Fig. 2 | The Journal of Antibiotics

Fig. 2

From: Targeting adenylate-forming enzymes with designed sulfonyladenosine inhibitors

Fig. 2

Structures of the nine classes of adenylate-forming enzymes. Top of ah: Overall protein fold with acyl-AMP intermediate or mimic (spheres) bound. Bottom of ah: Active site with acyl-AMP intermediate or mimic (ball-and-stick) bound; protein side chains within 4 Å of the ligand are shown (sticks); portions of structures that obscure the ligands are not shown. PDB ID codes are shown in parentheses. a Class I aminoacyl-tRNA synthetase Bacillus stearothermophilus tyrosyl-tRNA synthetase catalytic N-terminal domain with carbonyl-reduced intermediate mimic Tyr-CH2-AMP (tyrosinyl-AMP) (PDB ID: 3TS1) [44]. b Class II aminoacyl-tRNA synthetase Thermus thermophilus seryl-tRNA synthetase with adenylate mimic Ser-AMS (seryl-AMS) (PDB ID: 1SET) [134]. c ANL family enzyme B. subtilis DhbE with adenylate intermediate DHB-AMP (2,3-dihydroxybenzoyl-AMP) (PDB ID: 1MDB) [55]. d SUMO (small ubiquitin-like modifier) E1 activating enzyme human (Sae1/Uba2) with adenylate mimic SUMO-AMSN (SUMO1[T95C]-AMSN) (PDB ID: 3KYC) [60]. e Biotin protein ligase Escherichia coli BirA homodimer with carbonyl-reduced intermediate mimic Bio-CH2-AMP (biotinol-O-AMP) (PDB ID: 2EWN) [66]. f N-type ATP pyrophosphatase B. subtilis NAD+ synthetase homodimer with adenylate intermediate NAD-AMP (PDB ID: 2NSY) [68]. g YrdC-like carbamoyltransferase Sulfolobus tokodaii Sua5 with adenylate intermediate TC-AMP (threon-2-N-ylcarbamoyl-AMP) (PDB ID: 4E1B) [79, 80]. h NRPS-independent siderophore synthetase Petrobacterium chrysanthemi AcsD with substrate citrate and ATP fragments Ado (adenosine) and SO4 (sulfate) (PDB ID: 2W03) [91]. i BioW pimeloyl-CoA synthetase with adenylate intermediate pimeloyl-AMP (PDB ID: 5FLL) [40]. Abbreviations: AMP adenosine-5′-O-monophosphate, AMS adeonsine-5′-O-monosulfamate, AMSN 5′-(aminodeoxy)adenosine-5′-N-monosulfamide, ANL acyl-CoA synthetase/NRPS adenylation domain/luciferase, ATP adenosine-5′-O-triphosphate, CoA coenzyme A, NAD nicotinamide adenine dinucleotide, NRPS non-ribosomal peptide synthetase, tRNA transfer ribonucleic acid

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