2PHN

Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus

Summary for 2PHN

• Entry DOI: 10.2210/pdb2phn/pdb
• Related: 2G9I
• Descriptor: F420-0:gamma-glutamyl ligase, MANGANESE (II) ION, ACETATE ION, ... (7 entities in total)
• Functional Keywords: gamma-glutamyl ligase, coenzyme f420 biosynthesis, amide bond forming enzyme, metal dependent, new fold, gdp binding, mcsg, structural genomics, psi-2, protein structure initiative, midwest center for structural genomics, ligase
• Biological source: Archaeoglobus fulgidus DSM 4304
• Total number of polymer chains: 2
• Total formula weight: 57208.49

Authors

Nocek, B.,Evdokimova, E.,Kudritska, M.,Edwards, A.,Savchenko, A.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2007-04-11, release date: 2007-05-15, Last modification date: 2024-11-13)

Primary citation

Nocek, B.,Evdokimova, E.,Proudfoot, M.,Kudritska, M.,Grochowski, L.L.,White, R.H.,Savchenko, A.,Yakunin, A.F.,Edwards, A.,Joachimiak, A.
Structure of an Amide Bond Forming F(420):gammagamma-glutamyl Ligase from Archaeoglobus Fulgidus - A Member of a New Family of Non-ribosomal Peptide Synthases.
J.Mol.Biol., 372:456-469, 2007

PubMed Abstract: F(420) is a flavin-like redox-active coenzyme commonly used by archaea and some eubacteria in a variety of biochemical reactions in methanogenesis, the formation of secondary metabolites, the degradation of nitroaromatic compounds, activation of nitroimidazofurans, and F(420)-dependent photolysis in DNA repair. Coenzyme F(420)-2 biosynthesis from 7,8-didemethyl-8-hydroxy-5-deazariboflavin (Fo) and lactaldehyde involves six enzymatic steps and five proteins (CofA, CofB, CofC, CofD, and CofE). CofE, a F(420)-0:gamma-glutamyl ligase, is responsible for the last two enzymatic steps; it catalyses the GTP-dependent addition of two L-glutamate residues to F(420)-0 to form F(420)-2. CofE is found in archaea, the aerobic actinomycetes, and cyanobacteria. Here, we report the first crystal structure of the apo-F(420)-0:gamma-glutamyl ligase (CofE-AF) from Archaeoglobus fulgidus and its complex with GDP at 2.5 A and 1.35 A resolution, respectively. The structure of CofE-AF reveals a novel protein fold with an intertwined, butterfly-like dimer formed by two-domain monomers. GDP and Mn(2+) are bound within the putative active site in a large groove at the dimer interface. We show that the enzyme adds a glutamate residue to both F(420)-0 and F(420)-1 in two distinct steps. CofE represents the first member of a new structural family of non-ribosomal peptide synthases.

PubMed: 17669425
DOI: 10.1016/j.jmb.2007.06.063

Experimental method

X-RAY DIFFRACTION (1.35 Å)