Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine (ECMDB20210) (M2MDB001056)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (5)XML
Proteins (6)
Record Information
Version2.0
Creation Date2012-05-31 14:33:19 -0600
Update Date2015-06-03 17:19:33 -0600
Secondary Accession Numbers
  • ECMDB20210
Identification
Name:Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
DescriptionUndecaprenyl-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
Thumb
MOLSDFPDBSMILESInChI
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
Weight:Average: 1919.2547
Monoisotopic: 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
Description belongs to the class of organic compounds known as polyprenyl phospho carbohydrates. These are polyprenyl phosphates with a carbohydrate moiety attached to it.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassPolyprenols
Direct ParentPolyprenyl phospho carbohydrates
Alternative Parents
Substituents
  • Polyterpenoid
  • Bactoprenol diphosphate
  • Polyprenyl phospho carbohydrate
  • Alpha-oligopeptide
  • Polyprenyl monophosphate
  • Polyprenyl phosphate skeleton
  • Alpha peptide
  • Saccharolipid
  • Glutamine or derivatives
  • N-acyl-alpha-hexosamine
  • Disaccharide phosphate
  • N-acyl-alpha amino acid or derivatives
  • N-acyl-alpha-amino acid
  • Alpha-amino acid amide
  • Alanine or derivatives
  • O-glycosyl compound
  • Glycosyl compound
  • Disaccharide
  • L-alpha-amino acid
  • Organic pyrophosphate
  • Isoprenoid phosphate
  • Alpha-amino acid or derivatives
  • N-substituted-alpha-amino acid
  • Alpha-amino acid
  • Medium-chain fatty acid
  • Monoalkyl phosphate
  • Hydroxy fatty acid
  • Fatty acyl
  • Alkyl phosphate
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • N-acyl-amine
  • Fatty amide
  • Dicarboxylic acid or derivatives
  • Acetamide
  • Amino acid
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Primary carboxylic acid amide
  • Carboxamide group
  • Amino acid or derivatives
  • Oxacycle
  • Organoheterocyclic compound
  • Ether
  • Dialkyl ether
  • Carboxylic acid
  • Carboxylic acid derivative
  • Acetal
  • 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
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-3
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.0032 g/LALOGPS
logP3.39ALOGPS
logP15.47ChemAxon
logS-5.8ALOGPS
pKa (Strongest Acidic)1.72ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count33ChemAxon
Hydrogen Donor Count18ChemAxon
Polar Surface Area592.96 ŲChemAxon
Rotatable Bond Count64ChemAxon
Refractivity526.07 m³·mol⁻¹ChemAxon
Polarizability211.43 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol + Uridine diphosphate-N-acetylglucosamine > Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine 5'-diphosphate + Hydrogen ion
2 Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine > a peptidoglycan dimer (meso-diaminopimelate containing) + Undecaprenyl diphosphate + Hydrogen ion
SMPDB Pathways:
peptidoglycan biosynthesis I 2PW002062 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:Not Available
EcoCyc Pathways:
  • UDP-N-acetylmuramoyl-pentapeptide biosynthesis III (meso-DAP-containing) PWY-6387
  • peptidoglycan biosynthesis I (meso-diaminopimelate containing) PEPTIDOGLYCANSYN-PWY
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0ue9-2100320479-674e3b1ef5d838890eeeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f7k-3110120934-3f31646d2c856c516a38View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-053e-9402310822-24ee84e223ae02fa86f3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-2030001469-86998a81a17d1beb247bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-052b-7701001196-3028980a240f858f53e2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-6910002003-7b30b267a02c430fc13eView in MoNA
MSMass Spectrum (Electron Ionization)Not AvailableView in JSpectraViewer
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
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID11953874
Kegg IDC04882
ChemSpider ID10128173
Wikipedia IDNot Available
BioCyc IDC1
EcoCyc IDC1

Enzymes

Protein Details
1. Penicillin-binding protein 1A
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:
mrcA
Uniprot ID:
P02918
Molecular weight:
93636
Protein Details
2. 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
Uniprot ID:
P02919
Molecular weight:
94292
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
3. 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
4. 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
Uniprot ID:
P17443
Molecular weight:
37815
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
5. 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
Uniprot ID:
P76577
Molecular weight:
85066