{"entry": {"accession": "MF7000995", "general": {"name": "F420-gamma glutamyl ligase (Archaeoglobus fulgidus)", "pdb_id": "2phn", "exp_method": "X-ray", "resolution": "1.35", "assembly": "Homodimer", "source_organism": "Archaeoglobus fulgidus", "publication": {"pmid": "17669425", "authors": "Nocek B, Evdokimova E, Proudfoot M, Kudritska M, Grochowski LL, White RH, Savchenko A, Yakunin AF, Edwards A, Joachimiak A", "title": "Structure of an amide bond forming F(420):gamma-glutamyl ligase from Archaeoglobus fulgidus -- a member of a new family of non-ribosomal peptide synthases.", "journal": "J. Mol. Biol.", "year": "2007", "issue": "2", "volume": "372", "pages": "456-69", "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."}}, "function": {"molecular_function": {"go": [{"accession": "GO:0052618", "name": "coenzyme F420-0"}, {"accession": "GO:0052619", "name": "coenzyme F420-1"}, {"accession": "GO:0005525", "name": "GTP binding"}, {"accession": "GO:0046872", "name": "metal ion binding"}]}, "biological_process": {"go": {"accession": "GO:0052645", "name": "F420-0 metabolic process"}}}, "macromolecules": {"general": {"nr_of_chains": "2", "nr_of_unique_protein_segments": "1", "class": "Homooligomeric enzymes", "subclass": "Homodimeric enzymes", "note": "All chains according to the most probable oligomerization state stored in PDBe were considered."}, "chain": [{"id": "A", "name": "Coenzyme F420:L-glutamate ligase", "source_organism": "Archaeoglobus fulgidus", "uniprot": {"id": "O28028", "start": "2", "end": "249", "coverage": "99%", "sequence": "MRVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECVADEIAAFANLLMGEGGDGIPAVVVRGLNVAGEGSMEEIYRSEEEDVIRRCLKRCL", "length": "249"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "22", "region_end": "29"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "43", "region_end": "50"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "57", "region_end": "59"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "62", "region_end": "73"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "75", "region_end": "85"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "109", "region_end": "111"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "127", "region_end": "144"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "196", "region_end": "210"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "231", "region_end": "235"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "242", "region_end": "252"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "6", "region_end": "10"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "38", "region_end": "42"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "53", "region_end": "55"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "86", "region_end": "91"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "97", "region_end": "100"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "105", "region_end": "107"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "120", "region_end": "122"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "148", "region_end": "157"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "160", "region_end": "171"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "177", "region_end": "178"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "194", "region_end": "195"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "218", "region_end": "222"}, {"region_type": "pfam", "region_id": "PF01996", "region_name": "F420-0:Gamma-glutamyl ligase", "region_start": "11", "region_end": "220"}]}}, {"id": "B", "name": "Coenzyme F420:L-glutamate ligase", "source_organism": "Archaeoglobus fulgidus", "uniprot": {"id": "O28028", "start": "1", "end": "249", "coverage": "100%", "sequence": "MRVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECVADEIAAFANLLMGEGGDGIPAVVVRGLNVAGEGSMEEIYRSEEEDVIRRCLKRCL", "length": "249"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "22", "region_end": "29"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "43", "region_end": "50"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "57", "region_end": "59"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "62", "region_end": "73"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "75", "region_end": "85"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "109", "region_end": "111"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "127", "region_end": "144"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "196", "region_end": "210"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "231", "region_end": "235"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "242", "region_end": "252"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "6", "region_end": "10"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "38", "region_end": "42"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "53", "region_end": "55"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "86", "region_end": "91"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "97", "region_end": "100"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "105", "region_end": "107"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "120", "region_end": "122"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "148", "region_end": "157"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "160", "region_end": "171"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "177", "region_end": "178"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "194", "region_end": "195"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "218", "region_end": "222"}, {"region_type": "pfam", "region_id": "PF01996", "region_name": "F420-0:Gamma-glutamyl ligase", "region_start": "11", "region_end": "220"}]}}]}, "evidence": {"evidence_level": "Indirect evidence", "evidence_coverage": "The full structure participates in mutual synergistic folding.", "sequence_domain": "-", "complex_evidence": "The F420-gamma glutamyl ligase forms a tightly packed, highly intertwined, butterfly-like dimer formed by two-domain monomers. The dimer interface is very extensive and the putative active site lies in a large groove at the dimer interface. Also, the protein is a dimer in solution (SEC) which is in good agreement with its tight packing (PMID:17669425).", "chain_evidence": [{"chain_id": "A", "support": "N/A"}, {"chain_id": "B", "support": "N/A"}]}}}