Bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application.

The synthetic s-triazines are abundant, nitrogen-rich, heteroaromatic compounds used in a multitude of applications including, herbicides, plastics and polymers, and explosives. Their presence in the environment has led to the evolution of bacterial catabolic pathways in bacteria that allow use of these anthropogenic chemicals as a nitrogen source that supports growth. Herbicidal s-triazines have been used since the mid-twentieth century and are among the most heavily used herbicides in the world, despite being withdrawn from use in some areas due to concern about their safety and environmental impact. Bacterial catabolism of the herbicidal s-triazines has been studied extensively. Pseudomonas sp. strain ADP, which was isolated more than thirty years after the introduction of the s-triazine herbicides, has been the model system for most of these studies; however, several alternative catabolic pathways have also been identified. Over the last five years, considerable detail about the molecular mode of action of the s-triazine catabolic enzymes has been uncovered through acquisition of their atomic structures. These structural studies have also revealed insights into the evolutionary origins of this newly acquired metabolic capability. In addition, s-triazine-catabolizing bacteria and enzymes have been used in a range of applications, including bioremediation of herbicides and cyanuric acid, introducing metabolic resistance to plants, and as a novel selectable marker in fermentation organisms. In this review, we cover the discovery and characterization of bacterial strains, metabolic pathways and enzymes that catabolize the s-triazines. We also consider the evolution of these new enzymes and pathways and discuss the practical applications that have been considered for these bacteria and enzymes. One Sentence Summary: A detailed understanding of bacterial herbicide catabolic enzymes and pathways offer new evolutionary insights and novel applied tools.

Protein engineering: the potential of remote mutations.

Engineered proteins, especially enzymes, are now commonly used in many industries owing to their catalytic power, specific binding of ligands, and properties as materials and food additives. As the number of potential uses for engineered proteins has increased, the interest in engineering or designing proteins to have greater stability, activity and specificity has increased in turn. With any rational engineering or design pursuit, the success of these endeavours relies on our fundamental understanding of the systems themselves; in the case of proteins, their structure-dynamics-function relationships. Proteins are most commonly rationally engineered by targeting the residues that we understand to be functionally important, such as enzyme active sites or ligand-binding sites. This means that the majority of the protein, i.e. regions remote from the active- or ligand-binding site, is often ignored. However, there is a growing body of literature that reports on, and rationalises, the successful engineering of proteins at remote sites. This minireview will discuss the current state of the art in protein engineering, with a particular focus on engineering regions that are remote from active- or ligand-binding sites. As the use of protein technologies expands, exploiting the potential improvements made possible through modifying remote regions will become vital if we are to realise the full potential of protein engineering and design.

A novel decarboxylating amidohydrolase involved in avoiding metabolic dead ends during cyanuric acid catabolism in Pseudomonas sp. strain ADP.

Cyanuric acid is a common environmental contaminant and a metabolic intermediate in the catabolism of s-triazine compounds, including atrazine and other herbicides. Cyanuric acid is catabolized via a number of bacterial pathways, including one first identified in Pseudomonas sp. strain ADP, which is encoded by a single, five-gene operon (atzDGEHF) found on a self-transmissible plasmid. The discovery of two of the five genes (atzG and atzH) was reported in 2018 and although the function of atzG was determined, the role of atzH was unclear. Here, we present the first in vitro reconstruction of the complete, five-protein cyanuric acid catabolism pathway, which indicates that AtzH may be an amidase responsible for converting 1,3-dicarboxyurea (the AtzE product) to allophanate (the AtzF substrate). We have solved the AtzH structure (a DUF3225 protein from the NTF2 superfamily) and used it to predict the substrate-binding pocket. Site-directed mutagenesis experiments suggest that two residues (Tyr22 and Arg46) are needed for catalysis. We also show that atzH homologs are commonly found in Proteobacteria associated with homologs of the atzG and atzE genes. The genetic context of these atzG-atzE-atzH clusters imply that they have a role in the catabolism of nitrogenous compounds. Moreover, their presence in many genomes in the absence of homologs of atzD and atzF suggests that the atzG-atzE-atzH cluster may pre-date the evolution of the cyanuric acid catabolism operon.

Computer-Guided Surface Engineering for Enzyme Improvement.

Protein engineering strategies are often guided by our understanding of how the structure of a protein determines its function. However, our understanding is generally restricted to small regions of a protein, namely the active site and its immediate vicinity, while the remainder of the protein is something of an enigma. Studying highly homologous transaminases with strictly conserved active sites, but different substrate preferences and activities, we predict and experimentally validate that the surface of the protein far from the active site carries out a decisive role in substrate selectivity and catalytic efficiency. Using a unique molecular dynamics approach and novel trajectory analysis, we demonstrate the phenomenon of surface-directed ligand diffusion in this well-known protein family for the first time. Further, we identify the residues involved in directing substrate, design surface channel variants endowed for improved kinetic properties and establish a broadly applicable new approach for protein engineering.

An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme.

Cyanuric acid is a metabolic intermediate of s-triazines, such as atrazine (a common herbicide) and melamine (used in resins and plastics). Cyanuric acid is mineralized to ammonia and carbon dioxide by the soil bacterium Pseudomonas sp. strain ADP via three hydrolytic enzymes (AtzD, AtzE, and AtzF). Here, we report the purification and biochemical and structural characterization of AtzE. Contrary to previous reports, we found that AtzE is not a biuret amidohydrolase, but instead it catalyzes the hydrolytic deamination of 1-carboxybiuret. X-ray crystal structures of apo AtzE and AtzE bound with the suicide inhibitor phenyl phosphorodiamidate revealed that the AtzE enzyme complex consists of two independent molecules in the asymmetric unit. We also show that AtzE forms an α2ß2 heterotetramer with a previously unidentified 68-amino acid-long protein (AtzG) encoded in the cyanuric acid mineralization operon from Pseudomonas sp. strain ADP. Moreover, we observed that AtzG is essential for the production of soluble, active AtzE and that this obligate interaction is a vestige of their shared evolutionary origin. We propose that AtzEG was likely recruited into the cyanuric acid-mineralizing pathway from an ancestral glutamine transamidosome that required protein-protein interactions to enforce the exclusion of solvent from the transamidation reaction.

Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841.

Biuret deamination is an essential step in cyanuric acid mineralization. In the well-studied atrazine degrading bacterium Pseudomonas sp. strain ADP, the amidase AtzE catalyzes this step. However, Rhizobium leguminosarum bv. viciae 3841 uses an unrelated cysteine hydrolase, BiuH, instead. Herein, structures of BiuH, BiuH with bound inhibitor and variants of BiuH are reported. The substrate is bound in the active site by a hydrogen bonding network that imparts high substrate specificity. The structure of the inactive Cys175Ser BiuH variant with substrate bound in the active site revealed that an active site cysteine (Cys175), aspartic acid (Asp36) and lysine (Lys142) form a catalytic triad, which is consistent with biochemical studies of BiuH variants. Finally, molecular dynamics simulations highlighted the presence of three channels from the active site to the enzyme surface: a persistent tunnel gated by residues Val218 and Gln215 forming a potential substrate channel and two smaller channels formed by Val28 and a mobile loop (including residues Phe41, Tyr47 and Met51) that may serve as channels for co-product (ammonia) or co-substrate (water).

Diastereoselective C-H Bond Amination for Disubstituted Pyrrolidines.

We report herein the improved diastereoselective synthesis of 2,5-disubstituted pyrrolidines from aliphatic azides. Experimental and theoretical studies of the C-H amination reaction mediated by the iron dipyrrinato complex (Ad L)FeCl(OEt2 ) provided a model for diastereoinduction and allowed for systematic variation of the catalyst to enhance selectivity. Among the iron alkoxide and aryloxide catalysts evaluated, the iron phenoxide complex exhibited superior performance towards the generation of syn 2,5-disubstituted pyrrolidines with high diastereoselectivity.

Direct Comparison of C-H Bond Amination Efficacy through Manipulation of Nitrogen-Valence Centered Redox: Imido versus Iminyl.

Reduction of previously reported iminyl radical (ArL)FeCl(•N(C6H4-p-tBu)) (2) with potassium graphite furnished the corresponding high-spin (S = 5/2) imido (ArL)Fe(N(C6H4-p-tBu)) (3) (ArL = 5-mesityl-1,9-(2,4,6-Ph3C6H2)dipyrrin). Oxidation of the three-coordinate imido (ArL)Fe(NAd) (5) with chlorotriphenylmethane afforded (ArL)FeCl(•NAd) (6) with concomitant expulsion of Ph3C(C6H5)CPh2. The respective aryl/alkyl imido/iminyl pairs (3, 2; 5, 6) have been characterized by EPR, zero-field 57Fe Mössbauer, magnetometry, single crystal X-ray diffraction, XAS, and EXAFS for 6. The high-spin (S = 5/2) imidos exhibit characteristically short Fe-N bonds (3: 1.708(4) Å; 5: 1.674(11) Å), whereas the corresponding iminyls exhibit elongated Fe-N bonds (2: 1.768(2) Å; 6: 1.761(6) Å). Comparison of the pre-edge absorption feature (1s → 3d) in the X-ray absorption spectra reveals that the four imido/iminyl complexes share a common iron oxidation level consistent with a ferric formulation (3: 7111.5 eV, 2: 7111.5 eV; 5: 7112.2 eV, 6: 7112.4 eV) as compared with a ferrous amine adduct (ArL)FeCl(NH2Ad) (7: 7110.3 eV). N K-edge X-ray absorption spectra reveal a common low-energy absorption present only for the iminyl species 2 (394.5 eV) and 6 (394.8 eV) that was assigned as a N 1s promotion into a N-localized, singly occupied iminyl orbital. Kinetic analysis of the reaction between the respective iron imido and iminyl complexes with toluene yielded the following activation parameters: Ea (kcal/mol) 3: 12.1, 2: 9.2; 5: 11.5, 6: 7.1. The attenuation of the Fe-N bond interaction on oxidation from an imido to an iminyl complex leads to a reduced enthalpic barrier [Δ(ΔH‡) ≈ 5 kcal/mol]; the alkyl iminyl 6 has a reduced enthalpic barrier (1.84 kcal/mol) as compared with the aryl iminyl 2 (3.84 kcal/mol), consistent with iminyl radical delocalization into the aryl substituent in 2 as compared with 6.

High-Spin Iron Imido Complexes Competent for C-H Bond Amination.

Reduction of previously reported (ArL)FeCl with potassium graphite furnished a low-spin (S = 1/2) iron complex (ArL)Fe which features an intramolecular η6-arene interaction and can be utilized as an FeI synthon (ArL = 5-mesityl-1,9-(2,4,6-Ph3C6H2)dipyrrin). Treatment of (ArL)Fe with adamantyl azide or mesityl azide led to the formation of the high-spin (S = 5/2), three-coordinate imidos (ArL)Fe(NAd) and (ArL)Fe(NMes), respectively, as determined by EPR, zero-field 57Fe Mössbauer, magnetometry, and single crystal X-ray diffraction. The high-spin iron imidos are reactive with a variety of substrates: (ArL)Fe(NAd) reacts with azide yielding a ferrous tetrazido (ArL)Fe(κ2-N4Ad2), undergoes intermolecular nitrene transfer to phosphine, abstracts H atoms from weak C-H bonds (1,4-cyclohexadiene, 2,4,6-tBu3C6H2OH) to afford ferrous amido product (ArL)Fe(NHAd), and can mediate intermolecular C-H amination of toluene [PhCH3/PhCD3 kH/kD: 15.5(3); PhCH2D kH/kD: 11(1)]. The C-H bond functionalization reactivity is rationalized from a two-step mechanism wherein each step occurs via maximal energy and orbital overlap between the imido fragment and the C-H bond containing substrate.

An improved and general streamlined phylogenetic protocol applied to the fatty acid desaturase family.

Numerous tools to generate phylogenetic estimates are available, but there is no single protocol that will produce an accurate phylogenetic tree for any dataset. Here, we investigated some of those tools, paying particular attention to different alignment algorithms, in order to produce a phylogeny for the integral membrane fatty acid desaturase (FAD) family. Herein, we report a novel streamlined protocol which utilises peptide pattern recognition (PPR). This protocol can theoretically be applied universally to generate accurate multiple sequence alignments and improve downstream phylogenetic analyses. Applied to the desaturases, the protocol generated the first detailed phylogenetic estimates for the family since 2003, which suggested they may have evolved from three functionally distinct desaturases and further, that desaturases evolved first in cyanobacteria. In addition to the phylogenetic outputs, we mapped PPR sequence motifs onto an X-ray protein structure to provide insights into biochemical function and demonstrate the complementarity of PPR and phylogenetics.

Heterobimetallic Complexes Comprised of Nb and Fe: Isolation of a Coordinatively Unsaturated NbIII/Fe0 Bimetallic Complex Featuring a Nb≡Fe Triple Bond.

Heterometallic multiple bonds between niobium and other transition metals have not been reported to date, likely owing to the highly reactive nature of low-valent niobium centers. Herein, a C3-symmetric tris(phosphinoamide) ligand framework is used to construct a Nb/Fe heterobimetallic complex Cl-Nb(iPrNPPh2)3Fe-Br (2), which features a Fe→Nb dative bond with a metal-metal distance of 2.4269(4) Å. Reduction of 2 in the presence of PMe3 affords Nb(iPrNPPh2)3Fe-PMe3 (6), a compound with an unusual trigonal pyramidal geometry at a NbIII center, a Nb≡Fe triple bond, and the shortest bond distance (2.1446(8) Å) ever reported between Nb and any other transition metal. Complex 6 is thermally unstable and degrades via P-N bond cleavage to form a NbV═NR imide complex, iPrN═Nb(iPrNPPh2)3Fe-PMe3 (9). The heterobimetallic complexes iPrN═Nb(iPrNPPh2)3Fe-Br (8) and 9 are independently synthesized, revealing that the strongly π-bonding imido functionality prevents significant metal-metal interactions. The 57Fe Mössbauer spectra of 2, 6, 8, and 9 show a clear trend in isomer shift (δ), with a decrease in δ as metal-metal interactions become stronger and the Fe center is reduced. The electronic structure and metal-metal bonding of 2, 6, 8, and 9 are explored through computational studies, and cyclic voltammetry is used to better understand the effect of metal-metal interaction in early/late heterobimetallic complexes on the redox properties of the two metals involved.

High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes.

The Toblerone fold was discovered recently when the first structure of the cyclic amide hydrolase, AtzD (a cyanuric acid hydrolase), was elucidated. We surveyed the cyclic amide hydrolase family, finding a strong correlation between phylogenetic distribution and specificity for either cyanuric acid or barbituric acid. One of six classes (IV) could not be tested due to a lack of expression of the proteins from it, and another class (V) had neither cyanuric acid nor barbituric acid hydrolase activity. High-resolution X-ray structures were obtained for a class VI barbituric acid hydrolase (1.7 Å) from a Rhodococcus species and a class V cyclic amide hydrolase (2.4 Å) from a Frankia species for which we were unable to identify a substrate. Both structures were homologous with the tetrameric Toblerone fold enzyme AtzD, demonstrating a high degree of structural conservation within the cyclic amide hydrolase family. The barbituric acid hydrolase structure did not contain zinc, in contrast with early reports of zinc-dependent activity for this enzyme. Instead, each barbituric acid hydrolase monomer contained either Na+ or Mg2+, analogous to the structural metal found in cyanuric acid hydrolase. The Frankia cyclic amide hydrolase contained no metal but instead formed unusual, reversible, intermolecular vicinal disulfide bonds that contributed to the thermal stability of the protein. The active sites were largely conserved between the three enzymes, differing at six positions, which likely determine substrate specificity.IMPORTANCE The Toblerone fold enzymes catalyze an unusual ring-opening hydrolysis with cyclic amide substrates. A survey of these enzymes shows that there is a good correlation between physiological function and phylogenetic distribution within this family of enzymes and provide insights into the evolutionary relationships between the cyanuric acid and barbituric acid hydrolases. This family of enzymes is structurally and mechanistically distinct from other enzyme families; however, to date the structure of just two, physiologically identical, enzymes from this family has been described. We present two new structures: a barbituric acid hydrolase and an enzyme of unknown function. These structures confirm that members of the CyAH family have the unusual Toblerone fold, albeit with some significant differences.

Crystal structure of a putrescine aminotransferase from Pseudomonas sp. strain AAC.

The putrescine aminotransferase KES24511 from Pseudomonas sp. strain AAC was previously identified as an industrially relevant enzyme based on the discovery that it is able to promiscuously catalyse the transamination of 12-aminododecanoic acid. Here, the cloning, heterologous expression, purification and successful crystallization of the KES24511 protein are reported, which ultimately generated crystals adopting space group I2. The crystals diffracted X-rays to 2.07 Šresolution and data were collected using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replacement, with a monomer from PDB entry 4a6t as the search model.

X-ray crystal structure of a malonate-semialdehyde dehydrogenase from Pseudomonas sp. strain AAC.

The NAD-dependent malonate-semialdehyde dehydrogenase KES23460 from Pseudomonas sp. strain AAC makes up half of a bicistronic operon responsible for ß-alanine catabolism to produce acetyl-CoA. The KES23460 protein has been heterologously expressed, purified and used to generate crystals suitable for X-ray diffraction studies. The crystals belonged to space group P212121 and diffracted X-rays to beyond 3 Šresolution using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replacement, with a monomer from PDB entry 4zz7 as the search model.

Exploring Trends in Metal-Metal Bonding, Spectroscopic Properties, and Conformational Flexibility in a Series of Heterobimetallic Ti/M and V/M Complexes (M = Fe, Co, Ni, and Cu).

To understand the metal-metal bonding and conformational flexibility of first-row transition metal heterobimetallic complexes, a series of heterobimetallic Ti/M and V/M complexes (M = Fe, Co, Ni, and Cu) have been investigated. The titanium tris(phosphinoamide) precursors ClTi(XylNPiPr2)3 (1) and Ti(XylNPiPr2)3 (2) have been used to synthesize Ti/Fe (3), Ti/Ni (4, 4THF), and Ti/Cu (5) heterobimetallic complexes. A series of V/M (M = Fe (7), Co (8), Ni (9), and Cu (10)) complexes have been generated starting from the vanadium tris(phosphinoamide) precursor V(XylNPiPr2)3 (6). The new heterobimetallic complexes were characterized and studied by NMR spectroscopy, X-ray crystallography, electron paramagnetic resonance, and Mössbauer spectroscopy, where applicable, and computational methods (DFT). Compounds 3, 4THF, 7, and 8 are C3-symmetric with three bridging phosphinoamide ligands, while compounds 9 and 10 adopt an asymmetric geometry with two bridging phosphinoamides and one phosphinoamide ligand bound η2 to vanadium. Compounds 4 and 5, on the other hand, are asymmetric in the solid state but show evidence for fluxional behavior in solution. A correlation is established between conformational flexibility and metal-metal bond order, which has important implications for the future reactivity of these and other heterobimetallic molecules.

A ß-Alanine Catabolism Pathway Containing a Highly Promiscuous ω-Transaminase in the 12-Aminododecanate-Degrading Pseudomonas sp. Strain AAC.

UNLABELLED: We previously isolated the transaminase KES23458 from Pseudomonas sp. strain AAC as a promising biocatalyst for the production of 12-aminododecanoic acid, a constituent building block of nylon-12. Here, we report the subsequent characterization of this transaminase. It exhibits activity with a broad substrate range which includes α-, ß-, and ω-amino acids, as well as α,ω-diamines and a number of other industrially relevant compounds. It is therefore a prospective candidate for the biosynthesis of a range of polyamide monomers. The crystal structure of KES23458 revealed that the protein forms a dimer containing a large active site pocket and unusual phosphorylated histidine residues. To infer the physiological role of the transaminase, we expressed, purified, and characterized a dehydrogenase from the same operon, KES23460. Unlike the transaminase, the dehydrogenase was shown to be quite selective, catalyzing the oxidation of malonic acid semialdehyde, formed from ß-alanine transamination via KES23458. In keeping with previous reports, the dehydrogenase was shown to catalyze both a coenzyme A (CoA)-dependent reaction to form acetyl-CoA and a significantly slower CoA-independent reaction to form acetate. These findings support the original functional assignment of KES23458 as a ß-alanine transaminase. However, a seemingly well-adapted active site and promiscuity toward unnatural compounds, such as 12-aminododecanoic acid, suggest that this enzyme could perform multiple functions for Pseudomonas sp. strain AAC. IMPORTANCE: We describe the characterization of an industrially relevant transaminase able to metabolize 12-aminododecanoic acid, a constituent building block of the widely used polymer nylon-12, and we report the biochemical and structural characterization of the transaminase protein. A physiological role for this highly promiscuous enzyme is proposed based on the characterization of a related gene from the host organism. Molecular dynamics simulations were carried out to compare the conformational changes in the transaminase protein to better understand the determinants of specificity in the protein. This study makes a substantial contribution that is of interest to the broad biotechnology and enzymology communities, providing insights into the catalytic activity of an industrially relevant biocatalyst as well as the biological function of this operon.

Spin transitions in bis(amidinato)-N-heterocyclic carbene iron(II) and iron(III) complexes.

In contrast to high spin pyridyl diimine iron(ii) dichloride complexes, analogous bis(amidinato)-N-heterocyclic carbene iron(ii) and iron(iii) complexes demonstrate complex magnetic behaviour. In the solid state, they are best described as intermediate spin complexes at low temperatures that demonstrate gradual spin transitions beginning near or below room temperature. Treating the bis(amidinato)-N-heterocyclic carbene iron(ii) complex with an aryl azide revealed enhanced reactivity compared to analogous complexes supported by pyridyl diimine ligands.

Identification of novel transaminases from a 12-aminododecanoic acid-metabolizing Pseudomonas strain.

A Pseudomonas species [Pseudomonas sp. strain amino alkanoate catabolism (AAC)] was identified that has the capacity to use 12-aminododecanoic acid, the constituent building block of homo-nylon-12, as a sole nitrogen source. Growth of Pseudomonas sp. strain AAC could also be supported using a range of additional ω-amino alkanoates. This metabolic function was shown to be most probably dependent upon one or more transaminases (TAs). Fourteen genes encoding putative TAs were identified from the genome of Pseudomonas sp. AAC. Each of the 14 genes was cloned, 11 of which were successfully expressed in Escherichia coli and tested for activity against 12-aminododecanoic acid. In addition, physiological functions were proposed for 9 of the 14 TAs. Of the 14 proteins, activity was demonstrated in 9, and of note, 3 TAs were shown to be able to catalyse the transfer of the ω-amine from 12-aminododecanoic acid to pyruvate. Based on this study, three enzymes have been identified that are promising biocatalysts for the production of nylon and related polymers.

300-Fold increase in production of the Zn2+-dependent dechlorinase TrzN in soluble form via apoenzyme stabilization.

Microbial metalloenzymes constitute a large library of biocatalysts, a number of which have already been shown to catalyze the breakdown of toxic chemicals or industrially relevant chemical transformations. However, while there is considerable interest in harnessing these catalysts for biotechnology, for many of the enzymes, their large-scale production in active, soluble form in recombinant systems is a significant barrier to their use. In this work, we demonstrate that as few as three mutations can result in a 300-fold increase in the expression of soluble TrzN, an enzyme from Arthrobacter aurescens with environmental applications that catalyzes the hydrolysis of triazine herbicides, in Escherichia coli. Using a combination of X-ray crystallography, kinetic analysis, and computational simulation, we show that the majority of the improvement in expression is due to stabilization of the apoenzyme rather than the metal ion-bound holoenzyme. This provides a structural and mechanistic explanation for the observation that many compensatory mutations can increase levels of soluble-protein production without increasing the stability of the final, active form of the enzyme. This study provides a molecular understanding of the importance of the stability of metal ion free states to the accumulation of soluble protein and shows that differences between apoenzyme and holoenzyme structures can result in mutations affecting the stability of either state differently.

Cyanuric acid hydrolase: evolutionary innovation by structural concatenation.

The cyanuric acid hydrolase, AtzD, is the founding member of a newly identified family of ring-opening amidases. We report the first X-ray structure for this family, which is a novel fold (termed the 'Toblerone' fold) that likely evolved via the concatenation of monomers of the trimeric YjgF superfamily and the acquisition of a metal binding site. Structures of AtzD with bound substrate (cyanuric acid) and inhibitors (phosphate, barbituric acid and melamine), along with mutagenesis studies, allowed the identification of the active site. The AtzD monomer, active site and substrate all possess threefold rotational symmetry, to the extent that the active site possesses three potential Ser-Lys catalytic dyads. A single catalytic dyad (Ser85-Lys42) is hypothesized, based on biochemical evidence and crystallographic data. A plausible catalytic mechanism based on these observations is also presented. A comparison with a homology model of the related barbiturase, Bar, was used to infer the active-site residues responsible for substrate specificity, and the phylogeny of the 68 AtzD-like enzymes in the database were analysed in light of this structure-function relationship.