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Literature summary for 2.7.7.23 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.
    View publication on PubMed

Application

Application Comment Organism
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)

Crystallization (Comment) Organism
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

Metals/Ions

Metals/Ions Comment Organism Structure
Co2+ a cobalt ion substitutes for Mg2+A in the crystal structure Mycobacterium tuberculosis
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)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
UTP + N-acetyl-alpha-D-glucosamine 1-phosphate Mycobacterium tuberculosis
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diphosphate + UDP-N-acetyl-alpha-D-glucosamine
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r

Organism

Organism UniProt Comment Textmining
Mycobacterium tuberculosis P9WMN3
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-

Reaction

Reaction Comment Organism Reaction ID
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)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
UTP + N-acetyl-alpha-D-glucosamine 1-phosphate
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Mycobacterium tuberculosis diphosphate + UDP-N-acetyl-alpha-D-glucosamine
-
r

Subunits

Subunits Comment Organism
trimer GlmU forms a biological trimer, and two independent domains in each monomer catalyze two independent reactions in the protein Mycobacterium tuberculosis

Synonyms

Synonyms Comment Organism
GlmU
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Mycobacterium tuberculosis
N-acetylglucosamine-1-phosphate uridyltransferase
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Mycobacterium tuberculosis

General Information

General Information Comment Organism
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
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
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