Conserved YjgF Protein Family Deaminates Reactive Enamine/Imine Intermediates of Pyridoxal 5′-Phosphate (PLP)-dependent Enzyme Reactions

Lambrecht, Jennifer A.; Flynn, Jeffrey M.; Downs, Diana M.

doi:10.1074/jbc.m111.304477

Cited by 100 publications

(158 citation statements)

References 43 publications

(38 reference statements)

Supporting

Mentioning

155

Contrasting

Order By: Relevance

“…Based on the structures of EcDAPAL and its comparison with homologous enzymes, a plausible catalytic scenario could be envisaged (Fig. 7) (49) or by assistance of other cellular proteins (50).…”

Section: Resultsmentioning

confidence: 99%

Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis

Bisht

Radha

Bharath

et al. 2012

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: DAPAL is a novel PLP-dependent enzyme involved in the degradation of DAP, a nonstandard amino acid. Results: Striking structural differences were observed between apo-and holo-EcDAPAL, and structure with a PLP-aminoacrylate intermediate bound at the active site was obtained. Conclusion: Enzyme undergoes apo to holo structural transitions and follows a two-base mechanism of catalysis. Significance: The results provide insights into the catalytic mechanism of DAPAL.

show abstract

Section: Resultsmentioning

confidence: 99%

Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis

Bisht

Radha

Bharath

et al. 2012

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…The deduced amino acid sequence of Der f 34 contains seven amino acid residues (Tyr-19, Gly-33, Asn-59, Asn-91, Arg-105, Pro-114, and Glu-120; indicated in red in Fig. 1A) predicted to be involved in an active site structure or in a catalytic domain for enamine/imine metabolisms (27).…”

Section: Resultsmentioning

confidence: 99%

“…Rid family proteins share catalytically critical arginine residues for their enamine/imine deaminase enzymatic activity and serve to hydrolyze the reactive enamine/imines generated by pyridoxal 5Ј-phosphate-dependent enzymes or FAD-dependent amine oxidases (27). The deduced amino acid sequence of Der f 34 contains seven amino acid residues (Tyr-19, Gly-33, Asn-59, Asn-91, Arg-105, Pro-114, and Glu-120; indicated in red in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…We also analyzed the imine deaminase activity for the mutant of Der f 34, whose conserved seven amino acid residues for enamine/imine deaminase activity were substituted for alanine. RidA protein from Salmonella enterica (NCBI GenBank TM accession number AF095578) and a nonfunctional variant (RidA R105A ) were used as a positive and negative control for the imine deaminase assay (27,36). The imine deaminase activity was determined as an inhibitory activity to produce semicarbazone, which was produced by a reaction with imine and semicarbazide (37).…”

Section: Resultsmentioning

confidence: 99%

“…Der f 34 showed that imine deaminase activity involved in amino acid metabolisms cooperated with amino acid oxygenase or hydrogenase. Imine deaminase catalyzes the hydrolysis of imine to produce ammonia and ketone (27). Rid family proteins are highly conserved in various species, including prokaryotes and eukaryotes, and their sequences for the UPF0076 signature pattern and residues for enamine/imine deaminase activity are highly conserved (Fig.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Der f 34, a Novel Major House Dust Mite Allergen Belonging to a Highly Conserved Rid/YjgF/YER057c/UK114 Family of Imine Deaminases

ElRamlawy

Fujimura

Baba

et al. 2016

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

The high prevalence of house dust mite (HDM) allergy is a growing health problem worldwide, and the characterization of clinically important HDM allergens is a prerequisite for the development of diagnostic and therapeutic strategies. Here, we report a novel HDM allergen that belongs structurally to the highly conserved Rid/YjgF/YER057c/UK114 family (Rid family) with imine deaminase activity. Isolated HDM cDNA, named der f 34, encodes 128 amino acids homologous to Rid-like proteins. This new protein belongs to the Rid family and has seven conserved residues involved in enamine/imine deaminase activity. Indeed, we demonstrated that purified Der f 34 had imine deaminase activity that preferentially acted on leucine and methionine. Native Der f 34 showed a high IgE binding frequency as revealed by two-dimensional immunoblotting (62.5%) or ELISA (68%), which was comparable with those of a major HDM allergen Der f 2 (77.5 and 79%, respectively). We also found that Der f 34 showed cross-reactivity with another prominent indoor allergen source, Aspergillus fumigatus. This is the first report showing that the Rid family imine deaminase represents an additional important pan-allergen that is conserved across organisms.Asthma is a serious global health problem that significantly reduces quality of life. In a cross-sectional World Health Organization survey of 178,215 individuals from 70 countries conducted in 2002-2003, it was estimated that 4.3% of adults (range, 0.2-21.0%) had been diagnosed with asthma by a medical doctor (1). Inhaled airborne allergens cause allergic inflammation via the cross-linking of allergen-specific IgEs bound on high affinity IgE receptor (FceRI) located on the surface of airway or lung mast cells, causing the secretion of inflammatory chemical mediators (e.g. histamine and leukotrienes) from activated mast cells. House dust mites (HDMs) 5 and fungi are major sources of airborne allergens and trigger asthmatic attacks in allergic patients concomitant with air pollutants (2).Allergen-specific immunotherapy (AIT) is the only curative treatment for allergic asthma that changes the natural course of an allergy (3). AIT induces allergen-specific tolerance by administering increasing doses of causative allergens subcutaneously or sublingually (4). The precise mechanisms underlying AIT remain to be fully elucidated, but the involvement of regulatory T cells and B cells or the induction of T cell anergy is suggested to be a key mechanism for an efficient AIT. AIT induces antigen-specific immunomodulatory cells or the anergic response of T cells specific to major allergens included in an allergen extract as an AIT vaccine. Therefore, the standardization of AIT vaccines using important major allergens and the characterization of major component allergens in an allergen source are important issues for the development of an effective AIT (5, 6).

show abstract

Fe‐S‐Basedl‐Serine Dehydratases

Holden

Thoden

Grant

2016

Encyclopedia of Inorganic and Bioinorganic Chemistry

View full text Add to dashboard Cite

Enzyme; L-serine dehydratase; L-serine ammonia lyase; L-serine deaminase; L-serine hydro-lyase (deaminating); L-hydroxyamino acid dehydratase; EC 4.3.1.17; an ironsulfur containing L-serine dehydratase with a cubane [4Fe-4S] 2+ cluster; most commonly referred to as L-serine dehydratase (LSD).LSD catalyzes the conversion of L-serine to pyruvate and ammonia. 1-6 The enzyme is very specific for L-serine and only shows a very low activity (<1%) with L-threonine. 6-10

show abstract

Conserved YjgF Protein Family Deaminates Reactive Enamine/Imine Intermediates of Pyridoxal 5′-Phosphate (PLP)-dependent Enzyme Reactions

Cited by 100 publications

References 43 publications

Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis

Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis

Der f 34, a Novel Major House Dust Mite Allergen Belonging to a Highly Conserved Rid/YjgF/YER057c/UK114 Family of Imine Deaminases

Fe‐S‐Basedl‐Serine Dehydratases

Contact Info

Product

Resources

About