UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine (ECMDB24251) (M2MDB006368)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2015-09-08 17:50:25 -0600
Update Date2015-09-14 16:46:45 -0600
Secondary Accession Numbers
  • ECMDB24251
Identification
Name:UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
DescriptionUDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine is an intermediate in peptidoglycan biosynthesis I (meso-diaminopimelate containing) in E.coli. It is a substrate for the enzyme phospho-N-acetylmuramoyl-pentapeptide transferase which catalyzes the reaction UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + di-trans,octa-cis-undecaprenyl phosphate -> undecaprenyldiphospho-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP. It is also a product for enzyme D-alanyl-D-alanine-adding enzyme which catalyzes reaction D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimelate + ATP → UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + ADP + phosphate + H+ (BioCyc compound: C1).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:Not Available
Chemical Formula:C41H61N9O28P2
Weight:Average: 1189.924
Monoisotopic: 1189.312320676
InChI Key:IMWOXEZVYQDRDF-UHFFFAOYSA-J
InChI:InChI=1S/C41H65N9O28P2/c1-15(32(58)45-17(3)37(62)63)44-35(61)21(8-6-7-20(42)38(64)65)47-25(53)10-9-22(39(66)67)48-33(59)16(2)43-34(60)18(4)74-31-27(46-19(5)52)40(76-23(13-51)29(31)56)77-80(71,72)78-79(69,70)73-14-24-28(55)30(57)36(75-24)50-12-11-26(54)49-41(50)68/h11-12,15-18,20-24,27-31,36,40,51,55-57H,6-10,13-14,42H2,1-5H3,(H,43,60)(H,44,61)(H,45,58)(H,46,52)(H,47,53)(H,48,59)(H,62,63)(H,64,65)(H,66,67)(H,69,70)(H,71,72)(H,49,54,68)/p-4
CAS number:Not Available
IUPAC Name:2-azaniumyl-6-[4-carboxylato-4-(2-{2-[(2-{[({[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxy)phosphinato]oxy}-3-acetamido-5-hydroxy-6-(hydroxymethyl)oxan-4-yl)oxy]propanamido}propanamido)butanamido]-6-({1-[(1-carboxylatoethyl)carbamoyl]ethyl}carbamoyl)hexanoate
Traditional IUPAC Name:2-ammonio-6-(4-carboxylato-4-{2-[2-({2-[({[5-(2,4-dioxo-3H-pyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxyphosphinato)oxy]-3-acetamido-5-hydroxy-6-(hydroxymethyl)oxan-4-yl}oxy)propanamido]propanamido}butanamido)-6-({1-[(1-carboxylatoethyl)carbamoyl]ethyl}carbamoyl)hexanoate
SMILES:CC(NC(=O)C(C)NC(=O)C(CCCC([NH3+])C([O-])=O)NC(=O)CCC(NC(=O)C(C)NC(=O)C(C)OC1C(O)C(CO)OC(OP([O-])(=O)OP([O-])(=O)OCC2OC(C(O)C2O)N2C=CC(=O)NC2=O)C1NC(C)=O)C([O-])=O)C([O-])=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine nucleotide sugars
Direct ParentPyrimidine nucleotide sugars
Alternative Parents
Substituents
  • Pyrimidine nucleotide sugar
  • Pyrimidine ribonucleoside diphosphate
  • Alpha peptide
  • Pentose-5-phosphate
  • Pentose phosphate
  • N-acyl-alpha-hexosamine
  • N-acyl-alpha amino acid or derivatives
  • N-acyl-alpha-amino acid
  • Alanine or derivatives
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Alpha-amino acid or derivatives
  • Alpha-amino acid
  • Tricarboxylic acid or derivatives
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Amino acid
  • Secondary alcohol
  • Amino acid or derivatives
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Ether
  • Dialkyl ether
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Organic anion
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-4
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility1.86 g/LALOGPS
logP-0.99ALOGPS
logP-9.6ChemAxon
logS-2.9ALOGPS
pKa (Strongest Acidic)1.52ChemAxon
pKa (Strongest Basic)9.3ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count25ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area588.6 ŲChemAxon
Rotatable Bond Count31ChemAxon
Refractivity294.87 m³·mol⁻¹ChemAxon
Polarizability106.98 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate + D-Alanyl-D-alanine + Adenosine triphosphate > Adenosine diphosphate + Phosphate + Hydrogen ion + UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + ADP
UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + di-trans,octa-cis-undecaprenyl phosphate > Uridine 5'-monophosphate + Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
SMPDB Pathways:
peptidoglycan biosynthesis IPW000906 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0f6x-2940000000-8b57a6ddd508848b307cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-9740000000-e916809296850c7fc402View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000f-9200000000-3ae64b09ac9cb99d44d6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-9730000000-ed2b9134718d45200a14View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0f76-9220000000-d1de6e789f13a1fe3104View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-000x-9300000000-aee82f584bf1d0e5eec1View in MoNA
References
References:Not Available
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound IDNot Available
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Phospho-N-acetylmuramoyl-pentapeptide-transferase
General function:
Involved in phospho-N-acetylmuramoyl-pentapeptide-transferase activity
Specific function:
First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
Gene Name:
mraY
Uniprot ID:
P0A6W3
Molecular weight:
39875
Reactions
UDP-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala) + undecaprenyl phosphate = UMP + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol.
Protein Details
2. UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
General function:
Involved in ATP binding
Specific function:
Involved in cell wall formation. Catalyzes the final step in the synthesis of UDP-N-acetylmuramoyl-pentapeptide, the precursor of murein
Gene Name:
murF
Uniprot ID:
P11880
Molecular weight:
47447
Reactions
ATP + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysine + D-alanyl-D-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine.