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. Author manuscript; available in PMC: 2011 Feb 16.
Published in final edited form as: Biochemistry. 2010 Feb 16;49(6):1226–1235. doi: 10.1021/bi901812p

Structure Determination and Characterization of the Vitamin B6 Degradative Enzyme 2-(Acetamidomethylene)succinate Hydrolase†,‡

Kathryn M McCulloch □, Tathagata Mukherjee □, Tadhg P Begley §,*, Steven E Ealick □,*
PMCID: PMC2849673  NIHMSID: NIHMS173944  PMID: 20099871

Abstract

The gene identification and kinetic characterization of E-2-(acetamidomethylene)succinate (E-2AMS) hydrolase has recently been described. This enzyme catalyzes the final reaction in the degradation of vitamin B6 and produces succinic semialdehyde, acetate, ammonia, and carbon dioxide from E-2AMS. The structure of E-2AMS hydrolase was determined to 2.3 Å using SAD phasing. E-2AMS hydrolase is a member of the α/β hydrolase superfamily and utilizes a serine/histidine/aspartic acid catalytic triad. Mutation of either the nucleophilic serine or the aspartate resulted in inactive enzyme. Mutation of an additional serine residue in the active site causes the enzyme to be unstable and is likely structurally important. The structure also provides insight into the mechanism of hydrolysis of E-2AMS and identifies several potential catalytically important residues.

Vitamin B6 is an essential vitamin whose active cofactor, pyridoxal 5′-phosphate (PLP), plays an important role within the cell to stabilize carbanion intermediates adjacent to an amino group (1). Vitamin B6 degradation was first shown to occur in select microorganisms in the late 1950s by culturing bacteria on minimal media where the only carbon and nitrogen sources were different B6 vitamers (2). Two pathways for the degradation of vitamin B6 have been described; the first has been characterized in Pseudomonas sp. MA-1 and the second in Pseudomonas IA and Arthrobacter Cr-7 (2). None of the PLP catabolic genes in these microorganisms were identified. Gene identification was greatly facilitated when the genome of Mesorhizobium loti MAFF303099 was sequenced in 2000 (3). Shortly thereafter, the pyridoxine 4-oxidase gene was identified, suggesting that this bacterium was capable of degrading vitamin B6 (4). Six other catabolic genes were rapidly identified completing the vitamin B6 degradative pathway in M. loti, shown in Figure 1 (5–11). Crystal structures have been determined for three of these enzymes (12–14). The M. loti degradative pathway is slightly different from that observed in Pseudomonas sp. MA-1.

Figure 1.

Figure 1

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Vitamin B6 degradative pathway found in M. loti. 1, pyridoxine; 2, pyridoxal; 3, 4-pyridoxolactone; 4, 4-pyridoxic acid; 5, 5-formyl-2-methyl-3-hydroxypyridine-4-carboxylic acid; 6, 2-methyl-3-hydroxypyridine-4,5-dicarboxylic acid; 7, 2-methyl-3-hydroxypyridine-5-carboxylic acid; 8, 2-(acetamidomethylene)succinic acid; 9, succinic semialdehyde. Other final products are ammonia, acetate, and carbon dioxide.

E-2-(acetamidomethylene)succinate (E-2AMS) hydrolase is the last enzyme to be biochemically characterized on the vitamin B6 catabolic pathway. This enzyme catalyzes the hydrolysis of E-2AMS to succinic semialdehyde, ammonia, acetate, and carbon dioxide. The products of this reaction have been conclusively identified and the steady state kinetics of the enzyme have been characterized (7, 10). A similar reaction in nicotinate catabolism, catalyzing the amide hydrolysis of 2-(enamine)-glutarate, is performed by an enamidase, a member of the amidohydrolase superfamily (15). The primary sequence of E-2AMS hydrolase, however, indicated that this enzyme was most similar to members of the α/β hydrolase superfamily, although the sequence homology was low. This superfamily often utilizes a catalytic triad consisting of an active site nucleophile, an absolutely conserved histidine residue, and an acidic residue. Sequence alignments failed to identify this acidic residue and it was unclear how this enzyme catalyzed its metal-independent hydrolysis reaction (10). The structure reported here identifies this acidic residue and also suggests several other residues within the active site that could be involved in substrate binding and catalysis.

MATERIALS AND METHODS

Cloning, Overexpression, and Purification of E-2AMS Hydrolase

The molecular cloning of the mlr6787 gene from M. loti MAFF303099 has been previously described (7). The resulting pMl5331.XF1 plasmid contains the mlr6787 gene with an N-terminal polyhistidine tag and was transformed into Escherichia coli B834(DE3), a cell line auxotrophic for methionine. Overnight cultures were grown by transferring a single colony to 10 mL LB medium with 150 µg/mL ampicillin at 37 °C with shaking. Selenomethionyl-incorporated (SeMet) protein was grown using a minimal medium supplemented with 0.4% glucose, 20 mg/L of all amino acids except methionine, 50 mg/L L-selenomethionine, 1× MEM vitamin mix (Invitrogen), 2 mM MgSO4, 0.1 mM CaCl2, 25 mg/L FeSO4, and 150 µg/mL ampicillin. The overnight culture, grown in LB, was harvested at 4 °C at 2,000 × g for 15 min then resuspended in the minimal medium for inoculation of 1 L cultures. The large culture was allowed to grow at 37 °C with shaking to an OD595 of 0.6. The temperature was then lowered to 15 °C and overexpression of protein was induced overnight with 1 mM isopropyl β-D-thiogalactopyranoside (IPTG). After 16 h, cells were pelleted by centrifugation at 6,000 × g and stored frozen at −20 °C. For native protein overexpression, 1 L of LB medium with 150 µg/mL ampicillin was inoculated with 5 mL of overnight culture, then grown at 37 °C with shaking to an OD595 of 0.6 and induced with 1 mM IPTG. The cells were harvested as described for the SeMet protein preparation.

Purification of both native and SeMet protein followed the same protocol. Frozen cell pellet was resuspended in 30 mL of purification buffer (50 mM NaH2PO4 at pH 8.0, 300 mM NaCl, 3 mM β-mercaptoethanol) with 10 mM imidazole and lysed by sonication. After lysis, the cell extract was clarified by centrifugation at 40,000 × g for 1 h at 4 °C. The supernatant was then twice passed over a 2 mL Ni-NTA column (Qiagen) pre-equilibrated with purification buffer. The column was then washed with 50 mL of purification buffer and nonspecifically binding contaminants were removed by washing with 25 mL of purification buffer containing 20 mM imidazole. The protein was eluted from the column using purification buffer containing 250 mM imidazole. The resulting sample was further purified using size exclusion chromatography (HiLoad 26/60 Superdex 75 pg, GE Healthcare) to greater than 95% homogeneity as judged by SDS-PAGE analysis (results not shown). The protein samples were concentrated to ~8 mg/mL as measured by Bradford assay and stored at −80 °C in storage buffer (20 mM Tris pH 8.0, 50 mM NaCl), with 1 mM dithiothreitol (DTT) added to the SeMet sample (16).

Activity Assay for E-2AMS Hydrolase

The assay used for determining the activity of E-2AMS hydrolase has previously been described (7). Briefly, freshly purified enzyme was buffer exchanged into 50 mM phosphate buffer containing a quantified amount of E-2AMS and the decrease in absorbance at 261 nm is monitored. This assay was used to determine the steady state kinetic parameters previously reported (7, 10).

Crystallization of E-2AMS Hydrolase

The hanging-drop vapor diffusion method was used to crystallize E-2AMS hydrolase by mixing equal volumes of protein sample with reservoir solution and allowing the drop to equilibrate against 500 µL of reservoir solution at 22 °C. Initial hits were determined for the native protein using commercially available sparse matrix screens (Hampton Research, Emerald BioSystems). Optimized reservoir conditions consisted of 8–12% PEG 8000, 200 mM MgCl2, and 100 mM Tris buffer, pH 7.4–8.0 and 1.5 µL of reservoir solution was mixed with an equal volume of protein solution. Tetragonal bipyramidal crystals grew to 200 µm × 50 µm within two days. SeMet E-2AMS hydrolase crystals grew under the same conditions, but required an additional microseeding step. Briefly, native crystals were transferred to a seed stabilization solution of 9% PEG 8000, 200 mM MgCl2, 100 mM Tris at pH 7.8, then crushed using Seed Bead (Hampton Research). The freshly prepared seeds were then serially diluted and 0.5 µL of seed solution was added to SeMet hanging drops pre-equilibrated overnight. Crystals began growing within 20 min of seeding and reached full size overnight. Native and SeMet E-2AMS hydrolase crystals both belong to the space group P212121 with average unit cell parameters of a = 115 Å, b = 179 Å, and c = 189 Å. The asymmetric unit consists of twelve chains, corresponding to a Matthew’s coefficient of 2.40 Å3/Da and a solvent content of 49% (17).

X-Ray Data Collection and Processing

Protein crystals were cryoprotected in the crystallization solution supplemented with 17% glycerol and then flash frozen by plunging into liquid nitrogen. A single wavelength anomalous dataset was collected on a single SeMet E-2AMS hydrolase crystal on the NE-CAT 24-ID-C beamline at the Advanced Photon Source. A fluorescence scan was performed on a SeMet crystal to determine the maximum f″ for selenium, and the data were collected at this wavelength to a maximum resolution of 2.7 Å over a total rotation range of 180°. A native crystal diffracted to 2.3 Å resolution and data were collected over 110° on the NE-CAT 24-ID-E beamline. Both datasets were collected using Quantum315 detectors (Area Detector Systems Corp.) and used a 0.5° oscillation range to minimize reflection overlaps. The data were then indexed, integrated, and scaled using the HKL2000 suite of programs (18). Data collection statistics are given in Table 1.

Table 1.

Summary of Data Collection Statistics

SeMet Native
Source APS 24-ID-C APS 24-ID-E
Resolution (Å) 2.70 2.26
Wavelength (eV) 12662 12667
Space Group P212121 P212121
a (Å) 115.2 115.2
b (Å) 179.0 178.5
c (Å) 189.2 189.3
Matthew’s Coef. 2.4 2.4
   % solvent 49 49
   Mol/a.s.u. 12 12
Measured Reflections 531900 727191
Unique reflectionsa 207285 (20629) b 168768 (12441)
Average I/σ 11.7 (2.4) 13.1 (1.7)
Redundancy 2.6 (2.5) 4.3 (2.1)
Completeness (%) 99.9 (99.4) 91.6 (68.2)
Rsymc (%) 7.9 (35.7) 10.3 (45.8)
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a

Unique reflections include Bijvoet pairs for anomalous data.

b

Values in parentheses are for the highest resolution shell.

c

Rsym = ΣΣi|Ii − 〈I〉|/Σ〈I〉, where 〈I〉 is the mean intensity of the N reflections with intensities Ii and common indicies h,k,l.

Structure Determination, Model Building, and Refinement

Positions for 36 of a possible 60 selenium atoms were determined using the SAD dataset to 2.7 Å and the program hkl2map (19–21). These heavy atom coordinates were then used for SAD phasing, followed by density modification and calculation of initial electron density maps in CNS (22). RESOLVE was then used to perform phase extension to 2.3 Å with the native data and automated model building (23, 24). The initial model, consisting of 1511 out of 3336 residues in the asymmetric unit, required extensive manual model building in COOT (25). Once twelve chains had been positioned in the asymmetric unit relying solely on the experimental phase information, iterative rounds of refinement were performed in CNS followed by additional manual model building. Strict non-crystallographic symmetry (NCS) restraints were utilized and gradually lessened throughout refinement (26). Water molecules were added during later rounds of refinement using CNS. The final model, consisting of residues 11–278 for twelve chains, was analyzed using PROCHECK; Ser106 and Asp257 were each identified as having geometry that falls within the disallowed region, although each residue has clear electron density (27). Final refinement statistics are summarized in Table 2. Figures were generated using PYMOL and ChemDraw (28).

Table 2.

Summary of Data Refinement Statistics

E-2AMS Hydrolase
Resolution (Å) 50.00 – 2.30
No. of protein atoms 24444
No. of ligand atoms 12
No. of water atoms 1387
Reflections in working set 279026
Reflections in test set 18821
R factora(%) 20.4
Rfreeb (%) 24.5
Rmsd from ideal
   Bonds (Å) 0.0058
   Angles (°) 1.2
Average B-factor (Å3) 28.4
Ramachandran Plot
   Most favored (%) 87.6
   Additionally allowed (%) 11.9
   Generously allowed (%) 0.1
   Disallowed (%) 0.4
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a

R factor = Σhkl‖Fobs| − k|Fcal‖/Σhkl │Fobs│ where Fobs and Fcal are observed and calculated structure factors, respectively.

b

For Rfree, the sum is extended over a subset of reflections (5%) excluded from all stages of refinement.

Mutagenesis of E-2AMS Hydrolase

Mutants of E-2AMS hydrolase were prepared using standard procedures for site-directed mutagenesis (29). The plasmid p5331.XFI in E. coli Mach1 cell line was used as template DNA. Primers used for generating S106A are as follows: 5′-(for)CCA TCC TCG TCG GAC ACG CGC TTG GTG CTC GAA ATT CGG-3′; 5′-(rev)CCG AAT TTC GAG CAC CAA GCG CGT GTC CGA CGA GGA TGG-3′. The D130N mutant was prepared using the following primers: 5′-(for)GGT GCG GTC GGT CGT CGC GAT TAA CTT TAC GCC GTA CAT CGA G-3′; 5′-(rev)C TCG ATG TAC GGC GTA AAG TTA ATC GCG ACG ACC GAC CGC ACC-3′. To generate the S230A mutant, the following primers were used: 5′-(for)CGT TCG GGG CGA GTC CGC CAA GTT GGT TTC TGC G-3′; 5′-(rev)C GCA GAA ACC AAC TTG GCG GAC TCG CCC CGA ACG-3′. Additionally, the S230C and S230N mutants were generated by replacing the underlined bases in the forward primer with CTG and TTG and CAG and CAA, respectively. These mutants were each overexpressed and purified as described for the wild-type E-2AMS hydrolase. The S106A mutant was crystallized using the seeding procedure required for the SeMet sample.

RESULTS

Packing of E-2AMS Hydrolase

A typical diffraction pattern from an E-2AMS hydrolase dataset is shown in Figure 2A. At low resolution, it is clear that every third row of diffraction maxima exhibited a much greater intensity than the intervening two rows of maxima. This pattern indicated the possibility of pseudo-translational symmetry (30), which was confirmed by the structure. Twelve chains were built into the asymmetric unit and resulted in 49% solvent content. Figure 2B shows one layer of monomers in the unit cell, which consists of three unique protomers from the asymmetric unit and their crystallographic equivalents. The pseudo-translational symmetry occurs along the B-axis, where the spacing between protomers is nearly equal for two of the three pairs and nearly 10 Å further for the final spacing.

Figure 2.

Figure 2

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Pseudo-translational symmetry in E-2AMS hydrolase crystals. A. A typical diffraction pattern for E-2AMS hydrolase. At low resolution, every third row of reflections is much more intense than other rows. B. Crystal packing of E-2AMS hydrolase. For clarity only one third of the unit cell is shown, with the three unique chains colored blue, red and green. The crystallographically related protomers are shown in grey.

Overall Structure of E-2AMS Hydrolase

The structure of E-2AMS hydrolase was solved using SeMet SAD phasing at 2.7 Å resolution followed by phase extension with native data to 2.3 Å. Each of the twelve protomers within the asymmetric unit consists of residues 11–278; the first ten residues and the polyhistidine tag are not visible in the electron density. Figure 3 shows the final model of E-2AMS hydrolase. The overall fold of this enzyme indicates that E-2AMS hydrolase belongs to the α/β hydrolase superfamily. The core of the enzyme is an eight-stranded mostly parallel β-sheet where β2 is the only strand running antiparallel (β1↑β2↓β4↑β3↑β5↑β6↑β9↑β10↑). The β-sheet has a very tight twist so that β10 is oriented nearly perpendicular to β1 when looking down the β-sheet. One side of the β-sheet is flanked by three α-helices, α2, α10, and α11. A bundle of α-helices, consisting of α1, α3, α8, and α9, packs on the other side of the β-sheet. A cap domain is inserted between β6 and β9 and sits at the N-terminal side of the β-sheet. This lid is made up of four α-helices (α4, α5, α6, and α7) and a small two-stranded antiparallel β-sheet (β7↑β8↓).

Figure 3.

Figure 3

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Monomeric structure of E-2AMS hydrolase. A. Stereoview ribbon diagram of E-2AMS hydrolase with the secondary structures labelled. β-strands are shown in green and α-helices are shown in blue. B. Topology diagram of E-2AMS hydrolase, using the same color scheme as A. C. Ribbon diagram of E-2AMS hydrolase illustrating the sharp twist in the β-sheet running through the core of the enzyme and the cap domain.

The twelve protomers of E-2AMS hydrolase in the asymmetric unit form six pairs of dimers with identical interfaces. The two protomers are related to each other by local twofold symmetry. The β-sheets of each chain face in the same direction, but twist in opposite directions, as seen in Figure 4. The dimer interface involves the loop region between α9 and β10, residues from β10, and the C-terminal end of α10 from both protomers. Each dimer is about 95 Å long with a total surface area of nearly 20,000 Å2. Roughly 2000 Å2 is buried at the dimer interface (31). Two hydrogen bonds are formed between the carbonyl oxygen and amide nitrogen atoms of the protein backbone at Val250 and Val250* (where * indicates the second protomer of the dimer). A salt bridge is formed between Arg243 and Glu228*, a hydrogen bond is found between Asn274 and Aps247*, and Arg124 forms interactions with the oxygen atoms of the carboxy terminus at Ala278*. Additionally, Phe275, Pro221, Leu223, Pro 249, Val250, Val251, and Ala271 from each protomer form an extended hydrophobic patch at the dimer interface.

Figure 4.

Figure 4

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Dimeric structure of E-2AMS hydrolase. Each chain is colored differently, one red and the second blue. The second orientation obtained by rotating the first orientation by 90° along the horizontal axis.

Active Site of E-2AMS Hydrolase

The putative active site was identified through sequence and structural homology with other α/β hydrolases and is located at the C-terminal end of the β-sheet and is shielded from solvent by the cap domain. Three positively charged residues, Arg146, Arg167, and Lys231, are present at the entrance to the active site. The active site pocket has two distinct environments. The narrow cleft adjacent to Ser106 is lined with primarily hydrophobic residues, including Ile41, Leu207, Leu143, Leu232, and Phe131. The second half of the active site, however, is more hydrophilic. This pocket, roughly 10 Å deep and 6 Å wide, is filled with water molecules coordinated to hydrophilic residues. Arg179 forms hydrogen bonds to two water molecules and is oriented in the active site by Glu262. Three tyrosine residues, Tyr184, Tyr168, and Tyr259, are positioned so the hydroxyl group faces into the active site and forms hydrogen bonds with water molecules. Other hydrophilic residues in the active site include Thr42, Ser43, and His105.

The putative nucleophilic residue, Ser106, adopts a strained conformation at the C-terminal end of β5 and is hydrogen bonded to a structurally conserved water molecule, which is also coordinated to the backbone amide nitrogen atoms of Leu107 and Leu41. A chloride ion is bound in a pocket next to Ser106. The chloride ion is bound in an oxyanion hole, coordinated to Ser106 2.9 Å away and is also forming interactions with two backbone amide nitrogen atoms from Ile41 and Leu107 (3.2 and 3.3 Å, respectively). His258, located after β10, is 3.0 Å from Ser106 and is itself positioned by Asp130, 2.5 Å away. Asp130 is found at the end of β6 and Ser230 occurs after β9. Ser230 forms a strong hydrogen bond with Asp130 (2.7 Å) and a second hydrogen bond with the amide nitrogen atom from the protein backbone of Leu232. These interactions are shown in Figure 5.

Figure 5.

Figure 5

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Stereoview ball and stick diagram of the active site of E-2AMS hydrolase. Water molecules are shown as red nonbonded spheres and the chloride ion is shown as a nonbonded grey sphere. Key protein interactions are shown as dashed lines.

Activity of E-2AMS Hydrolase Mutants

The extinction coefficient at 261 nm for E-2AMS is 18600 M−1 cm−1 as previously determined, and the KM and kcat values for E-2AMS hydrolase have also been reported (7, 10, 32). The activity of the active site mutants S106A, D130N, and S230C were assayed by measuring the decrease in the absorbance at 261 nm, the λmax for E-2AMS as previously described (7, 10). Each of these mutants was found to be completely inactive relative to the native enzyme, which retained an activity comparable to published results. The active site mutants S230A and S230N could not be assayed because these proteins precipitated in the assay buffer. The inactive S106A mutant was then used for cocrystallization and soaking experiments with E-2AMS, which were unsuccessful in producing an enzyme-substrate complex.

DISCUSSION

Comparison of E-2AMS Hydrolase to Other Members of the α/β Hydrolase Superfamily

The α/β hydrolase superfamily comprises a very large class of enzymes, catalyzing myriad reactions and related through similar tertiary structures. This family has been structurally well characterized and includes esterases, lipases, epoxidases, alkane dehalogenases, carbon-carbon bond hydrolases, amidohydrolases, and thioesterases (33, 34). Previous analysis of the primary sequence for E-2AMS hydrolase using BLAST suggested that this enzyme was a member of the α/β hydrolase superfamily, despite a low sequence identity to this family of enzymes (10). A DALI search was performed using the structure of E-2AMS hydrolase and these results confirmed that E-2AMS hydrolase is a member of the α/β hydrolase family. Representative members of this superfamily are shown in Table 3 and their similarity to E-2AMS hydrolase is given by their Z-score, rmsd, sequence identity, and the number of residues aligned (34–40). The core of E-2AMS hydrolase is formed by an eight stranded β-sheet flanked on both sides by α-helices with a strand order that agrees with the other members of this superfamily (41, 42). The cap domain is an insertion between β6 and β9, with a short two stranded antiparallel β-sheet and four α-helices. The cap domain acts to shield the active site from solvent. While this second domain is not part of the α/β hydrolase fold, insertions are common after the fifth β-strand of the core β-sheet (42). Additionally, the cap domain is not conserved. For example, the cap domains of the serine hydrolase CarC and the carbon-carbon hydrolase MhpC (34, 37) are composed of three long α-helices and the cap domain from an α/β hydrolase of Novosphingobium aromaticivorans DSM 12444 has a three stranded antiparallel β-sheet flanked by four α-helices (PBD ID: 3BWX).

Table 3.

Enzymes Identified as Structurally Similar to E-2AMS Hydrolase through DALI

Protein PDB ID Z Score RMSD %
Identical		 # aligned residues
α/βHydrolase,
YP_496220.1 		3BWX 30.4 2.4 23 263
Serine hydrolase (CarC) 1J1I 29.1 2.2 21 238
Chloroperoxidase L 1A88 28.7 2.4 21 246
Arylesterase (PFE) 1VA4 28.7 2.5 23 247
Esterase (EST) 1ZOI 28.5 2.5 21 247
Esterase (ybfF) 3BF7 27.5 2.5 21 242
Fluoroacetate dehalogenase 1Y37 27.3 2.7 24 246
C-C bond hydrolase
(MhpC)		 1U2E 26.3 2.6 18 251
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Figure 6 shows a sequence alignment of similar enzymes identified through DALI (43, 44). The “nucleophilic elbow” begins at the C-terminal end of β5 in E-2AMS hydrolase and is identified using the fingerprint motif Gly-X-Nu-X-Gly, where X is any amino acid and Nu is the nucleophilic amino acid necessary for catalysis. In E-2AMS hydrolase, the nucleophile is Ser106. The sequence alignment identified few conserved residues; the majority being glycine residues, presumably important for proper folding. An absolutely conserved histidine residue required for catalysis in the α/β hydrolase family is found after the last β-strand in the core domain. Additionally, the seventh β-strand of the eight stranded β-sheet is mostly conserved, with hydrophobic residues forming interactions with neighboring β-strands.

Figure 6.

Figure 6

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Sequence alignment of E-2AMS hydrolase with other enzymes identified as structurally homologous by DALI. Included enzymes are the α/β hydrolase YP_496220.1 (3BWX), CarC (1J1I), chloroperoxidase L (1A88), the PFE arylesterase (1VA4), the EST esterase (1ZOI), ybfF (3BF7), fluoroacetate dehalogenase (1Y37), and MhpC (1U2E). The nucleophile is marked with a green circle, the catalytic histidine is labelled with a blue star, and the different active site acids are labelled using triangles. The expected acidic residues have a purple triangle, while the location of the acidic residue in E-2AMS hydrolase has a yellow triangle.

Active Site Comparison

The α/β hydrolase superfamily utilizes a catalytic triad consisting of a nucleophile, a strictly conserved histidine residue, and an acidic residue, usually an aspartate residue. The nucleophile, identified as Ser106, and the catalytic histidine residue, His258, are located in structurally conserved positions at the interface of the two domains of E-2AMS hydrolase. However, the third residue of the catalytic triad is not located at the C-terminal end of the seventh β-strand as expected. Instead, His258 forms a hydrogen bond with Asp130 found after β6 with Ser230 occupying the turn between β9 and α9. Figure 7 shows the superposition of the active site of E-2AMS hydrolase (green) with the esterase ybfF (white) from E. coli (PDB ID: 3BF7) and the carbon-carbon bond hydrolase MhpC (purple) from E. coli (PDB ID: 1U2E) (34, 40). All three structures have an oxyanion hole formed by the amide nitrogen atoms of the protein backbone using the residue adjacent to the nucleophile (Leu107 in E-2AMS hydrolase) and a residue at the C-terminal end of the fourth β-strand (Ile41 at the end of β3 in E-2AMS hydrolase). The catalytic triads observed in E-2AMS hydrolase and ybfF are similar. The histidine responsible for activation of the nucleophile is 3.0 Å from Ser106 and 2.9 Å in the ybfF structure. The histidine residues in these two structures are each then coordinated to one oxygen atom of the carboxylate group of the acidic residue at the end of β6. The catalytic triad seen in MhpC, shown in purple in Figure 7, adopts the more common arrangement. The nucleophile, Ser110, is positioned 3.3 Å from the Nε2 atom of the side chain of His263. The aspartate residue responsible for activation of His263, Asp235, is coordinated to the Nδ1 atom of the histidine side chain using both oxygen atoms of the carboxylate side chain. Asp235 is located at the end of the seventh β-strand of the β-sheet. The remaining residues lining the active site are not conserved and show no sequence similarity. However, careful sequence analysis has identified several residues apart from the catalytic triad that can help identify the reaction catalyzed and suggest E-2AMS hydrolase is quite similar to the esterase subclass of the α/β hydrolase superfamily (45, 46). The residue preceding the active site nucleophile is a histidine and two residues before the catalytic histidine is a hydrophobic residue in esterases (His105 and Ala261, respectively, in E-2AMS hydrolase). While the reaction catalyzed is a hydrolysis of an amide bond instead of an ester linkage, the requirements and chemistry are very similar. Additionally, the arrangement of active site residues in which the acidic residue is found at the end of β6 and a fourth catalytic residue, a serine at the C-terminal end of the seventh β-strand, is not uncommon in esterases (40).

Figure 7.

Figure 7

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Stereoview ball and stick diagram comparing the active site of E-2AMS hydrolase to other members of the α/β hydrolase superfamily. The E-2AMS hydrolase structure is shown with green carbon atoms, ybfF is shown using magenta carbon atoms, and the carbon-carbon bond hydrolase MhpC has white carbon atoms. All residues of E-2AMS hydrolase are labelled and the catalytic residues of ybfF and MhpC are labelled.

Mechanistic Implications for E-2AMS Hydrolase

Previous characterization of E-2AMS hydrolase has suggested a possible mechanism for the hydrolysis of E-2AMS to form succinic semialdehyde, acetate, ammonia, and carbon dioxide, shown in Figure 8 (7). This mechanism utilizes an active site base to activate a water molecule for nucleophilic attack on the carbonyl carbon atom of the amide group. Collapse of the tetrahedral intermediate then leads to the loss of acetate. Tautomerization of intermediate 11 is followed by loss of carbon dioxide and release of ammonia through the addition of water. The last two steps could also occur in the reverse order. Direct addition of an active site nucleophile to the amide carbonyl carbon atom is also a possibility (Figure 8, Mechanism 2). Direct attack by the active site nucleophile is most commonly observed in serine proteases, which are not members of the α/β superfamily but have a similar active site triad, composed of serine, histidine, and aspartate (47). However, an aryl esterase from Pseudomonas fluorescens, which has the α/β hydrolase fold, is believed to function through direct attack of the nucleophilic serine residue (35). A third possibility for the hydrolysis of E-2AMS to form intermediate 10 utilizes His258 to deprotonate water for attack on the carbonyl carbon, leading to loss of acetate and intermediate 11. In this mechanism, Ser106 might stabilize the negatively charged tetrahedral intermediate found in the oxyanion hole. This general base mechanism has precedence; the carbon-carbon bond hydrolase MhpC from E. coli is believed to use His263 for activation of water and Ser110 for stabilization of a tetrahedral intermediate (34, 48, 49).

Figure 8.

Figure 8

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Proposed mechanisms for the hydrolysis of E-2AMS to produce succinic semialdehyde, acetate, ammonia, and carbon dioxide. Mechanism 1 utilizes Ser106 to activate a water molecule for attack at the carbonyl carbon of the amide bond, while Mechanism 2 utilizes a direct attack on E-2AMS by Ser106.

Although all attempts at cocrystallization or soaking E-2AMS into crystals of E-2AMS hydrolase or into crystals of the E-2AMS hydrolase S106A mutant were unsuccessful, examination of the active site suggests several residues that could play important roles in both the binding of E-2AMS and the catalysis of E-2AMS hydrolase. The catalytic triad, shown in Figure 5, consists of Ser106, His258, and Asp130 and most likely functions as seen in other α/β hydrolase enzymes (42). Briefly, Asp130 activates His258 for deprotonation of Ser106, which could act as a nucleophile for direct attack on the E-2AMS, or activate a water molecule for attack on the substrate. Mutation of Ser106 to alanine abolished all catalytic activity, confirming this residue’s critical importance for activity. The D130N mutant also showed no activity, indicating that the activation and stabilization of the catalytic histidine residue is necessary for catalysis. Ser230, found after β9 in the position most commonly occupied by the acidic residue of the catalytic triad, is more than 4 Å from His258 but forms a strong hydrogen bond (2.7 Å) with Asp130. Ser230 may play an important role in the structural integrity of the enzyme because the S230A, S230C and S230N mutants were all unstable. It is possible the slightly larger sulphur atom of cysteine in the S230C mutant could disrupt this sharp turn between β9 and α9. Other interactions involving Ser230 include two hydrogen bonds to amide nitrogen atoms of the protein backbone of Leu232 and Val233 in a β-turn.

The active site has several positively charged residues which could be involved in coordination to the carboxylate groups of E-2AMS (Figure 5). Three arginine residues, Arg146, Arg167, and Arg179, face into the active site. Additionally, Arg179 forms two salt bridges with Glu262 to help orient Arg179 within the active site. Manual placement of the substrate, such that the carbonyl carbon of the amide group is located near Ser106 in the active site and the carbonyl oxygen points towards the oxyanion hole, suggests Arg146 and Arg179 are both likely candidates for coordination to the carboxylate groups and could play a role in the proper orientation of E-2AMS within the active site (Figure 9). Either arginine residue could also stabilize the enol intermediate and serve as a proton donor in the first mechanism. Protonation of the enol intermediate 11 could utilize Tyr166, Tyr259, or His105, either directly or using an activated water molecule. These same residues could also be involved in catalyzing the decarboxylation reaction leading to succinic semialdehyde.

Figure 9.

Figure 9

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Possible coordination of E-2AMS within the active site. A. Schematic diagram where E-2AMS (shown in red) was manually positioned such that either Ser106 or an activated water molecule could attack the carbonyl carbon of the amide group. Potential hydrogen bonds are shown as dashed lines. B. Stereoview ball and stick diagram of the E-2AMS hydrolase active site with E-2AMS manually positioned in the active site. Carbon atoms of E-2AMS hydrolase are colored green and carbon atoms of E-2AMS are colored gray. Possible interactions and hydrogen bonds important for active site orientation are shown in dashed lines.

ACKNOWLEDGEMENT

We are grateful to Dr. Yasunobu Ohkawa of the National Institute of Agrobiological Sciences, Ibaraki, Japan for sharing the M. loti MAFF303099 strain with us. We would also like to thank Dr. Cynthia Kinsland and the Cornell Protein Facility for providing the clones and performing the site-directed mutagenesis. We thank Leslie Kinsland for her assistance in preparing this manuscript. Lastly, the assistance provided by the beamline staff scientists at NE-CAT during data collection is appreciated.

ABBREVIATIONS

PLP

Pyridoxal 5′-phosphate

M. loti

Mesorhizobium loti

E-2AMS

E-2-(acetamidomethylene)succinate

E. coli

Escherichia coli

SeMet

selenomethionyl

IPTG

isopropyl β-D-thiogalactopyranoside

DTT

dithiothreitol

NCS

noncrystallographic symmetry

Footnotes

†

This work is based upon research conducted at the Northeastern Collaborative Access Team beam lines of the Advanced Photon Source, supported by award RR-15301 from the National Center for Research Resources at the National Institute of Health. Use of the Advanced Photon Source is supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under contract No. W-31-109-ENG-38. This research was supported by a grant from the National Institutes of Health (GM069618) and a NIH Chemistry and Biology Interface Training Grant (GM008500).

‡

The Brookhaven Protein Data Bank code for E-2AMS hydrolase is 3KXP.

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