P. aeruginosa Metabolome Database: UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate (PAMDB000650)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB000650

Identification

Name:

UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate

Description:

UDP-n-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate is a member of the chemical class known as Peptides. These are compounds containing an amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another. It is a key component of peptidoglycan synthesis. The peptidoglycan synthesis pathway starts at the cytoplasm, where in six steps the peptidoglycan precursor a UDP-N-acetylmuramoyl-pentapeptide is synthesized. This precursor is then attached to the memberane acceptor all-trans-undecaprenyl phosphate, generating a N-acetylmuramoyl-pentapeptide-diphosphoundecaprenol, also known as lipid I. Another transferase then adds UDP-N-acetyl-alpha-D-glucosamine, yielding the complete monomeric unit a lipid , also known as lipid . This final lipid intermediate is transferred through the membrane. The peptidoglycan monomers are then polymerized on the outside surface by glycosyltransferases, which form the linear glycan chains, and transpeptidases, which catalyze the formation of peptide crosslinks.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelate
UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate
UDP-Aagm-diaminoheptanedioate
UDP-Aagm-diaminoheptanedioic acid
UDP-MurNAc-L-Ala-D-Glu-meso-A₂pm
UDP-MurNAc-L-Ala-D-Glu-meso-A2pm
UDP-MurNAc-L-Ala-D-Glu-mesoA2pm
UDP-n-Acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelate
UDP-n-Acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelic acid
UDP-N-acetylmuramoyl-L-alanyl-D-γ-glutamyl-meso-2,6-diaminopimelate
UDP-N-Acetylmuramoyl-L-alanyl-D-γ-glutamyl-meso-2,6-diaminopimelate
UDP-N-Acetylmuramoyl-L-alanyl-D-γ-glutamyl-meso-2,6-diaminopimelic acid
UDP-N-Acetylmuramoyl-L-alanyl-D-g-glutamyl-meso-2,6-diaminopimelate
UDP-N-Acetylmuramoyl-L-alanyl-D-g-glutamyl-meso-2,6-diaminopimelic acid
UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate
UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelic acid
UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioic acid
UDP-N-Acetylmuramoyl-L-alanyl-D-γ-glutamyl-meso-2,6-diaminopimelate
UDP-N-Acetylmuramoyl-L-alanyl-D-γ-glutamyl-meso-2,6-diaminopimelic acid
UDP-N-Acetylmuramoyl-L-alanyl-g-D-glutamyl-meso-diaminopimelate
UDP-N-Acetylmuramoyl-L-alanyl-g-D-glutamyl-meso-diaminopimelic acid
UDP-N-Acetylmuramoyl-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate
UDP-N-Acetylmuramoyl-L-alanyl-gamma-D-glutamyl-meso-diaminopimelic acid
UDP-N-Acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelate
UDP-N-Acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelic acid

Chemical Formula:

C₃₅H₅₁N₇O₂₆P₂

Average Molecular Weight:

1047.7583

Monoisotopic Molecular Weight:

1047.235897863

InChI Key:

QUHLBZKCGUXHGP-BHBBPGSKSA-J

InChI:

InChI=1S/C35H55N7O26P2/c1-13(28(50)40-18(33(56)57)7-8-21(45)39-17(32(54)55)6-4-5-16(36)31(52)53)37-29(51)14(2)64-27-23(38-15(3)44)34(66-19(11-43)25(27)48)67-70(61,62)68-69(59,60)63-12-20-24(47)26(49)30(65-20)42-10-9-22(46)41-35(42)58/h9-10,13-14,16-20,23-27,30,34,43,47-49H,4-8,11-12,36H2,1-3H3,(H,37,51)(H,38,44)(H,39,45)(H,40,50)(H,52,53)(H,54,55)(H,56,57)(H,59,60)(H,61,62)(H,41,46,58)/p-4/t13-,14+,16+,17-,18+,19+,20+,23+,24+,25+,26+,27+,30+,34+/m0/s1

CAS number:

Not Available

IUPAC Name:

(4R)-N-[(1S,5R)-5-amino-1,5-dicarboxypentyl]-4-carboxy-4-{[(2S)-2-{[(2R)-2-{[(2R,3R,4R,5S,6R)-2-({[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-oxido-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-5-hydroxy-6-(hydroxymethyl)-3-[(1-oxidoethylidene)amino]oxan-4-yl]oxy}-1-hydroxypropylidene]amino}-1-oxidopropylidene]amino}butanecarboximidate

Traditional IUPAC Name:

(4R)-N-[(1S,5R)-5-amino-1,5-dicarboxypentyl]-4-carboxy-4-{[(2S)-2-{[(2R)-2-{[(2R,3R,4R,5S,6R)-2-[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-oxido-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-5-hydroxy-6-(hydroxymethyl)-3-[(1-oxidoethylidene)amino]oxan-4-yl]oxy}-1-hydroxypropylidene]amino}-1-oxidopropylidene]amino}butanecarboximidate

SMILES:

[H][C@@](N)(CCC[C@]([H])(N=C([O-])CC[C@@]([H])(N=C([O-])[C@]([H])(C)N=C(O)[C@@]([H])(C)O[C@@]1([H])[C@]([H])(O)[C@@]([H])(CO)O[C@]([H])(OP(O)(=O)OP(O)(=O)OC[C@@]2([H])O[C@@]([H])(N3C=CC([O-])=NC3=O)[C@]([H])(O)[C@]2([H])O)[C@]1([H])N=C(C)[O-])C(O)=O)C(O)=O)C(O)=O

Chemical Taxonomy

Taxonomy Description

This compound 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.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine nucleotide sugars

Direct Parent

Pyrimidine nucleotide sugars

Alternative Parents

Substituents

Pyrimidine nucleotide sugar
Pyrimidine ribonucleoside diphosphate
Alpha peptide
Saccharolipid
N-acyl-alpha-hexosamine
N-acyl-alpha amino acid or derivatives
Glucosamine
Amino sugar
N-glycosyl compound
Glycosyl compound
L-alpha-amino acid
Organic pyrophosphate
Monosaccharide phosphate
Alpha-amino acid or derivatives
Alpha-amino acid
Tricarboxylic acid or derivatives
Monoalkyl phosphate
Amino saccharide
Pyrimidone
Amino fatty acid
Fatty acyl
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Organic phosphate
Monosaccharide
Hydropyrimidine
Saccharide
Heteroaromatic compound
Oxolane
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Ether
Dialkyl ether
Carboxylic acid
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Not Available

Charge:

-3

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	4.0 mg/mL	ALOGPS
logP	-0.82	ALOGPS
logP	-3.4	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	1.72	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	29	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	543.4 Å²	ChemAxon
Rotatable Bond Count	27	ChemAxon
Refractivity	263.32 m³·mol^-1	ChemAxon
Polarizability	92.98 Å³	ChemAxon
Number of Rings	3	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:

Pathways:

Lysine biosynthesis pae00300
Peptidoglycan biosynthesis pae00550

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-052b-9000000000-93b5c36a79fcf09f13d5	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btc-9000000000-51746bb1471a6d81a5a9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9100000110-8a01cd074258d2ff07f3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4m-9000000000-f58d2052cef4e479229a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0aba-9000000000-4b079078403481aad574	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-06uu-9300000000-8c1109c8031b33c29738	View in MoNA

References

References:

Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
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

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	28639
HMDB ID	Not Available
Pubchem Compound ID	25243985
Kegg ID	C04877
ChemSpider ID	34448900
Wikipedia ID	Not Available
BioCyc ID	UDP-AAGM-DIAMINOHEPTANEDIOATE
EcoCyc ID	UDP-AAGM-DIAMINOHEPTANEDIOATE

Enzymes

Protein Details

• 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
Locus Tag:: PA4416
Molecular weight:: 47.4 kDa

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.

Protein Details

• UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase

General function:: Involved in ATP binding
Specific function:: Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan. Is also able to use many meso-diaminopimelate analogs as substrates, although much less efficiently, but not L-lysine
Gene Name:: murE
Locus Tag:: PA4417
Molecular weight:: 51.3 kDa

Reactions

ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diamino-heptanedioate.

Protein Details

• Murein tetrapeptide carboxypeptidase

General function:: Defense mechanisms
Specific function:: Releases the terminal D-alanine residue from the cytoplasmic tetrapeptide recycling product L-Ala-gamma-D-Glu-meso- Dap-D-Ala. To a lesser extent, can also cleave D-Ala from murein derivatives containing the tetrapeptide, i.e. MurNAc-tetrapeptide, UDP-MurNAc-tetrapeptide, GlcNAc-MurNAc-tetrapeptide, and GlcNAc- anhMurNAc-tetrapeptide. Does not act on murein sacculi or cross- linked muropeptides. The tripeptides produced by the lcdA reaction can then be reused as peptidoglycan building blocks; lcdA is thereby involved in murein recycling. Is also essential for viability during stationary phase
Gene Name:: ldcA
Locus Tag:: PA1818
Molecular weight:: 82.8 kDa

Reactions

GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine + H(2)O = GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate + D-alanine.

Protein Details

• UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase

General function:: Involved in ATP binding
Specific function:: Reutilizes the intact tripeptide L-alanyl-gamma-D- glutamyl-meso-diaminopimelate by linking it to UDP-N-acetylmuramic acid
Gene Name:: mpl
Locus Tag:: PA4020
Molecular weight:: 48.5 kDa

UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate (PAMDB000650)

Structure for UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate (PAMDB000650)

Enzymes

Reactions

Reactions

Reactions