Kinetic and structural characterization of a cis -3-Chloroacrylic acid dehalogenase homologue in Pseudomonas sp. UW4: A potential step between subgroups in the tautomerase superfamily

LeVieux, Jake A.; Baas, Bert‐Jan; Kaoud, Tamer S.; Davidson, Rebecca M.; Babbitt, Patricia C.; Zhang, Yan Jessie; Whitman, Christian P.

doi:10.1016/j.abb.2017.10.018

Cited by 9 publications

(25 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The positioning of these sequences in the tree, however, suggests that some of them may be good targets for structural characterization that might help to fill out the similarity path in more detail. As a case in point, the identification of Linker 1 led to our targeting of that protein for structural characterization (PDB ID: 5UIF ) ( 57 ), allowing us to include it in the structure-guided alignment shown in Fig. 5 .…”

Section: Resultsmentioning

confidence: 99%

A global view of structure–function relationships in the tautomerase superfamily

Davidson

Baas²,

Akiva

et al. 2018

Journal of Biological Chemistry

Self Cite

163

View full text Add to dashboard Cite

The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure–function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence similarity network to guide classification into distinct subgroups. Our results indicate that TSF members are found in all domains of life, with most being present in bacteria. The eukaryotic members of the cis-3-chloroacrylic acid dehalogenase subgroup are limited to fungal species, whereas the macrophage migration inhibitory factor subgroup has wide eukaryotic representation (including mammals). Unexpectedly, we found that 346 TSF sequences lack Pro-1, of which 85% are present in the malonate semialdehyde decarboxylase subgroup. The computed network also enabled the identification of similarity paths, namely sequences that link functionally diverse subgroups and exhibit transitional structural features that may help explain reaction divergence. A structure-guided comparison of these linker proteins identified conserved transitions between them, and kinetic analysis paralleled these observations. Phylogenetic reconstruction of the linker set was consistent with these findings. Our results also suggest that contemporary TSF members may have evolved from a short 4-oxalocrotonate tautomerase–like ancestor followed by gene duplication and fusion. Our new linker-guided strategy can be used to enrich the discovery of sequence/structure/function transitions in other enzyme superfamilies.

show abstract

Section: Resultsmentioning

confidence: 99%

A global view of structure–function relationships in the tautomerase superfamily

Davidson

Baas²,

Akiva

et al. 2018

Journal of Biological Chemistry

Self Cite

163

View full text Add to dashboard Cite

show abstract

“…Previously Zhang et al ( 2017 ) identified conserved residues in the superfamily that relate to DNA binding within the photolyase, defining which substrate is recognised and repaired by the photolyase (Table 1 and Fig. 3 ).…”

Section: Resultsmentioning

confidence: 99%

A Case Study of Eukaryogenesis: The Evolution of Photoreception by Photolyase/Cryptochrome Proteins

et al. 2020

View full text Add to dashboard Cite

Eukaryogenesis, the origin of the eukaryotes, is still poorly understood. Herein, we show how a detailed all-kingdom phylogenetic analysis overlaid with a map of key biochemical features can provide valuable clues. The photolyase/cryptochrome family of proteins are well known to repair DNA in response to potentially harmful effects of sunlight and to entrain circadian rhythms. Phylogenetic analysis of photolyase/cryptochrome protein sequences from a wide range of prokaryotes and eukaryotes points to a number of horizontal gene transfer events between ancestral bacteria and ancestral eukaryotes. Previous experimental research has characterised patterns of tryptophan residues in these proteins that are important for photoreception, specifically a tryptophan dyad, a canonical tryptophan triad, an alternative tryptophan triad, a tryptophan tetrad and an alternative tetrad. Our results suggest that the spread of the different triad and tetrad motifs across the kingdoms of life accompanied the putative horizontal gene transfers and is consistent with multiple bacterial contributions to eukaryogenesis.

show abstract

“…The gene encoding fused 4-OT from Burkholderia lata (ATCC 17760, UniProt accession: Q392K7) (designated "fused 4-OT") was codon-optimized for expression in E. coli, synthesized, and cloned into the expression vectors pJ411 (pJ411-F4-OT) by DNA2.0, Inc., now ATUM (Newark, CA). 19…”

Section: Bacterial Strains Plasmids and Growth Conditionsmentioning

confidence: 99%

Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer

et al. 2019

Self Cite

View full text Add to dashboard Cite

A 4-oxalocrotonate tautomerase (4-OT) trimer has been isolated from Burkholderia lata and a kinetic, mechanistic, and structural analysis has been performed. The enzyme is the third described oligomer state for 4-OT along with a homo-and heterohexamer. The 4-OT trimer is part of a small subset of sequences (133 sequences) within the 4-OT subgroup of the tautomerase superfamily (TSF). The TSF has two distinct features: members are composed of a single β-α-β unit (homo-and heterohexamer) or two consecutively joined β-α-β units (trimer) and generally have a catalytic amino-terminal proline. The enzyme, designated fused 4-OT, functions as a 4-OT where the active site groups (Pro-1, Arg-39, Arg-76, Phe-115, Arg-127) mirror those in the canonical 4-OT from Pseudomonas putida mt-2. Inactivation by 2-oxo-3-pentynoate suggests that Pro-1 of fused 4-OT has a low pK a enabling the prolyl nitrogen to function as a general base. A remarkable feature of the fused 4-OT is the absence of P3 rotational symmetry in the structure (1.5 Å resolution). The asymmetric arrangement of the trimer is not due to the fusion of the two β-α-β building blocks because an engineered "unfused" variant that breaks the covalent bond between the two units (to generate a heterohexamer) assumes the same asymmetric oligomerization state. It

show abstract

Kinetic and structural characterization of a cis -3-Chloroacrylic acid dehalogenase homologue in Pseudomonas sp. UW4: A potential step between subgroups in the tautomerase superfamily

Cited by 9 publications

References 41 publications

A global view of structure–function relationships in the tautomerase superfamily

A global view of structure–function relationships in the tautomerase superfamily

A Case Study of Eukaryogenesis: The Evolution of Photoreception by Photolyase/Cryptochrome Proteins

Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer

Contact Info

Product

Resources

About