Crystal structure of Escherichia coli ArnA (PmrI) decarboxylase domain. A key enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance.
Gram-negative bacteria including Escherichia coli, Salmonella typhimurium, and Pseudomonas aeruginosa can modify the structure of lipid A in their outer membrane with 4-amino-4-deoxy-l-arabinose (Ara4N). Such modification results in resistance to cationic antimicrobial peptides of the innate immune system and antibiotics such as polymyxin. ArnA is a key enzyme in the lipid A modification pathway, and its deletion abolishes both the Ara4N-lipid A modification and polymyxin resistance. ArnA is a bifunctional enzyme. It can catalyze (i) the NAD(+)-dependent decarboxylation of UDP-glucuronic acid to UDP-4-keto-arabinose and (ii) the N-10-formyltetrahydrofolate-dependent formylation of UDP-4-amino-4-deoxy-l-arabinose. We show that the NAD(+)-dependent decarboxylating activity is contained in the 360 amino acid C-terminal domain of ArnA. This domain is separable from the N-terminal fragment, and its activity is identical to that of the full-length enzyme. The crystal structure of the ArnA decarboxylase domain from E. coli is presented here. The structure confirms that the enzyme belongs to the short-chain dehydrogenase/reductase (SDR) family. On the basis of sequence and structure comparisons of the ArnA decarboxylase domain with other members of the short-chain dehydrogenase/reductase (SDR) family, we propose a binding model for NAD(+) and UDP-glucuronic acid and the involvement of residues T(432), Y(463), K(467), R(619), and S(433) in the mechanism of NAD(+)-dependent oxidation of the 4''-OH of the UDP-glucuronic acid and decarboxylation of the UDP-4-keto-glucuronic acid intermediate.
Gatzeva-Topalova
Petia Z
PZ
Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA.
May
Andrew P
AP
Sousa
Marcelo C
MC
D000595:Amino Acid Sequence; D000606:Amino Sugars / Q000737:chemistry*; D001665:Binding Sites; D002262:Carboxy-Lyases / Q000737:chemistry* / Q000378:metabolism; D003460:Crystallization; D018360:Crystallography, X-Ray; D024881:Drug Resistance, Bacterial; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D019877:Hydroxymethyl and Formyl Transferases / Q000737:chemistry; D008050:Lipid A / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000737:chemistry / Q000378:metabolism; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D011113:Polymyxins / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity; D014534:UDPglucose 4-Epimerase / Q000737:chemistry / Q000378:metabolism; D014535:Uridine Diphosphate Glucuronic Acid / Q000737:chemistry / Q000378:metabolism
D000606:Amino Sugars; D029968:Escherichia coli Proteins; D008050:Lipid A; D009097:Multienzyme Complexes; D010446:Peptide Fragments; D011113:Polymyxins; D014535:Uridine Diphosphate Glucuronic Acid; C040134:4-amino-4-deoxyarabinose; D019877:Hydroxymethyl and Formyl Transferases; D002262:Carboxy-Lyases; C023257:UDPglucuronate decarboxylase; D014534:UDPglucose 4-Epimerase