Structure of an antibiotic-synthesizing UDP-glucuronate 4-epimerase MoeE5 in complex with substrate

Sun, Hanjun; Ko, Tzu‐Ping; Liu, W.; Zheng, Yingying; Chen, Chun‐Chi; Guo, Rey‐Ting

doi:10.1016/j.bbrc.2019.10.035

Cited by 25 publications

(14 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The glucuronic acid faces the nicotinamide ring of NAD + with a geometry that is perfectly suited for the hydride transfer and 4-keto-hexose-uronic acid intermediate generation (Scheme 1). As observed in MoeE5 (22), the sugar adopts the chair conformation to position its 4'-carbon at 3.2 Å distance from the C4 atom of the NAD +. The substrate 4'-H atom is thereby predicted to point exactly towards the C4 of the nicotinamide ring (Fig.…”

Section: Structure Of the Michaelis Complexmentioning

confidence: 62%

“…The intermediate is then reduced by NADH, leading to the inversion of the C4' configuration (18,21). The same catalytic strategy has been hypothesized also for the epimerases acting on UDP-GlcA (22). As demonstrated by recent work, these enzymes fine tune the rates of the individual redox steps to prevent the accumulation of the 4-keto-hexoseuronic acid, minimizing the undesired decarboxylation and/or release of this reactive intermediate (23).…”

Section: Introductionmentioning

confidence: 81%

“…1). Structural comparisons using the Dali server (32) indicate that the overall structure of BcUGAepi is similar to the structures of UDPgalactose 4-epimerase from Escherichia coli (PDB entry 1UDA) (27)(28)(29) and MoeE5 (a UDPglucuronic acid epimerase from Streptomyces viridosporus; PDB entry 6KV9) (22) with Z scores of 37.2 and 42.8 and sequence identities of 30% and 38%, respectively. NAD + remains tightly associated to the enzyme during the entire purification process ( Fig.…”

Section: Overall Structurementioning

confidence: 93%

See 2 more Smart Citations

Crystallographic snapshots of UDP-glucuronic acid 4-epimerase ligand binding, rotation, and reduction

Iacovino

Savino

Borg

et al. 2020

Journal of Biological Chemistry

View full text Add to dashboard Cite

UDP-glucuronic acid is converted to UDP-galacturonic acid en route to a variety of sugar-containing metabolites. This reaction is performed by a NAD+-dependent epimerase belonging to the short-chain dehydrogenase/reductase family. We present several high-resolution crystal structures of the UDP-glucuronic acid epimerase from Bacillus cereus. The geometry of the substrate-NAD+ interactions is finely arranged to promote hydride transfer. The exquisite complementarity between glucuronic acid and its binding site is highlighted by the observation that the unligated cavity is occupied by a cluster of ordered waters whose positions overlap the polar groups of the sugar substrate. Co-crystallization experiments led to a structure where substrate- and product-bound enzymes coexist within the same crystal. This equilibrium structure reveals the basis for a “swing & flip” rotation of the pro-chiral 4-keto-hexose-uronic acid intermediate that results from glucuronic acid oxidation, placing the C4’ atom in position for receiving a hydride ion on the opposite side of the sugar ring. The product-bound active site is almost identical to that of the substrate-bound structure and satisfies all hydrogen-bonding requirements of the ligand. The structure of the apo-enzyme together with kinetic isotope effect and mutagenesis experiments further outlines a few flexible loops that exist in discrete conformations, imparting structural malleability required for ligand rotation while avoiding leakage of the catalytic intermediate and/or side-reactions. These data highlight the double nature of the enzymatic mechanism: the active site features a high degree of precision in substrate recognition combined with the flexibility required for intermediate rotation.

show abstract

Section: Structure Of the Michaelis Complexmentioning

confidence: 62%

Section: Introductionmentioning

confidence: 81%

Section: Overall Structurementioning

confidence: 93%

See 1 more Smart Citation

Crystallographic snapshots of UDP-glucuronic acid 4-epimerase ligand binding, rotation, and reduction

Iacovino

Savino

Borg

et al. 2020

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…This pathway is comparable to that involving UDP-glucuronate 4-epimerase (UGA4E, EC 5.1.3.6), an enzyme that catalyzes the interconversion of UDP-GlcA and UDP-d-galacturonic acid (UDP-GalA) ( Figure 1). The latter serves as a donor for GalA incorporation in plant cell walls, bacterial lipopolysaccharides, or antibiotics [16][17][18][19][20]. UGA4E is also present in the CEP1 family [3].…”

Section: Selection Of a Uga5e Sequencementioning

confidence: 99%

“…This hypothesis is supported by a more detailed sequence analysis. Sun et al recently solved the first crystal structure of an UGA4E (i.e., from Streptomyces viridosporus, PDB 6KV9) and found that crucial interactions are formed with the substrate at positions G92 and R192 [20]. Moreover, R192 is believed to favor the sugar ring rotation that is needed for C4-epimerization, and its correct orientation would be ensured by the adjacent D194.…”

Section: Analysis Of the Uga5e Specificitymentioning

confidence: 99%

Novel Insights into the Existence of the Putative UDP-Glucuronate 5-Epimerase Specificity

et al. 2020

View full text Add to dashboard Cite

C5-epimerases are promising tools for the production of rare l-hexoses from their more common d-counterparts. On that account, UDP-glucuronate 5-epimerase (UGA5E) attracts attention as this enzyme could prove to be useful for the synthesis of UDP-l-iduronate. Interestingly, l-iduronate is known as a precursor for the production of heparin, an effective anticoagulant. To date, the UGA5E specificity has only been detected in rabbit skin extract, and the respective enzyme has not been characterized in detail or even identified at the molecular level. Accordingly, the current work aimed to shed more light on the properties of UGA5E. Therefore, the pool of putative UGA5Es present in the UniProt database was scrutinized and their sequences were clustered in a phylogenetic tree. However, the examination of two of these enzymes revealed that they actually epimerize UDP-glucuronate at the 4- rather than 5-position. Furthermore, in silico analysis indicated that this should be the case for all sequences that are currently annotated as UGA5E and, hence, that such activity has not yet been discovered in nature. The detected l-iduronate synthesis in rabbit skin extract can probably be assigned to the enzyme chondroitin-glucuronate C5-epimerase, which catalyzes the conversion of d-glucuronate to l-iduronate on a polysaccharide level.

show abstract

Enzymatische C4‐Epimerisierung von UDP‐Glucuronsäure: präzise gesteuerte Rotation eines transienten 4‐Ketointermediats für eine invertierende Reaktion ohne Decarboxylierung

Borg

Esquivias²,

Coines³

et al. 2022

Angewandte Chemie

View full text Add to dashboard Cite

UDP-Glucuronsäure(UDP-GlcA)-4-Epimerase repräsentiert eine wichtige Fragestellung in der Enzymkatalyse: die Balance zwischen konformativer Flexibilität und genauer Positionierung. Das Enzym koordiniert die C4-Oxidation des Substrats durch NAD + mit der Rotation eines leicht decarboxylierbaren β-Ketosäure-Intermediats im aktiven Zentrum zur Ermöglichung der stereoinvertierenden Reduktion der Ketogruppe durch NADH. Wir zeigen hier die nur schwer erfassbare Rotationskoordinate des 4-Ketointermediats. Distorsion des Zuckerrings in eine Boot-Konformation erzeugt torsionale Mobilität in der Bindungstasche des Enzyms. Die Endpunkte der Rotation zeigen den 4-Ketozucker in einer unverformten 4 C 1 -Sesselkonformation. Die äquatorial positionierte Carboxylatgruppe ist ungünstig für die 4-Ketozucker-Decarboxylierung. Varianten der Epimerase zeigen Decarboxylierung, wenn sie die Bindung mit der Carboxylatgruppe im entgegengesetzten Rotationsisomer des Substrats entfernen. R185A/D-Substitutionen wandeln die Epimerase in UDP-Xylose-Synthasen um, welche UDP-GlcA in stereospezifischen, konfigurationserhaltenden Reaktionen decarboxylieren.

show abstract

Structure of an antibiotic-synthesizing UDP-glucuronate 4-epimerase MoeE5 in complex with substrate

Cited by 25 publications

References 19 publications

Crystallographic snapshots of UDP-glucuronic acid 4-epimerase ligand binding, rotation, and reduction

Crystallographic snapshots of UDP-glucuronic acid 4-epimerase ligand binding, rotation, and reduction

Novel Insights into the Existence of the Putative UDP-Glucuronate 5-Epimerase Specificity

Enzymatische C4‐Epimerisierung von UDP‐Glucuronsäure: präzise gesteuerte Rotation eines transienten 4‐Ketointermediats für eine invertierende Reaktion ohne Decarboxylierung

Contact Info

Product

Resources

About