Conserved main‐chain peptide distortions: A proposed role for Ile203 in catalysis by dihydrodipicolinate synthase

Dobson, Renwick C. J.; Griffin, Michael D. W.; Devenish, Sean R. A.; Pearce, F. Grant; Hutton, Craig A.; Gerrard, Juliet A.; Jameson, Geoffrey B.; Perugini, Matthew A.

doi:10.1110/ps.037440.108

Cited by 31 publications

(35 citation statements)

References 41 publications

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“…The refinement statistics are provided in Table 4. For Av-DHDPS, Ramachandran statistics showed 91.3% in the preferred region, 8.3% in the additionally allowed region and 0.4% in the disallowed region consistent with previous structural reports152162. For Av-DHDPR, Ramachandran statistics showed 89.5% in the preferred region, 8.8% in the additionally allowed region and 1.3% in the generously allowed region consistent with previous studies313233343536.…”

Section: Methodssupporting

confidence: 90%

Structure and Function of Cyanobacterial DHDPS and DHDPR

Christensen

Costa

Faou

et al. 2016

Sci Rep

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Lysine biosynthesis in bacteria and plants commences with a condensation reaction catalysed by dihydrodipicolinate synthase (DHDPS) followed by a reduction reaction catalysed by dihydrodipicolinate reductase (DHDPR). Interestingly, both DHDPS and DHDPR exist as different oligomeric forms in bacteria and plants. DHDPS is primarily a homotetramer in all species, but the architecture of the tetramer differs across kingdoms. DHDPR also exists as a tetramer in bacteria, but has recently been reported to be dimeric in plants. This study aimed to characterise for the first time the structure and function of DHDPS and DHDPR from cyanobacteria, which is an evolutionary important phylum that evolved at the divergence point between bacteria and plants. We cloned, expressed and purified DHDPS and DHDPR from the cyanobacterium Anabaena variabilis. The recombinant enzymes were shown to be folded by circular dichroism spectroscopy, enzymatically active employing the quantitative DHDPS-DHDPR coupled assay, and form tetramers in solution using analytical ultracentrifugation. Crystal structures of DHDPS and DHDPR from A. variabilis were determined at 1.92 Å and 2.83 Å, respectively, and show that both enzymes adopt the canonical bacterial tetrameric architecture. These studies indicate that the quaternary structure of bacterial and plant DHDPS and DHDPR diverged after cyanobacteria evolved.

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Section: Methodssupporting

confidence: 90%

Structure and Function of Cyanobacterial DHDPS and DHDPR

Christensen

Costa

Faou

et al. 2016

Sci Rep

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“…It has also been proposed that highly nonplanar residues are biased toward active sites (14), and a number of descriptions of protein structures emphasized nonplanar peptide bonds in the active site (14)(15)(16)(17). The question of conformation dependence was revisited by Esposito,et al (8) using structures refined at better than 1.2 Å resolution, and a correlation with the handedness of the chain twist was not found.…”

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confidence: 99%

Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites

Berkholz

Driggers

Shapovalov

et al. 2011

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

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The planarity of peptide bonds is an assumption that underlies decades of theoretical modeling of proteins. Peptide bonds strongly deviating from planarity are considered very rare features of protein structure that occur for functional reasons. Here, empirical analyses of atomic-resolution protein structures reveal that trans peptide groups can vary by more than 25°from planarity and that the true extent of nonplanarity is underestimated even in 1.2 Å resolution structures. Analyses as a function of the φ,ψ-backbone dihedral angles show that the expected value deviates by 8°from planar as a systematic function of conformation, but that the large majority of variation in planarity depends on tertiary effects. Furthermore, we show that those peptide bonds in proteins that are most nonplanar, deviating by over 20°from planarity, are not strongly associated with active sites. Instead, highly nonplanar peptides are simply integral components of protein structure related to local and tertiary structural features that tend to be conserved among homologs. To account for the systematic φ,ψ-dependent component of nonplanarity, we present a conformation-dependent library that can be used in crystallographic refinement and predictive protein modeling.omega torsion angle | peptide planarity | protein geometry | kernal density regression | strain T he prediction of the dominant forms of secondary structure in proteins, α-helices and β-strands, was enabled by the simplifying assumption that the peptide bond was planar, consistent with its expected partial double-bond character and evidence from small-molecule crystal structures (1-3). Pauling, et al. were aware that deformations from planarity associated with an energetic cost could occur, but the expectation was that the minimumenergy conformation was always planar (2, 4). In proteins, the ω torsion angle measures peptide planarity, with ω ¼ 180°and ω ¼ 0°representing planar trans and cis peptides, respectively. In an early large-scale empirical study of peptide planarity, MacArthur and Thornton (5) found that in proteins determined at better than 2 Å resolution and in small-molecule peptides, the ω-distributions were Gaussian-like with averages of 179.6°( σ ¼ 4.7°) and 179.7°(σ ¼ 5.9°), respectively. These authors further proposed that the smaller spread seen in proteins was an artifact due to the planarity restraints used in crystallographic refinements. This study and that of Karplus (6) also showed that the average ω-value varies as a function of the conformation of the backbone torsion angles φ and ψ, with MacArthur and Thornton suggesting that the direction of nonplanarity was related to the handedness of the φ,ψ-associated chain twist (5).As more structures were analyzed at ultrahigh (≤1.2 Å) resolutions (7), higher deviations in planarity have emerged (8-13). It has also been proposed that highly nonplanar residues are biased toward active sites (14), and a number of descriptions of protein structures emphasized nonplanar peptide bonds in the active site (14-17). The...

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“…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: 76%

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

et al. 2015

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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...

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Conserved main‐chain peptide distortions: A proposed role for Ile203 in catalysis by dihydrodipicolinate synthase

Cited by 31 publications

References 41 publications

Structure and Function of Cyanobacterial DHDPS and DHDPR

Structure and Function of Cyanobacterial DHDPS and DHDPR

Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites

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

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