Structure and mechanism of a sub-family of enzymes related to N -acetylneuraminate lyase 1 1Edited by F. E. Cohen

Lawrence, Michael C.; Barbosa, J.A.R.G.; Smith, Brian J.; Hall, Nathan E.; Pilling, Patricia A.; Ooi, Hua Chee; Marcuccio, Sebastian M.

doi:10.1006/jmbi.1996.0769

Cited by 100 publications

(112 citation statements)

References 65 publications

(82 reference statements)

Supporting

Mentioning

107

Contrasting

Order By: Relevance

“…2)], similar to the mechanism proposed for the inactivation of Nacetylneuraminate lyase (NAL) 44 and dihydrodipicolinate synthase (DHDPS) 45 by 3-HP. Subsequent deprotonation of the Schiff base (presumably by His 297) would yield an enol or enolate [i.e., enol(ate)] (86 Da), which could tautomerize to yield a covalent aldehyde adduct.…”

supporting

confidence: 54%

“…A possible mechanism accounting for our observations involves the reversible formation of a Schiff base (imine) between the ε-NH2 group of Lys 166 and the α-carbonyl of 3-HP [C2 mechanism (Scheme 2)], similar to the mechanism proposed for the inactivation of Nacetylneuraminate lyase (NAL) 44 and dihydrodipicolinate synthase (DHDPS) 45 by 3-HP. Subsequent deprotonation of the Schiff base (presumably by His 297) would yield an enol or enolate [i.e., enol(ate)] (86 Da), which could tautomerize to yield a covalent aldehyde adduct.…”

Section: Mechanism Of Inactivationmentioning

confidence: 75%

“…3-HP inactivates NAL from Clostridium fringens 56 and E. coli 44 and DHDPS from E. coli, 45 and the X-ray crystal structures of the covalently modified NAL and DHDPS enzymes revealed the presence of an aldehyde/enol(ate)-lysine adduct similar to the one we observe for MR inactivated by 3-HP. 44,45 Although the mechanism-based inhibition of these two NAL superfamily members by 3-HP also proceeds via initial Schiff-base formation followed by deprotonation, 44,45 the apparent second-order rate constant for the inactivation of MR exceeds that observed for inactivation of DHDPS (0.56 M -1 s -1 ) by ∼138-fold. This observation is in accord with the active site of MR being optimized to promote enolate formation.…”

Section: Mechanistic Link Between Superfamiliesmentioning

confidence: 99%

See 2 more Smart Citations

Inactivation of Mandelate Racemase by 3-Hydroxypyruvate Reveals a Potential Mechanistic Link between Enzyme Superfamilies

et al. 2015

View full text Add to dashboard Cite

Mandelate racemase (MR), a member of the enolase superfamily, catalyzes the Mg 2+ -dependent interconversion of the enantiomers of mandelate. Several α-keto acids are modest competitive inhibitors of MR [e.g., mesoxalate (Ki = 1.8 ± 0.3 mM) and 3-fluoropyruvate (Ki = 1.3 ± 0.1 mM)], but, surprisingly, 3-hydroxypyruvate (3-HP) is an irreversible, time-dependent inhibitor (kinact/KI = 83 ± 8 M -1 s -1 ). Protection from inactivation by the competitive inhibitor benzohydroxamate, trypsinolysis and electrospray ionization tandem mass spectrometry analyses, and X-ray crystallographic studies reveal that 3-HP undergoes Schiff-base formation with Lys 166 at the active site, followed by formation of an aldehyde/enol(ate) adduct. Such a reaction is unprecedented in the enolase superfamily and may be a relic of an activity possessed by a promiscuous progenitor enzyme. The ability of MR to form and deprotonate a Schiff-base intermediate furnishes a previously unrecognized mechanistic link to other α/β-barrel enzymes utilizing Schiff-base chemistry and is in accord with the sequence-and structure-based hypothesis that members of the metal-dependent enolase superfamily and the Schiff-baseforming N-acetylneuraminate lyase superfamily and aldolases share a common ancestor.One of the first enzyme superfamilies recognized was the enolase superfamily, 1 whose members share a common partial reaction (i.e., the metal-assisted, Brønsted-base-catalyzed abstraction of the α-proton from a carboxylate substrate to form an enolate) 2-5 and a common protein fold [i.e., a modified (α/β)8-barrel (TIM barrel) bearing the catalytic residues at the C-terminal ends of the β-strands and an N-terminal domain that caps the active site conferring substrate specificity and excluding solvent]. [6][7][8] Studies of members of the enolase superfamily have afforded important insights into enzyme evolution and developing strategies for assigning the correct functions to proteins identified in genome projects. 3,[9][10][11][12] The well-characterized NOT THE PUBLISHED VERSION; this is the author's final, peer-reviewed manuscript. The published version may be accessed by following the link in the citation at the bottom of the page.Biochemistry, Vol 54, No. 17 (May 5, 2015): pg. 2747-2757. DOI. This article is © American Chemical Society and permission has been granted for this version to appear in e-Publications@Marquette. American Chemical Society does not grant permission for this article to be further copied/distributed or hosted elsewhere without the express permission from American Chemical Society. 3archetype of this superfamily, mandelate racemase (MR, EC 5.1.2.2) from Pseudomonas putida, catalyzes the Mg 2+ -dependent, 1,1-proton transfer reaction that interconverts the enantiomers of mandelate and has served as a useful paradigm for understanding how enzymes catalyze the rapid α-deprotonation of a carbon acid substrate with a relatively high pKa value. 13 MR utilizes a two-base mechanism with Lys 166 and His 297 abstracting the α-proton fr...

show abstract

supporting

confidence: 54%

Section: Mechanism Of Inactivationmentioning

confidence: 75%

Section: Mechanistic Link Between Superfamiliesmentioning

confidence: 99%

See 1 more Smart Citation

Inactivation of Mandelate Racemase by 3-Hydroxypyruvate Reveals a Potential Mechanistic Link between Enzyme Superfamilies

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Although the DHDPS, NAL, HBPHA, and DOGDH enzymes function in disparate pathways, they all share a reaction mechanism with a covalent Schiff base intermediate that forms between the substrate (which varies, depending on the enzyme) and a completely conserved lysine residue in the active site (47). A tyrosine residue in the substrate binding pocket is also completely conserved and is predicted to be involved directly in the reaction mechanism or to function in stabilizing the position of the lysine (47,48).…”

Section: Resultsmentioning

confidence: 99%

“…A tyrosine residue in the substrate binding pocket is also completely conserved and is predicted to be involved directly in the reaction mechanism or to function in stabilizing the position of the lysine (47,48). The similarities of the sequences of HypD and LhpC to those of the other characterized members of this group and the fact that both have the conserved active-site lysine and tyrosine residues (see Fig.…”

Section: Resultsmentioning

confidence: 99%

l-Hydroxyproline andd-Proline Catabolism in Sinorhizobium meliloti

et al. 2016

View full text Add to dashboard Cite

Sinorhizobium meliloti IMPORTANCEHydroxyproline is abundant in proteins in animal and plant tissues and serves as a carbon and a nitrogen source for bacteria in diverse environments, including the rhizosphere, compost, and the mammalian gut. While the main biochemical features of bacterial hydroxyproline catabolism were elucidated in the 1960s, the genetic and molecular details have only recently been determined. Elucidating the genetics of hydroxyproline catabolism will aid in the annotation of these genes in other genomes and metagenomic libraries. This will facilitate an improved understanding of the importance of this pathway and may assist in determining the prevalence of hydroxyproline in a particular environment.4-Hydroxyproline and 3-hydroxyproline in animal and plant proteins are formed through the posttranslational modification of proline residues by the enzyme proline hydroxylase. In some bacteria, hydroxyproline is synthesized from free L-proline, where it is employed in the synthesis of secondary metabolites (1, 2). 4-Hydroxyproline has two chiral carbon atoms, and of its four isomeric forms, trans-4-hydroxy-L-proline (trans-4-L-Hyp) and cis-4-hydroxy-D-proline (cis-4-D-Hyp) appear to be the two most common isomers. trans-4-

show abstract

Structure and inhibition ofN‐acetylneuraminate lyase from methicillin‐resistantStaphylococcus aureus

et al. 2016

View full text Add to dashboard Cite

N-Acetylneuraminate lyase is the first committed enzyme in the degradation of sialic acid by bacterial pathogens. In this study, we analyzed the kinetic parameters of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus (MRSA). We determined that the enzyme has a relatively high K of 3.2 mm, suggesting that flux through the catabolic pathway is likely to be controlled by this enzyme. Our data indicate that sialic acid alditol, a known inhibitor of N-acetylneuraminate lyase enzymes, is a stronger inhibitor of MRSA N-acetylneuraminate lyase than of Clostridium perfringens N-acetylneuraminate lyase. Our analysis of the crystal structure of ligand-free and 2R-sialic acid alditol-bound MRSA N-acetylneuraminate lyase suggests that subtle dynamic differences in solution and/or altered binding interactions within the active site may account for species-specific inhibition.

show abstract

Structure and mechanism of a sub-family of enzymes related to N -acetylneuraminate lyase 1 1Edited by F. E. Cohen

Cited by 100 publications

References 65 publications

Inactivation of Mandelate Racemase by 3-Hydroxypyruvate Reveals a Potential Mechanistic Link between Enzyme Superfamilies

Inactivation of Mandelate Racemase by 3-Hydroxypyruvate Reveals a Potential Mechanistic Link between Enzyme Superfamilies

l-Hydroxyproline andd-Proline Catabolism in Sinorhizobium meliloti

Structure and inhibition ofN‐acetylneuraminate lyase from methicillin‐resistantStaphylococcus aureus

Contact Info

Product

Resources

About