P. aeruginosa Metabolome Database: Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine (PAMDB001056)

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

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB001056

Identification

Name:

Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine

Description:

Undecaprenyl-diphospho-n-acetylmuramoyl-(n-acetylglucosamine)-l-alanyl-d-glutaminyl-meso-2,6-diaminopimeloyl-d-alanyl-d-alanine is a peptide. 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-D-glucosamine, yielding the complete monomeric unit a lipid II, also known as lipid II. 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-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine
UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate- D-alanyl-D-alanine
UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
UDP-MurNAcAlaGludAHeAlaAla
UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine
UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate- D-alanyl-D-alanine
UDP-n-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioic acid- D-alanyl-D-alanine
UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioic acid- D-alanyl-D-alanine
UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine

Chemical Formula:

C₉₅H₁₅₇N₉O₂₇P₂

Average Molecular Weight:

1919.2547

Monoisotopic Molecular Weight:

1918.066413887

InChI Key:

LKSKDJLUCDKSHW-WJEGFZIFSA-N

InChI:

InChI=1S/C95H157N9O27P2/c1-58(2)30-19-31-59(3)32-20-33-60(4)34-21-35-61(5)36-22-37-62(6)38-23-39-63(7)40-24-41-64(8)42-25-43-65(9)44-26-45-66(10)46-27-47-67(11)48-28-49-68(12)54-55-125-132(121,122)131-133(123,124)130-95-82(102-74(18)108)86(85(79(57-106)128-95)129-94-81(101-73(17)107)84(111)83(110)78(56-105)127-94)126-72(16)89(114)98-70(14)88(113)103-77(52-53-80(97)109)91(116)104-76(51-29-50-75(96)93(119)120)90(115)99-69(13)87(112)100-71(15)92(117)118/h30,32,34,36,38,40,42,44,46,48,54,69-72,75-79,81-86,94-95,105-106,110-111H,19-29,31,33,35,37,39,41,43,45,47,49-53,55-57,96H2,1-18H3,(H2,97,109)(H,98,114)(H,99,115)(H,100,112)(H,101,107)(H,102,108)(H,103,113)(H,104,116)(H,117,118)(H,119,120)(H,121,122)(H,123,124)/b59-32+,60-34+,61-36+,62-38+,63-40+,64-42+,65-44+,66-46+,67-48+,68-54+/t69-,70+,71-,72?,75+,76-,77-,78-,79-,81-,82-,83-,84-,85-,86-,94+,95?/m1/s1

CAS number:

Not Available

IUPAC Name:

(2S,6R)-2-amino-6-{[(1R)-1-{[(1R)-1-carboxyethyl]-C-hydroxycarbonimidoyl}ethyl]-C-hydroxycarbonimidoyl}-6-{[(2R)-2-{[(2S)-2-[(2-{[(2R,3S,4R,5R)-3-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-6-{[hydroxy({[hydroxy({[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaen-1-yl]oxy})phosphoryl]oxy})phosphoryl]oxy}-5-[(1-hydroxyethylidene)amino]-2-(hydroxymethyl)oxan-4-yl]oxy}-1-hydroxypropylidene)amino]-1-hydroxypropylidene]amino}-1-hydroxy-4-(C-hydroxycarbonimidoyl)butylidene]amino}hexanoic acid

Traditional IUPAC Name:

(2S,6R)-2-amino-6-{[(1R)-1-{[(1R)-1-carboxyethyl]-C-hydroxycarbonimidoyl}ethyl]-C-hydroxycarbonimidoyl}-6-{[(2R)-2-{[(2S)-2-[(2-{[(2R,3S,4R,5R)-3-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-6-{[hydroxy({hydroxy[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaen-1-yl]oxyphosphoryl}oxy)phosphoryl]oxy}-5-[(1-hydroxyethylidene)amino]-2-(hydroxymethyl)oxan-4-yl]oxy}-1-hydroxypropylidene)amino]-1-hydroxypropylidene]amino}-1-hydroxy-4-(C-hydroxycarbonimidoyl)butylidene]amino}hexanoic acid

SMILES:

OC[C@@]1([H])O[C@@]([H])(O[C@]2([H])[C@@]([H])(CO)OC([H])(OP(O)(=O)OP(O)(=O)OC\C([H])=C(/C)CC\C([H])=C(/C)CC\C([H])=C(/C)CC\C([H])=C(/C)CC\C([H])=C(/C)CC\C([H])=C(/C)CC\C([H])=C(/C)CC\C([H])=C(/C)CC\C([H])=C(/C)CC\C([H])=C(/C)CCC=C(C)C)[C@]([H])(N=C(C)O)[C@@]2([H])OC(C)([H])C(O)=N[C@](C)([H])C(O)=N[C@]([H])(CCC(=N)O)C(O)=N[C@]([H])(CCC[C@@](N)([H])C(=O)O)C(O)=N[C@@](C)([H])C(O)=N[C@@](C)([H])C(=O)O)[C@]([H])(N=C(C)O)[C@](O)([H])[C@@]1(O)[H]

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as polyprenyl phospho carbohydrates. These are polyprenyl phosphates with a carbohydrate moiety attached to it.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Polyprenols

Direct Parent

Polyprenyl phospho carbohydrates

Alternative Parents

Substituents

Polyterpenoid
Bactoprenol diphosphate
Polyprenyl phospho carbohydrate
Alpha peptide
Saccharolipid
N-acyl-alpha-hexosamine
Disaccharide phosphate
N-acyl-aliphatic-alpha amino acid
N-acyl-alpha amino acid or derivatives
N-acyl-alpha-amino acid
Glucosamine
Amino sugar
O-glycosyl compound
Glycosyl compound
Disaccharide
D-alpha-amino acid
Organic pyrophosphate
Isoprenoid phosphate
Alpha-amino acid or derivatives
Alpha-amino acid
Medium-chain fatty acid
Monoalkyl phosphate
Amino saccharide
Amino fatty acid
Fatty acyl
Alkyl phosphate
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Organic phosphate
Dicarboxylic acid or derivatives
Secondary alcohol
1,2-diol
Oxacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Ether
Dialkyl ether
Carboxylic acid
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Acetal
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	0.00325 mg/mL	ALOGPS
logP	3.39	ALOGPS
logP	15.47	ChemAxon
logS	-5.8	ALOGPS
pKa (Strongest Acidic)	1.72	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	33	ChemAxon
Hydrogen Donor Count	18	ChemAxon
Polar Surface Area	592.96 Å²	ChemAxon
Rotatable Bond Count	64	ChemAxon
Refractivity	526.07 m³·mol^-1	ChemAxon
Polarizability	211.43 Å³	ChemAxon
Number of Rings	2	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:

Membrane

Reactions:

Pathways:

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ue9-2100320479-674e3b1ef5d838890eee	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0f7k-3110120934-3f31646d2c856c516a38	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-053e-9402310822-24ee84e223ae02fa86f3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-2030001469-86998a81a17d1beb247b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-052b-7701001196-3028980a240f858f53e2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-6910002003-7b30b267a02c430fc13e	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

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	Not Available
HMDB ID	Not Available
Pubchem Compound ID	11953874
Kegg ID	C04882
ChemSpider ID	10128173
Wikipedia ID	Not Available
BioCyc ID	C1
EcoCyc ID	C1

Enzymes

Protein Details

• Penicillin-binding protein 1B

General function:: Involved in catalytic activity
Specific function:: Cell wall formation. Synthesis of cross-linked peptidoglycan from the lipid intermediates. The enzyme has a penicillin-insensitive transglycosylase N-terminal domain (formation of linear glycan strands) and a penicillin-sensitive transpeptidase C-terminal domain (cross-linking of the peptide subunits)
Gene Name:: mrcB
Locus Tag:: PA4700
Molecular weight:: 85.5 kDa

Reactions

(GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n)-diphosphoundecaprenol + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = (GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n+1)-diphosphoundecaprenol + undecaprenyl diphosphate.

Protein Details

• 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
Locus Tag:: PA4415
Molecular weight:: 39.7 kDa

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

• UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase

General function:: Involved in undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase activity
Specific function:: Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc- (pentapeptide)GlcNAc (lipid intermediate II)
Gene Name:: murG
Locus Tag:: PA4412
Molecular weight:: 37.8 kDa

Reactions

UDP-N-acetylglucosamine + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = UDP + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol.

Protein Details

• Penicillin-binding protein 1C

General function:: Involved in catalytic activity
Specific function:: Cell wall formation. The enzyme has a penicillin- insensitive transglycosylase N-terminal domain (formation of linear glycan strands) and a transpeptidase C-terminal domain which may not be functional
Gene Name:: pbpC
Locus Tag:: PA2272
Molecular weight:: 61.1 kDa

Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine (PAMDB001056)

Structure for Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine (PAMDB001056)

Enzymes

Reactions

Reactions

Reactions