L-Seryl-AMP (ECMDB20608) (M2MDB001407)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2012-05-31 14:53:09 -0600
Update Date2015-06-03 17:20:22 -0600
Secondary Accession Numbers
  • ECMDB20608
Identification
Name:L-Seryl-AMP
DescriptionL-Seryl-AMP is an enzyme-bound intermediate found in the protein EntF. EntF is the enzyme responsible for serine activation during the biosynthesis of enterobactin (a cyclic trimer of N-dihydroxybenzoyl serine) in Escherichia coli. Serine adenylate is also an intermediate in the charging of Seryl-tRNA-synthetase. In particular, Mg.ATP and serine react to form seryl-adenylate on the protein. The serine is subsequently transferred to the 3'-end of the tRNA. Seryl-tRNA synthetase is also capable of synthesizing diadenosine tetraphosphate (Ap4A) from the enzyme-bound seryl-adenylate intermediate and a second molecule of ATP.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • (L-Seryl)adenylate
  • (L-Seryl)adenylic acid
  • L-Serine adenylate
  • L-Serine adenylic acid
  • L-Serine AMP
  • L-Seryl-adenylate
  • L-Seryl-adenylic acid
  • Serine adenylate
  • Serine adenylic acid
  • Serine AMP
  • Seryl adenylate
  • Seryl adenylic acid
  • Seryl-AMP
  • SRP
Chemical Formula:C13H19N6O9P
Weight:Average: 434.2985
Monoisotopic: 434.095112748
InChI Key:UVSYURUCZPPUQD-MACXSXHHSA-N
InChI:InChI=1S/C13H19N6O9P/c14-5(1-20)13(23)28-29(24,25)26-2-6-8(21)9(22)12(27-6)19-4-18-7-10(15)16-3-17-11(7)19/h3-6,8-9,12,20-22H,1-2,14H2,(H,24,25)(H2,15,16,17)/t5-,6+,8+,9+,12+/m0/s1
CAS number:52435-67-3
IUPAC Name:{[(2S)-2-amino-3-hydroxypropanoyl]oxy}({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy})phosphinic acid
Traditional IUPAC Name:L-seryl-AMP
SMILES:[H][C@](N)(CO)C(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])O
Chemical Taxonomy
Description belongs to the class of organic compounds known as 5'-acylphosphoadenosines. These are ribonucleoside derivatives containing an adenoside moiety, where the phosphate group is acylated.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine ribonucleotides
Direct Parent5'-acylphosphoadenosines
Alternative Parents
Substituents
  • 5'-acylphosphoadenosine
  • Pentose phosphate
  • Pentose-5-phosphate
  • Serine or derivatives
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • Alpha-amino acid or derivatives
  • Monosaccharide phosphate
  • Imidazopyrimidine
  • Purine
  • Phosphoethanolamine
  • Acyl phosphate
  • Aminopyrimidine
  • Beta-hydroxy acid
  • Monoalkyl phosphate
  • Pyrimidine
  • Imidolactam
  • Monosaccharide
  • Phosphoric acid ester
  • N-substituted imidazole
  • Alkyl phosphate
  • Organic phosphoric acid derivative
  • Hydroxy acid
  • Imidazole
  • Heteroaromatic compound
  • Azole
  • Tetrahydrofuran
  • Amino acid or derivatives
  • Carboxylic acid salt
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Oxacycle
  • Carboxylic acid derivative
  • Azacycle
  • Organoheterocyclic compound
  • Organonitrogen compound
  • Organic salt
  • Alcohol
  • Organic oxygen compound
  • Primary amine
  • Carbonyl group
  • Primary aliphatic amine
  • Hydrocarbon derivative
  • Organic oxide
  • Organic nitrogen compound
  • Amine
  • Organopnictogen compound
  • Primary alcohol
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility3.07 g/LALOGPS
logP-2.3ALOGPS
logP-4.6ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)0.77ChemAxon
pKa (Strongest Basic)6.83ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area238.39 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity92.62 m³·mol⁻¹ChemAxon
Polarizability38.14 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
3 (2,3-Dihydroxybenzoyl)adenylic acid + 3 L-Seryl-AMP >6 Adenosine monophosphate + Enterochelin +9 Hydrogen ion
Adenosine triphosphate + Hydrogen ion + L-Serine <> Pyrophosphate + L-Seryl-AMP
Adenosine triphosphate + L-Serine <> Pyrophosphate + L-Seryl-AMP
(2,3-Dihydroxybenzoyl)adenylic acid + L-Seryl-AMP <> Hydrogen ion + Enterochelin + Adenosine monophosphate
Adenosine triphosphate + L-Serine > Pyrophosphate + L-Seryl-AMP
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_15) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-9710300000-3cfe079a874c6fbca08bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-7900000000-8013312117d41dfcc35bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-5900000000-8d25b0d18e7dfa7c855bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00o0-3904400000-12b9aeba0543a4b758ffView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-4900000000-996f0b24784859aa0857View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-003r-9500000000-e072b2c35ed00139f040View in MoNA
MSMass Spectrum (Electron Ionization)Not AvailableView in JSpectraViewer
References
References:
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID61645
HMDB IDNot Available
Pubchem Compound ID5289403
Kegg IDNot Available
ChemSpider ID4451381
Wikipedia IDNot Available
BioCyc IDSERYL-AMP
EcoCyc IDSERYL-AMP
Ligand ExpoSRP

Enzymes

Protein Details
1. Enterobactin synthase component F
General function:
Involved in ligase activity
Specific function:
Activates the carboxylate group of L-serine via ATP- dependent PPi exchange reactions to the aminoacyladenylate, preparing that molecule for the final stages of enterobactin synthesis. Holo-entF acts as the catalyst for the formation of the three amide and three ester bonds present in the cyclic (2,3- dihydroxybenzoyl)serine trimer enterobactin, using seryladenylate and acyl-holo-entB (acylated with 2,3-dihydroxybenzoate by entE)
Gene Name:
entF
Uniprot ID:
P11454
Molecular weight:
141990
Reactions
ATP + L-serine = diphosphate + L-serine-adenylate.
Protein Details
2. 4'-phosphopantetheinyl transferase entD
General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the transfer of the 4'-phosphopantetheine moiety from coenzyme A to apo-domains of both entB (an ArCP domain) and entF (a PCP domain). Plays an essential role in the assembly of the enterobactin
Gene Name:
entD
Uniprot ID:
P19925
Molecular weight:
23604
Reactions
CoA + apo-EntB/F = adenosine 3',5'-bisphosphate + holo-EntB/F.