The Reaction Coordinate of a Bacterial GH47 α‐Mannosidase: A Combined Quantum Mechanical and Structural Approach

Thompson, Andrew J.; Dabin, Jérôme; Iglésias-Fernández, Javier; Ardèvol, Albert; Dinev, Zoran; Williams, Spencer J.; Bande, Omprakash; Siriwardena, Aloysius; Moreland, Carl; Hu, Ting‐Chou; Smith, David K.; Gilbert, Harry J.; Rovira, Carme; Davies, G.J.

doi:10.1002/ange.201205338

Cited by 10 publications

(18 citation statements)

References 33 publications

(20 reference statements)

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“…S 1 sugar conformations (14,(16)(17)(18)(19)) that mimic intermediates in the proposed conformational itinerary during catalysis (14,19). In the ERManI-and GMIA-La 3+ -substrate complexes the mannose residue in the −1 subsite assumed a 1 C 4 chair conformation and also retained normal glycosidic bond lengths to the +1 mannose residue (Fig.…”

Section: +mentioning

confidence: 94%

“…These data demonstrate that ion coordination can influence the conformation of the bound glycone residue in the respective structures. By comparison, several inhibitors bound to GH47 enzymes in 1 C 4 chair conformations (16,17,19), whereas mannoimidazole bound in the proposed 3 H 4 half-chair transition state conformation (19 (Fig. 5B).…”

Section: The Michaelis Complex Demonstrates the Glycone Conformationalmentioning

confidence: 99%

“…Previous studies characterized interactions with glycone-mimicking inhibitors within the −1 subsite (14,(16)(17)(18)(19) and a thiodisaccharide substrate analog that bridged the −1 and the adjoining +1 subsites (14, 19) through a highly conserved collection of hydrophobic and H-bonding interactions as well as direct coordination with the Ca 2+ ion. In contrast to the highly conserved −1 and +1 subsites, the topologies of the broad clefts (≥+1 subsites) leading to the active-site cores are distinct among the GH47 family members (10,(16)(17)(18)(19)(20); these distinct topologies have been proposed to account for the differences in branch specificities (20). For example, protein-glycan complexes were obtained for both mouse GMIA (20) and the yeast ERManI (10), in which the equivalent of Man 5 GlcNAc 2 enzymatic products occupied the ≥+1 subsites as ligands, but the −1 glycone subsites remained unoccupied.…”

Section: Significancementioning

confidence: 99%

“…By contrast, prior studies on GH47 enzymes used glycone-mimicking inhibitors or poorly cleaved thiodisaccharide substrate analogs as surrogates for bound natural substrates. The thiodisaccharide complexes displayed glycone residues bound in 3 S 1 skew boat conformations (14,19) which may have been induced by the longer C-S-C bond lengths (∼1.8 Å) (Fig. S1).…”

Section: The Michaelis Complex Demonstrates the Glycone Conformationalmentioning

confidence: 99%

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Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway

Xiang

Karaveg

Moremen

2016

Proc. Natl. Acad. Sci. U.S.A.

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Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secreted glycoproteins. Multiple glycoside hydrolase family 47 (GH47) α-mannosidases, including endoplasmic reticulum (ER) α-mannosidase I (ERManI) and Golgi α-mannosidase IA (GMIA), are responsible for cleavage of terminal α1,2-linked mannose residues to produce uniquely trimmed oligomannose isomers that are necessary for ER glycoprotein quality control and glycan maturation. ERManI and GMIA have similar catalytic domain structures, but each enzyme cleaves distinct residues from tribranched oligomannose glycan substrates. The structural basis for branch-specific cleavage by ERManI and GMIA was explored by replacing an essential enzyme-bound Ca 2+ ion with a lanthanum (La 3+) ion. This ion swap led to enzyme inactivation while retaining high-affinity substrate interactions. Cocrystallization of La 3+ -bound enzymes with Man 9 GlcNAc 2 substrate analogs revealed enzyme-substrate complexes with distinct modes of glycan branch insertion into the respective enzyme active-site clefts. Both enzymes had glycan interactions that extended across the entire glycan structure, but each enzyme engaged a different glycan branch and used different sets of glycan interactions. Additional mutagenesis and time-course studies of glycan cleavage probed the structural basis of enzyme specificity. The results provide insights into the enzyme catalytic mechanisms and reveal structural snapshots of the sequential glycan cleavage events. The data also indicate that full steric access to glycan substrates determines the efficiency of mannose-trimming reactions that control the conversion to complex-type structures in mammalian cells.Asn-linked glycan processing | α-mannosidase | glycosidase mechanism | glycoside hydrolase | bioinorganic chemistry

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Section: +mentioning

confidence: 94%

Section: The Michaelis Complex Demonstrates the Glycone Conformationalmentioning

confidence: 99%

Section: Significancementioning

confidence: 99%

Section: The Michaelis Complex Demonstrates the Glycone Conformationalmentioning

confidence: 99%

See 2 more Smart Citations

Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway

Xiang

Karaveg

Moremen

2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Alternatively, mannoimidazole (MIm)-type inhibitors, for example, 2 , are qualitatively good models of a mannopyranosyl oxocarbenium ion-like transition state, with sp 2 hybridization of equivalent atoms and the potential for anti protonation7 of the imidazole functionality. Structural studies aimed at identifying the conformation of the transition state and flanking ground states on the reaction coordinate, utilizing 2 , and related inhibitors as transition-state and ground-state mimics, identified a 1 S 5 ↔ B 2,5 ≠ ↔ O S 2 conformational itinerary for mannosidases of families GH2,8 38,9 and 92,10 and a 3 S 1 → 3 H 4 ≠ → 1 C 4 itinerary for the α-mannosidases of GH47 11. However, it is now apparent that complexes with 2 can report on both the transition-state conformation and conformational itinerary 11.…”

mentioning

confidence: 99%

Combined Inhibitor Free‐Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate

et al. 2013

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Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole-type inhibitors are energetically poised to report faithfully on mannosidase transition-state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including β-mannanases from families GH26 and GH113. Isofagomine-type inhibitors are poor mimics of transition-state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar-shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active-site residues involved in substrate recognition.

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Combined Inhibitor Free‐Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate

Williams¹,

Iglésias-Fernández²,

Stepper³

et al. 2013

Angewandte Chemie

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Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole-type inhibitors are energetically poised to report faithfully on mannosidase transition-state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including b-mannanases from families GH26 and GH113. Isofagomine-type inhibitors are poor mimics of transition-state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugarshaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active-site residues involved in substrate recognition.

show abstract

The Reaction Coordinate of a Bacterial GH47 α‐Mannosidase: A Combined Quantum Mechanical and Structural Approach

Cited by 10 publications

References 33 publications

Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway

Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway

Combined Inhibitor Free‐Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate

Combined Inhibitor Free‐Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate

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