.3.0.0⁶,¹⁰]octadecane-3,12-dione

Traditional IUPAC Name:

cyclic di-GMP

SMILES:

[H][C@@]12COP(O)(=O)O[C@]3([H])[C@@]([H])(COP(O)(=O)O[C@@]1([H])[C@@]([H])(O)[C@@]([H])(O2)N1C=NC2=C1NC(=N)N=C2O)O[C@@]([H])(N1C=NC2=C1NC(=N)N=C2O)[C@]3([H])O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

D-alpha-amino acids

Alternative Parents

Substituents

D-alpha-amino acid
Carboxylic acid salt
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Organic oxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Organic salt
Organic zwitterion
Primary amine
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Alkyl chloride
Primary aliphatic amine
Organic oxide
Carbonyl group
Amine
Alkyl halide
Organopnictogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

chloroalanine (CHEBI:17092 )
D-alanine derivative (CHEBI:17092 )

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	3.77 g/L	ALOGPS
logP	-1	ALOGPS
logP	-3.5	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	1.53	ChemAxon
pKa (Strongest Basic)	5.18	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	343.02 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	164.59 m³·mol⁻¹	ChemAxon
Polarizability	60.01 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

2 Guanosine triphosphate <> 3',5'-Cyclic diGMP +2 Pyrophosphate + Cyclic di-3',5'-guanylate
3',5'-Cyclic diGMP + Water + Cyclic di-3',5'-guanylate <> Linear dimeric GMP
2 Guanosine triphosphate >2 Pyrophosphate + Cyclic di-3',5'-guanylate
Cyclic di-3',5'-guanylate + Water > 5'-phosphoguanylyl(3'->5')guanosine

SMPDB Pathways:

Not Available

KEGG Pathways:

Not Available

EcoCyc Pathways:

Not Available

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_22) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0902003000-e714278e50df8020df9d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-805d685a4a60cc6521c8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-0901000000-f966dd9a12345ea25d0c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f79-1700109000-5c992a7b596f80ec0b1d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-1900000000-a366df89a35ae5755147	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0ufr-6900000000-e76693b19ac5868f3b31	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Not Available

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	49537
HMDB ID	Not Available
Pubchem Compound ID	5287531
Kegg ID	C16463
ChemSpider ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	Not Available
Ligand Expo	C2E

Enzymes

Protein Details

1. Cyclic di-GMP phosphodiesterase yahA

General function:: Involved in two-component response regulator activity
Specific function:: Hydrolyzes c-di-GMP (cyclic bis(3'-5') dimeric GMP) to 5'-pGpG, known as PDE-A activity. PDE-B activity, that is hydrolysis of 5'-pGpG to GMP, proceeds only very slowly
Gene Name:: yahA
Uniprot ID:: P21514
Molecular weight:: 40725

Protein Details

2. Oxygen sensor protein DosP

General function:: Involved in phosphorus-oxygen lyase activity
Specific function:: In association with DosC is involved in the production and removal of the second messenger c-di-GMP in response to changing O(2) levels. Has phosphodiesterase (PDE) activity with c- di-GMP (PubMed:15995192), very poor activity on cAMP (PubMed:15995192) but not with cGMP, bis(p-nitrophenyl) phosphate or p-nitrophenyl phosphate (PubMed:11970957). Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria
Gene Name:: dosP
Uniprot ID:: P76129
Molecular weight:: 90260

Reactions

Cyclic di-3',5'-guanylate + H(2)O = 5'-phosphoguanylyl(3'->5')guanosine.

Protein Details

3. diguanylate cyclase; cold- and stationary phase-induced oxygen-dependent biofilm regulator; positively regulates csgBAC and pgaABCD

General function:: Not Available
Specific function:: Not Available
Gene Name:: dosC
Uniprot ID:: P0AA89
Molecular weight:: Not Available

Protein Details

4. diguanylate cyclase

General function:: Not Available
Specific function:: Not Available
Gene Name:: yeaP
Uniprot ID:: P76245
Molecular weight:: Not Available

Protein Details

5. Probable diguanylate cyclase AdrA

General function:: Signal transduction mechanisms
Specific function:: A probable diguanylate cyclase. The last member of a cascade of expressed proteins, its expression requires YdaM. AdrA production induces biosynthesis of cellulose in some E.coli isolates, but not in K12 strains. Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria
Gene Name:: adrA
Uniprot ID:: P0AAP1
Molecular weight:: 41537

Reactions

2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate.

Protein Details

6. Cyclic di-GMP phosphodiesterase Gmr

General function:: Signal transduction mechanisms
Specific function:: Part of a 2 protein system that seems to be dedicated to transcription of csgD. This protein decreases csgD transcription and thus decreases expression of adhesive curli fimbriae genes csgEFG, csgBAC/ymaD and adrA (yaic). Activity of this protein is antagonized by the diguanylate cyclase YdaM. In vitro has c-di-GMP phosphodiesterase activity. Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria
Gene Name:: gmr
Uniprot ID:: P77334
Molecular weight:: 74664

Reactions

Cyclic di-3',5'-guanylate + H(2)O = 5'-phosphoguanylyl(3'->5')guanosine.

Cyclic di-3',5'-guanylate (ECMDB23177) (M2MDB003567)

Structure for #<Compound:0x90cba350>

Enzymes

Reactions

Reactions

Reactions