Literature summary extracted from
Jagtap, P.K.; Verma, S.K.; Vithani, N.; Bais, V.S.; Prakash, B.
Crystal structures identify an atypical two-metal-ion mechanism for uridyltransfer in GlmU: its significance to sugar nucleotidyl transferases (2013), J. Mol. Biol., 425, 1745-1759.
Application
EC Number |
Application |
Comment |
Organism |
---|
2.7.7.23 |
drug development |
prokaryotic/microbial sugar nucleotidyl transferases are targets for design of selective inhibitors due to their different metal mechanisms compared to eukaryotes |
Mycobacterium tuberculosis |
Crystallization (Commentary)
EC Number |
Crystallization (Comment) |
Organism |
---|
2.7.7.23 |
GlmUMtb active site crystal structure analysis, PDB ID 3DJ4, and crystal structure of GlmU with both substrates (i.e., GlcNAc-1-P and UTP) in the presence of metal ions, soaking of GlmUMtb[Apo] crystals in a solution containing GlcNAc-1-P, UTP and MgCl2. the soaking solution consists of 10% PEG 8000, 100 mM HEPES, pH 7.5, 20 mM MgCl2, and 4 mM CoCl2, and substrate 50 mM GlcNAc-1-phosphate, with or without 10 mM UTP, for 4 h at 4°C, X-ray diffraction structure determination and analysis at 2.0 A resolution using molecular replacement with GlmUMtb[Apo] as a search model |
Mycobacterium tuberculosis |
Localization
EC Number |
Localization |
Comment |
Organism |
GeneOntology No. |
Textmining |
---|
Metals/Ions
EC Number |
Metals/Ions |
Comment |
Organism |
Structure |
---|
2.7.7.23 |
Co2+ |
a cobalt ion substitutes for Mg2+A in the crystal structure |
Mycobacterium tuberculosis |
|
2.7.7.23 |
Mg2+ |
required, two metal binding sites, site-A and site-B. The enzyme uses a two-metal ion mechanism (mechanism-B). Roles of the metal ions in substrate stabilization, nucleophile activation and transition-state stabilization, detailed overview. Mg2+A interacts with Asp114 and Asn239 and oxygens O1B and O2A of UDP-GlcNAc in addition to two water molecules. Mg2+B is coordinated with three water molecules and the oxygen atoms are contributed by UDP-GlcNAc and diphosphate. Mg2+A enables nucleophile activation and Mg2+B stabilizes the transition state |
Mycobacterium tuberculosis |
|
Natural Substrates/ Products (Substrates)
EC Number |
Natural Substrates |
Organism |
Comment (Nat. Sub.) |
Natural Products |
Comment (Nat. Pro.) |
Rev. |
Reac. |
---|
2.7.7.23 |
UTP + N-acetyl-alpha-D-glucosamine 1-phosphate |
Mycobacterium tuberculosis |
- |
diphosphate + UDP-N-acetyl-alpha-D-glucosamine |
- |
r |
|
Organism
EC Number |
Organism |
UniProt |
Comment |
Textmining |
---|
2.7.7.23 |
Mycobacterium tuberculosis |
P9WMN3 |
- |
- |
Reaction
EC Number |
Reaction |
Comment |
Organism |
Reaction ID |
---|
2.7.7.23 |
UTP + N-acetyl-alpha-D-glucosamine 1-phosphate = diphosphate + UDP-N-acetyl-alpha-D-glucosamine |
catalytic mechanism for the uridyltransfer reaction in the bifunctional enzyme GlmU, overview. The enzyme has distinct roles for Mg2+A and Mg2+B in substrate stabilization, nucleophile activation and transition-state stabilization |
Mycobacterium tuberculosis |
|
Substrates and Products (Substrate)
EC Number |
Substrates |
Comment Substrates |
Organism |
Products |
Comment (Products) |
Rev. |
Reac. |
---|
2.7.7.23 |
UTP + N-acetyl-alpha-D-glucosamine 1-phosphate |
- |
Mycobacterium tuberculosis |
diphosphate + UDP-N-acetyl-alpha-D-glucosamine |
- |
r |
|
Subunits
EC Number |
Subunits |
Comment |
Organism |
---|
2.7.7.23 |
trimer |
GlmU forms a biological trimer, and two independent domains in each monomer catalyze two independent reactions in the protein |
Mycobacterium tuberculosis |
Synonyms
EC Number |
Synonyms |
Comment |
Organism |
---|
2.7.7.23 |
GlmU |
- |
Mycobacterium tuberculosis |
2.7.7.23 |
N-acetylglucosamine-1-phosphate uridyltransferase |
- |
Mycobacterium tuberculosis |
General Information
EC Number |
General Information |
Comment |
Organism |
---|
2.7.7.23 |
evolution |
GlmU belongs to the large family of sugar nucleotidyl transferases, which can be classified into group-I, which employs the two-metal mechanism-B as in GlmU, and group-II that employs a variant one metal mechanism-B, wherein the role of Mg2+ A is substituted by a conserved lysine. Eukaryotic sugar nucleotidyl transferases appear confined to group-II, structure-based sequence comparisons of sugar nucleotidyl transferases |
Mycobacterium tuberculosis |
2.7.7.23 |
additional information |
GlmU forms a biological trimer, and two independent domains in each monomer catalyze two independent reactions in the protein. The enzyme uses a two-metal ion mechanism (mechanism-B). In contrast to well-established two-metal mechanism (mechanism-A) for enzymes acting on nucleic acids, mechanism-B is distinct in the way the two Mg2+ ions (Mg2+A and Mg2+B) are positioned and stabilized. Analysis of the catalytic mechanism for the uridyltransfer reaction in GlmU, role of metal ions in substrate binding, overview |
Mycobacterium tuberculosis |
2.7.7.23 |
physiological function |
N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) is exclusive to prokaryotes and a bifunctional enzyme that synthesizes UDP-GlcNAc, an important component of the cell wall of many microorganisms |
Mycobacterium tuberculosis |