4HCQ

Crystal structure of GLMU from mycobacterium tuberculosis in complex with glucosamine-1-phosphate

Summary for 4HCQ

• Entry DOI: 10.2210/pdb4hcq/pdb
• Descriptor: Bifunctional protein GlmU, 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose, COBALT (II) ION, ... (5 entities in total)
• Functional Keywords: acetyltransferase, bifunctional, pyrophosphorylase, rossmann-like fold, left-handed-beta-helix, cell shape, cell wall biogenesis/degradation, magnesium, metal-binding, multifunctional enzyme, nucleotidyltransferase, peptidoglycan synthesis, transferase, acyltransferase
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 1
• Total formula weight: 53176.52

Authors

Jagtap, P.K.A.,Verma, S.K.,Vithani, N. (deposition date: 2012-10-01, release date: 2013-03-13, Last modification date: 2023-11-08)

Primary citation

Jagtap, P.K.A.,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
J.Mol.Biol., 425:1745-1759, 2013

PubMed Abstract: N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU), exclusive to prokaryotes, is a bifunctional enzyme that synthesizes UDP-GlcNAc-an important component of the cell wall of many microorganisms. Uridyltransfer, one of the reactions it catalyzes, involves binding GlcNAc-1-P, UTP and Mg(2+) ions; however, whether one or two ions catalyze this reaction remains ambiguous. Here, we resolve this using biochemical and crystallographic studies on GlmU from Mycobacterium tuberculosis (GlmU(Mtb)) and identify 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 Mg(2+) ions (Mg(2+)A and Mg(2+)B) are positioned and stabilized. Further, attempts to delineate the roles of the metal ions in substrate stabilization, nucleophile activation and transition-state stabilization are presented. Interestingly, a detailed analysis of the available structures of sugar nucleotidyl transferases (SNTs) suggests that they too would utilize mechanism-B rather than mechanism-A. Based on this, SNTs could 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 Mg(2+)A is substituted by a conserved lysine. Strikingly, eukaryotic SNTs appear confined to Group-II. Recognizing these differences may be important in the design of selective inhibitors against microbial nucleotidyl transferases.

PubMed: 23485416
DOI: 10.1016/j.jmb.2013.02.019

Experimental method

X-RAY DIFFRACTION (2.6 Å)