A Structure Function Model for 1-Pyrroline-5’ Carboxylate Reductase

Shukla,V.B., Johnson, C.A and Hawes, J.W.

Department of Chemistry and Biochemistry

Miami University

Oxford, Ohio 45056

Phone: 513-529-8072

FAX: 513-529-5715

hawesjw@muohio.edu

Running Title- 1-Pyrroline-5’ Carboxylate Reductase

Abstract

We present a structure / function model for 1-pyrroline-5’ carboxylate reductase (P5CR)

based on enzymatic and structural similarity to the β-hydroxyacid dehydrogenase enzyme

family. P5CR is similar to the β-hydroxyacid dehydrogenases in that it is non-metal-dependant

and catalyzes redox chemistry with specific carboxylate substrates. Recombinant E. coli P5CR

displays circular dichroism spectra similar to that of β-hydroxyisobutyrate dehydrogenase,

suggesting similarities in secondary structural contents. P5CR amino acid sequences from

diverse species display homology in the regions corresponding to the known functional domains

of the β-hydroxyacid dehydrogenases. These include the N-terminal dinucleotide cofactor-

binding domain, the carboxylate substrate-binding domain, and the catalytic domain. Site-

directed mutagenesis of a conserved threonine residue in the proposed carboxylate-binding

domain of the E. coli P5CR produces mutant enzymes with reduced catalytic efficiency.

Treatment of the recombinant E. coli P5CR with either iodoacetamide or tetranitromethane

results in inactivation of the enzyme. Quantitation of nitrotyrosine residues shows that

inactivation occurs concomitant with the production of two moles of nitrotyrosine per mole of

enzyme. NADP+ protects the enzyme from inactivation with iodoacetamide but enhances

inactivation with tetranitromethane. E. coli P5CR has three tyrosine residues in its amino acid

sequence, all of which lie within the proposed functional domains. Semi-conservative

replacement of each of these tyrosine residues with phenylalanine results in distinct kinetic

effects, including increased catalytic efficiency. Neither proline nor a variety of β-hydroxyacids

inhibit P5CR; however, glutamate inhibits the enzyme at sub-millimolar concentrations. Based

on this model we propose that γ-glutamate semialdehyde (the straight-chain isomer of pyrroline

carboxylate) may actually be the true substrate for P5CR.

Key Words: Active site, Pyrroline-5-carboxylate, NADPH, proline, oxidoreductase, site directed

mutagensis, , L-thiazolidine-4-carboxylate, glutamate.

Introduction

Pyrroline-5’carboxylate (P5C) is an intermediate in the biosynthesis of the amino acid

proline, and is situated at a branch point between the citric acid cycle and the urea cycle through

conversion to ornithine. As a redox couple, proline and P5C are reported to form a cycle

capable of transferring reducing equivalents into mitochondria as proline and oxidizing potential

out as P5C (1). This cycle depends on the presence of proline oxidase in mitochondria and

pyrroline carboxylate reductase in the cytosol. P5C, as a precursor of proline, has multiple

physiological roles in plants (heavy metal and osmotic stress), bacteria, and animal tissues. (2-

10).

Pyrroline-5’-carboxylate reductase (P5CR; EC 1.5.1.2) is the enzyme which catalyzes the

final reaction in proline biosynthesis by converting P5C to proline with either NADH or NADPH

as cofactor. It may also regulate metabolism limited by NADP+ concentrations such as the

pentose phosphate pathway (11). P5CR is unusual compared to other oxidoredutases as it acts

unidirectionally with its natural substrate, catalyzing only the reduction of P5C and not the

oxidation of proline, whereas most oxidoreductase-catalyzed reactions are fully reversible. It

does, however, oxidize a proline analogue, L-thiazolidine-4-carboxylate. How this occurs,

mechanistically, is not known. Bacterial proline synthesis from glutamate occurs via three

enzymatic reactions catalyzed by -glutamyl kinase (proB gene product, EC 2.7.2.11), -glutamyl

phosphate reductase (proA gene product, EC 1.2.1.41) and P5CR (proC gene product). The E.

coli proC gene was shown to encode a pyrroline carboxylate reductase (4). For the majority of

bacteria the proB and proA genes constitute an operon which is distant from proC on the

chromosome (8). There are reports that synthesis of P5CR in E. coli is not subject to repression

by proline (12, 13). Rossi et. al reported that synthesis of P5CR is not repressed by growth in the

presence of proline, but it is inhibited by only high levels of the reaction end products, proline

and NADP+ (14). Deutch et.al. have demonstrated the co-purification of L-thiazolidine-4-

caboxylate dehydrogenase activity and P5CR activity, although proline was not oxidized to P5C

by this partially purified protein in the presence of NADP+ (15). Rossi et. al. also reported that

partially purified P5CR from E. coli catalysed conversion of P5C to proline but not the reverse

reaction (14). Fujii et al. demonstrated that P5CR also catalyzes the reduction of 1-piperideine-

6-carboxylate to L-pipecolic acid (16). However, oxidation of pipecolic acid was not analyzed.

Kenklies et. al. reported the purification and sequence of P5CR from Clostridium sticklandii, and

its expression (17). Deutch et. al. (18), and Rossi et. al. (14) reported the E. coli P5CR gene

sequence, protein over-expression, and purification of the enzyme. P5CR has also been purified

approximately 200 fold from crude extract of baker’s yeast (19). With this purified enzyme the

Km value for DL-P5C was 0.8 X 10-4; for NADH it was 4.8 X 10-5 and for NADPH was 5.6

X10-5. Several reports suggest that mammals express two distinct pyrroline carboxylate

reductases with differences in cofactor specificity (20). Examination of mammalian genome

databases clearly show at least two homologues, although no particular sequence elements in

these homologous sequences provide clear clues as to residues that might affect cofactor

specificity. No studies have focused on structure / function relationships in this enzyme from

any species; nor have any previous studies suggested any possible models for structure / function

relationships.

We report a unique structure / function model of P5CR based on structural and enzymatic

comparisons to the β-hydroxyacid dehydrogenases. The β-hydroxyacid dehydrogenases are a

family of enzymes with characteristic functional domain structure and substrate specificities for

various β-hydroxycarboxylic acids (21, 22). Some members of this family (such as tartronate

semialdehyde reductase) function physiologically in the reductive direction (22). We show that,

although there is limited overall amino acid sequence homology among these proteins, there is

conservation of critical structural features throughout the known functional domains of the β-

hydroxyacid dehydrogenases. Using recombinant E. coli P5CR, we have tested this model

through the application of specific chemical modifications and site-directed mutagenesis.

Results of specific mutations are consistent with a model based on structural and functional

similarity between β-hydroxyacid dehydrogenases and pyrroline-carboxylate reductase.

Inhibition of E. coli P5CR by glutamate, but not by proline suggests that γ-gluatamate

semialdehyde (the straight-chain isomer of pyrroline carboxylate) may actually be the true

substrate for P5CR.

Materials and Methods

Strains, media and growth conditions

E. coli DH10B was used in this study. Cultures were grown at 37◦C in TY broth

containing per liter: 10 g tryptone, 5 g yeast extract, and 0.5 g NaCl. Cultures were maintained

on solid medium (1.5% agar). Ampicillin (50 µg per ml) was included as appropriate for

recombinant cultures.

Cloning of Pyrroline-5’-Carboxylate Reductase (proC) gene

For this purpose PCR amplification of the E. coli proC gene was performed using

primers ECP5CR5’ (ATGGAAAAGAAAATCGGTTTTATT) and ECP5CR3’

(TCAGGATTTGCTG AGTTTTTCTG). High molecular weight E. coli genomic DNA (Sigma)

was used as template. The Biorad Icycler was used for PCR with one cycle at 95°C for 2 min, 45

cycles of: 95°C 33sec, 48°C 60sec, and 70°C 1.3min. The PCR product size was confirmed by

gel electrophoresis using 1 % agarose. After purification by alcohol precipitation, the PCR

product was cloned into pTrcHis-TOPO vector using pTrcHis TOPO TA Expression kit

(Invitrogen Life Technologies) and transformed into chemically competent E.coli DH10B. The

recombinant clones were selected with 50µg ml−1 ampicillin. Plasmids were purified using

Perfect Prep plasmid mini kit (Eppendorf), digested using BamH1 and EcoR1, and analyzed by

agarose gel electrophoresis to confirm the size of the cDNA insert. The orientation of the insert

was confirmed by PCR using pTrcHis Forward Primer (GAGGTATATATATTAATGTATCG)

and ECP5CR5’ primer (described above). The clones were sequenced using Dyenamic ET

terminator (Amersham Bioscience) and an Applied Biosystems 310 DNA Sequencer. Primers

used for sequence analysis were TOPO Express Forward (TATGGCTAGCATGACTGGT) and

T122SEQ (TGCTTAGCGAAATCACCTC).

Site-directed mutagenesis

For this purpose the QuickChange Site-Directed Mutagenesis Kit (Stratagene) was used.

The primers used for Y122 mutation were CGGAAAATTATCCGCGCCATGCCGAACGCTCC

CGCACTGGTTAATGCCGGGATGACC and GTCATCCCGGCATTAACCAGTGCGGGAGC

GTTCGGCATGGCGCGGATAATTTTCCG. For Y122S mutation, primers used were CGGA

AAATTATCCGCGCCATGCCGAACTCTCCCGCACTGGTTAATGCCGGGATGACC and G

GTCATCCCGGCATTAACCAGTGCGGGAGAGTTCGGCATGGCGCGGATAATTTTCCG.

The primers for Y35F mutation were GCAAATCTGGGTATTCACCCCCTCCCCG and

CGGGGAGGGGGTGAATACCCAGATTTGC. The primers for Y178F mutation were CGGT

TCTTCGCCAGCCTTCGTATTTATGTTTATCGA and TCGATAAACATAAATACGAAGG

CTGGCGAAGAACCG. The primers used for Y201F mutation wereCGCGCCCAGGCG TTT

AAATTTGCCGCTC and GAGCGGCAAATTTAAACGCCTGGGCGCG. The mutagenic PCR

was performed using purified plasmid DNA (from a verified clone of P5CR) as template with the

addition of 8% DMSO. The condition for mutagenic PCR was one cycle at 95°C for 30 sec, 16

cycles of : 95°C 30sec, 55°C 60sec, and 68°C 11min. The mutations were confirmed by

sequence analysis using either TOPO Express Forward primer or T122SEQ primer.

Recombinant Enzyme Purification

For expression of recombinant enzymes, cultures were grown at 37◦C in TY broth with

ampicillin (50 µg ml−1). When OD600 was reached between 0.5 – 0.8 (estimated using Ultraspec

2100 pro UV/visible spectrophotometer, Amershan Bioscience), 0.5 mM IPTG was then added

to induce production of the wild-type or mutant recombinant enzymes. After 24 hours of

induction, cell mass was harvested by centrifugation at 6000 X g, at 4◦C, using an RC5C

centrifuge (Sorvall Instrument) and was resuspended in 15 ml of 25 mM Tris-HCl buffer (pH

7.0) with 0.5% Tween-20. The suspension was sonicated 5 times on ice for 30 Sec with

intermittent gaps of 30 sec each at continuous mode using a Sonic Dismembrator (model 100

Fisher Scientific). The suspension was centrifuged at 12,000 X g, at 4◦C, for 20 min to remove

cell debris using an Eppendorf centrifuge 5810. Supernatant was mixed in equal quantities with

2X column buffer. The column buffer had composition 50mM Na2HPO4, 10mM 2-

mercaptoethanol, 250 mM NaCl, 5mM imidazole, pH 8.0. This solution was passed through 10

ml Ni-NTA Agarose beads (Qiagen) equilibrated in the same buffer. The columns were then

eluted with 30 ml of column buffer containing 20, 40, 60, and 200 mM imidazole. Protein

concentrations of all the 200mM imidazole fractions were analyzed using Bradford reagent

(BioRad), using BSA as a protein standard. The samples with detectable levels of proteins were

pooled and frozen in aliquots with 10% glycerol.

SDS –PAGE Analysis

For gel electrophoresis 25µl of the samples along with the protein markers were loaded

on 10% SDS-PAGE gels (23). After Commossie blue staining the gels were imaged using the

Versa Doc 3000 imaging system (Biorad). The corresponding bands of protein were excised

after successive washing and subjected to in-gel digestion with sequence grade trypsin in 10mM

ammonium bicarbonate (pH 9.0). The digested peptides were extracted and concentrated, and

suspended in 10% acetonitrite with 0.05% TFA. This was mixed in equal volume with 4-

hydroxy cinnamic acid (10mg/ml) in 50% acetonitrile with 0.05% TFA. MALDI-TOF mass

spectra were collected using a Brucker reflex mass spectrometer in reflectron mode.

Enzyme kinetic analysis

The enzyme activity was measured according to the method published by Deutch et. al

(2001) at 37°C measuring an increase in absorbance at 340 nm in a Cary 1E UV-Visible

spectrophotometer (Varian). Reaction mixtures normally contained 300 mM Tris-HCl, pH 7.2,

0 to 12.5 mM L-thiazolidine-4-carboxylate , and 0 to 50 µM NADP+ in a total volume of 1.0 ml.

Activities were calculated in mmoles of NADPH formed per min from the first 30 s of 2-min

assays, using a mM extinction coefficient of 6.22 for NADPH. For proline oxidation assays 0 to

10 mM concentration of L-proline were used as substrate in place of L-thiazolidine-4-

carboxylate.

Chemical Modifications and Inhibition

For treatment with iodoacetamide, aliquots of enzyme stored with 5 mM 2-

mercaptoethanol were diluted 5-fold in Tris-HCl buffer, pH 7.2 and treated with 5 mM

iodoacetamide from freshly prepared stock solutions made in the same buffer. P5CR activity

was then measured immediately, following the given incubation times, using L-thiazolidine-4-

carboxylate as substrate exactly as described above. For treatment with tetranitromethane

(TNM), aliquots of enzyme stored with 5 mM 2-mercaptoethanol were diluted in Tris-HCl

buffer, pH 7.2 and treated with 83 mM TNM from freshly prepared stock solutions in 95%

ethanol. Control reactions were prepared with equal volumes of ethanol alone. P5CR activity

was then measured immediately, following the given incubation times, using L-thiazolidine-4-

carboxylate exactly as described above. For measurement of the stoichiometry of nitrotyrosine

formation, frozen aliquots of wild-type or mutant enzyme were desalted by passage through pre-

packed PD10 gel filtration columns (Pharmacia) and treated with TNM exactly as described

above. Production of nitrotyrosine was monitored throughout the course of these reactions by

measurement of OD428. Moles of nitrotyrosine produced were calculated using a molar

extinction coefficient of 4100 as reported by Sokolovsky et al (24). Treatment with

phenylmethylsulfonyl fluoride (PMSF) was performed exactly as described above for TNM

accept for using PMSF stock solutions freshly prepared in 95% isopropanol. In this case,

isopropanol was added to control reactions.

CD Spectrapolarimetry

Circular dichroism spectra were recorded at 25°C using a Jasco J-810 spectrapolarimeter.

Spectra were recorded with a cell path length of 0.1 cm and a wavelength range of 300–200 nm.

Each spectrum was averaged from five separate recordings. Immediately before measuring the

spectra, protein samples were desalted using PD10 columns exatly as described above. 100 µg

of protein were used for each measurement. Protein was quantitated using the Bradford protein

assay (Biorad) with BSA employed as standard.

Structural Modeling

Structural modeling of enzyme substrates was performed using HyperChem software

(Hypercube, Inc.). Geometry optimization was performed using Polak-Ribiere (conjugate

gradient) method.

Results and Discussion

Comparison of Substrates and Reaction Characteristics

The reactions catalyzed by P5CR and those catalyzed by β-hydroxyacid dehydrogenases

are different but have certain features in common. P5CR does not catalyze the oxidation of a β-

hydroxyacid. It does however, catalyze the NAD(P)+-dependent oxidation / reduction of a

carbon distal to a carboxylate, which is structurally and mechanistically similar to reactions

catalyzed by known β-hydroxyacid dehydrogenases. P5CR also has enzymatic similarity to the

β-hydroxyacid dehydrogenases in that it is non-metal-dependant. A major difference between

P5CR and the β-hydroxyacid dehydrogenases is the fact that P5CR is unidirectional with its

natural substrate (P5C) and does not oxidize proline. It does, however, oxidize the substrate

analogue L-thiazolidine-4-carboxylate (thiaproline). It is not clear what structural features

provide for this difference in reaction characteristics between proline and thiaproline. We have

modeled these substrates and compared torsional bond angles in the most stable structures after

performing energy minimizing geometry optimizations (Fig 1). This analysis indicates that the

pyrroline carboxylate ring is stabilized by a significantly different conformation than the ring

structures of proline or thiaproline (thiazolidine-4-carboxylate). A major structural difference

between pyrroline carboxylate and proline is the position of the carboxylate atoms relative to the

nitrogen atom in the ring, reflected in the torsional bond angles between these atoms (Fig 1).

Comparison of the torsional bond angles between the carboxylate oxygen atoms and the ring

nitrogen show that the pyrroline and proline rings take on significantly different conformations

relative to the plane of the ring and the carboxylate (Fig 1). Torsional angles between C2 and the

C5 protons also reflect this difference between the pyrroline and proline rings. Torsional angles

between the carboxylate carbon and the C5 of the pyrroline, proline, and thiazolidine rings show

dramatic conformational differences between all three compounds. These structural differences

may explain, in part, the irreversible nature of the enzyme-catalyzed reduction of pyrroline

carboxylate, either through differences in binding of these compounds to the enzyme active site

or through structural inability of the enzyme to contact the appropriate proton in the proline ring

for hydride transfer to NADP+.

P5CR should require chemistry for carboxylate-binding and for acid/base catalysis

similar to the chemistry required of the β-hydroxyacid dehydrogenases. The features of the

P5CR-catalyzed reaction in common with that of the β-hydroxyacid dehydrogenases are

carboxylate-binding, dinucleotide cofactor-binding, acid/base catalysis and hydride transfer to

the cofactor. Judging based on the chemistry alone, what is likely most different is the nature of

the acid/base catalyst. Although the P5CR-catalyzed reaction was not previously believed to

involve an acid/base-catalyzed proton abstraction from a carbonyl group, our model indicates

that the architectural frame-work of this enzyme is likely similar to a family of enzymes that bind

specifically to β-hydroxyacids and semialdehydes. This model suggests the possibility that the

true substrate of P5CR may actually be γ-glutamate semialdehyde, an isomeric form of pyrroline

carboxylate (Fig 2). Previous studies related to proline biosynthesis assumed that pyrroline

carboxylate is the direct substrate for this enzyme and that it is produced in solution

spontaneously from γ-glutamate semialdehyde. We propose that γ-glutamate semialdehyde may

be the true substrate for this enzyme and the enzyme may facilitate conversion to pyrroline

carboxylate (Fig 2), which may be more efficient, metabolically, than the spontaneous

conversion of the semialdehyde to pyrroline carboxylate. Considering this possibility, we tested

the inhibition of P5CR by glutamate, proline, and β−hydroxyacids. Glutamate was indeed found

to be a much more potent inhibitor of purified recombinant P5CR than any other acids

previously tested. Gluatamate at concentrations between 250 µM and 1mM produced significant

inhibition in the NADP+-dependent oxidation of thiaproline whereas neither proline nor a variety

of other common acids inhibited the enzyme even at concentrations over 10 mM (Fig 3). Kinetic

analysis of this inhibition clearly showed that glutamate is not a competitive inhibitor of

thiaproline, but inhibits through a mixed uncompetitive mechanism involving changes in both

Vmax and Km. It is particularly notable that proline does not inhibit the enzyme even at high

concentrations. This level of inhibition and specificity is consistent with an enzyme-assisted

(non cofactor-dependent) conversion of glutamate-semialdehyde to pyrroline carboxylate

followed by the NADPH-dependent reduction to proline (Fig 2). This model, including the

structural differences in substrates shown in Figure 1, may explain, in part, the inability of the

enzyme to catalyze the oxidation of proline. Alternatively, glutamate might have sufficient free

rotation to be able to bind to an enzyme active site that ordinarily binds pyrroline carboxylate.

However, such this alternative might be expected to result in competitive inhibition.

Amino Acid Sequence Homology

Comparison of primary structures of P5CR and well-established β-hydroxyacid

dehydrogenases show only a low level of overall identity. Figure 4 shows an amino acid

sequence alignment of P5CR sequences from diverse species with those of several well-

established β-hydroxyacid dehydrogenases. Many of the glycine and alanine residues conserved

in the β-hydroxyacid dehydrogenases, as well as several highly conserved proline residues, are

also conserved in P5CR, probably demonstrating a common structural framework. Closer

inspection predicts putative structural elements that reflect a possible shared functional domain

structure. One of the most obvious and striking similarities between the pyrroline carboxylate

reductases and the β-hydroxyacid dehydrogenases is in the N-terminal dinucleotide cofactor-

binding domain, which is highly characteristic of this family. This domain consists of a motif

with a sequence of VGFIGXGXMGXXXAX5AG. The sequence conservation in the P5CRs fits

extremely well to this consensus sequence including the distribution of hydrophobic residues, the

conserved methionine residue, and the most highly conserved alanine and glycine residues (21).

The next major domain is the carboxylate-binding domain downstream from the cofactor-

binding domain. The homology of the P5CRs with the previously published consensus sequence

for this domain is less than that of the β-hydroxyacid dehydrogenases alone (21, 22). The beta-

hydroxyacid dehydrogenases display a highly conserved substrate-binding motif with a sequence

of DAPVSGGXXXA (21, 22), followed by a number of well-conserved glycine and alanine

residues. Upstream from this motif is a highly conserved serine residue directly preceded by a

stretch of considerably hydrophobic but otherwise non-conserved sequence. The P5CR

sequences share a number of important features in this domain. As with the N-terminus, most of

the conserved residues are glycines and alanines that probably reflect a similar structural

framework (Fig 4). The conserved serine residue (in the motif DAPVSGG) believed to be

functional in carboxylate-binding in the β-hydroxyacid dehydrogenases (21,22) is semi-

conserved as a threonine residue in the P5CR sequences and is invariant in the P5CRs (Fig 4).

This highly conserved residue was shown to make direct contact with a substrate carboxylate

oxygen atom in the crystal structure of 6-phosphogluconate dehydrogenase (25). Furthermore,

both of these conserved serine and threonine residues are preceded by a highly conserved proline

residue in either a PXS or PXT sequence (Fig 4). We predict that this conserved threonine

residue in P5CR may be specifically important to carboxylate-binding in P5CRs, and that this

motif further defines a conserved structure for carboxylate-binding among all of these enzymes.

This is not surprising given that all the β-hydroxyacid dehydrogenases, as well as P5CR, must

bind a carboxylate substrate in their active sites (non-acid analogues are not active substrates).

The catalytic domain is clearly conserved in structure, but differs between the β-

hydroxyacid dehydrogenases and P5CRs in several respects. The putative catalytic lysine

residue present in the β-hydroxyacid dehydrogenases (Fig 4) is absent in the P5CR sequences,

whereas other features of this domain are well conserved. Perhaps it should not be surprising

that this conserved catalytic residue in all known β-hydroxyacid dehydrogenases is absent in

P5CRs or that its function could be performed by another residue. There may be specific

residues to support the reduction of P5C, a reaction similar to (but somewhat different from) β-

hydroxyacid oxidation. However, these catalytic residues appear to be situated in a region with a

similar structural framework. There is a highly conserved GXXGXG consensus sequence in this

region, although it is shifted downstream slightly in the P5CR sequences (Fig 4). This motif

likely represents a conserved structural element such as a turn or bend in secondary structure that

may function in positioning of catalytic residues. The consensus sequence downstream from

this, containing highly conserved glutamate, alanine, and leucine residues, is highly conserved in

the P5CRs. A number of amino acid residues in this domain could possibly serve as specialized

acid/base catalysts for P5CR, and our hypothesis predicts that the most important catalytic

residues for P5CR will reside in this region, downstream from the GXXGXG motif.

This hypothetical model predicts a number of amino acid residues and domains that are

likely of structural and catalytic importance in P5CR, which would not have been predicted

without this structural comparison. These include the very distinct N-terminal dinucleotide

cofactor-binding domain, a carboxylate-binding domain with a conserved threonine residue, and

a catalytic domain with a number of conserved glycine, alanine, and proline residues. This

comparison now provides a model for further structure / function studies of P5CRs by site-

directed mutagenesis and chemical modifications.

Expression and Purification of Recombinant E. coli P5CR

The proC gene of E. coli was amplified by PCR using primers based on the known DNA

sequence and using purified E. coli genomic DNA as the template for PCR. This cDNA was

ligated in frame to the pTrcHisTOPO vector (Invitrogen) for over-expression in E. coli cultures.

Induction with IPTG led to the appearance of a largely over-expressed band of protein

approximately 30 kD in size. This protein was purified by nickel affinity chromatography as

described in Materials and Methods. The resulting protein was over 90% pure as estimated by

SDS-PAGE analysis and was verified as E. coli P5CR by trypsin digestion and MALDI-TOF

mass spectral analysis of the resulting peptides. This purified, wild-type enzyme was not active

in the oxidation of proline with either NADP+ or NAD+ as cofactor, but oxidized thiaproline in

the presence of NADP+ with a specific activity similar to that previously reported for the native

enzyme (Table 1) (15). Two mutations of a conserved threonine residue were produced as well

as three mutations of tyrosine residues. Each of these mutants were expressed at similar levels to

wild-type enzyme and each resulted in identical levels of purity when purified by nickel affinity

chromatography. The mutant enzymes were also analyzed by CD spectrapolarimetry and

displayed spectra identical to that of wild-type enzyme. These purified enzymes were found to

be stable for at least one month when stored at -20°C in the presence of β-mercaptoethanol and

glycerol. In the absence of β-mercaptoethanol the purified enzymes were only stable for several

days.

CD Spectral Comparison of P5CR and Hydroxyisobutyrate Dehydrogenase.

The sequence homology described above predicts a similar structural architecture

between P5CRs and β−hydroxyacid dehydrogenases, despite a relatively low overall sequence

identity. To test this hypothesis CD spectrapolarimetry was used to compare secondary

structural contents of E. coli P5CR with that of rat β-hydroxyisobutyrate dehydrogenase, one of

the most well-characterized β-hydroxyacid dehydrogenases. Examination of the CD spectra for

these two enzymes indicate that they have very similar secondary structures (Fig 5). Comparison

of the ellipticities at 208nm and 220nm suggest very similar content of α-helices (26).

Role of Conserved Threonine Residue

As described above, the sequence homology within the previously proposed carboxylate

substrate-binding domain suggests a role for a conserved threonine residue in P5CR. This

residue (T122 in the E. coli enzyme) is absolutely invariant in all known P5CR sequences, also

suggesting the possibility of a conserved functional role. To test whether this threonine residue

may be catalytically important, we performed site-directed mutagenesis substituting it with either

alanine or serine. As shown in Table 1, these substitutions both produced increased Km values

for thiaproline as well as lowered Kcat values, resulting in significantly reduced catalytic

efficiencies. Alanine substitution produced a greater increase in the Km for thiaproline

(approximately 10-fold) compared to serine substitution. Serine substitution also produced a

much less dramatic change in the Vmax. Both the alanine and serine substitutions led to changes

in the Km for NADP+; however, the serine substitution produced a greater increase in this

parameter than the alanine substitution. These results are consistent with a proposed role for

substrate binding by this conserved threonine residue.

Chemical Modification of Ser, Tyr and Cys Residues

To begin determining other possible active site residues, recombinant P5CR was tested

for inhibitory effects of a number of amino acid side chain-specific chemical modifiers.

Although there is a highly conserved serine residue at the N-terminal end of the substrate-

binding domain (Fig 4) there is no affect of PMSF even at high concentrations. This suggests

that there are no binding events or catalytic events involving acid/base chemistry with this

conserved serine residue or any other serine residue. PMSF usually reacts with specialized

serine residues with pKa values lowered by the structures within their local environment. This

must not be the case for the conserved serine residue in the β-hydroxyacid dehydrogenases and

P5CRs.

Treatment with iodoacetamide resulted in over 90% inactivation of recombinant E. coli

P5CR, with almost complete protection provided by the addition of NADP+ (Fig 6). This is

similar to the effects of cysteine modifiers on β-hydroxyacid dehydrogenases; however, there are

no specifically conserved cysteine residues in this family of enzymes, and none believed to be

involved in catalysis or substrate binding (21, 22, 27). Nevertheless, most of the β-hydroxyacid

dehydrogenases are sensitive to a variety of chemical modifiers of cysteine residues, and this

appears to be true of P5CR as well. There are no conserved cysteine residues in the amino acid

sequences for P5CR, but there is a unique cysteine residue directly within the proposed N-

terminal cofactor-binding domain of the E. coli P5CR sequence (Fig 4).

Treatment with tetranitromethane (TNM) also resulted in inactivation of E. coli P5CR.

Unlike the case with iodoacetamide, the presence of NADP+ did not protect the enzyme from

inactivation, but actually enhanced the inactivation with TNM (Fig 6). Measurement of

nitrotyrosine production by absorbance at 428 nm revealed that inactivation of wild-type E. coli

P5CR occurred concomitant with the production of 2 moles nitrotyrosine per mole of enzyme. It

is possible that cofactor alone cannot afford protection against TNM inactivation if inactivation

occurs through the labeling of multiple, functionally unrelated sites. These results are consistent

with the presence of tyrosine residues in the active site of E. coli P5CR. Indeed, there are only

three tyrosine residues in the E. coli P5CR sequence, and each of these residues lie within or

very near to the proposed functional domains shown in Figure 4. One of these tyrosine residues

(Y35 in the E. coli enzyme) lies in the N-terminal cofactor-binding domain. The other two

tyrosine resides lie directly within the proposed catalytic domain. One of these tyrosine residues

(Y178 in the E. coli enzyme) occurs just downstream from the characteristic GXXGXG motif in

the proposed catalytic domain and is completely conserved in the P5CR sequences from widely

variant species.

Site-directed mutagenesis of Tyrosine residues

The inactivation by TNM, the stoichiometry of nitrotyrosine production, and the presence

of tyrosine residues in the proposed functional domains of E. coli P5CR strongly suggest the

presence of active site tyrosine residues in this enzyme. To test the catalytic importance of these

residues, replacement with phenylalanine residues was performed by site-directed mutagenesis.

Surprisingly, each of these very semiconservative replacements resulted in increases in Vmax

and Kcat (Table 1). Although consistent with active site locations, it is not exactly clear why

these replacements should result in increased catalytic rate. Phenylalanine replacement of Y36

(located in the proposed cofactor-binding domain) resulted in relatively small changes in the Km

for either NADP+ or thiaproline, but produced approximately 5-fold increase in Vmax.

Phenylalanine replacement of Y178, the invariant tyrosine, resulted in relatively small changes in

Km values and also a smaller (2.7-fold) increase in Vmax compared to the Y36 mutation. This

result rules out an identity for this residue as a possible acid/base catalyst. Phenylalanine

replacement of Y201, also in the proposed catalytic domain, resulted in the most dramatic

changes, with a nearly 5-fold increase in the Km for NADP+, a 3-fold increase in the Km for

thiaproline, and a 6-fold increase in Vmax. It is not clear why this mutation should result in an

increased catalytic rate. It is possible that this structural change increases the rate-limiting step

in this reaction, which is presumably the release of reduced cofactor. Increases in the Km for

NADP+ cofactor may be consistent with this explanation. It is also possible that these surprising

increases in catalytic rate are related to an increased efficiency in binding of the unnatural

substrate analogue used in the assay, thiaproline. However, the observed increases in Km for

thiaproline, though small, are not consistent with this explanation.

Acknowledgements

We thank Dr. Mike Crowder and Dr. Rich Taylor (Miami University) for helpful discussion.

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Figure 1. Structural Features of Substrates and Products of Pyrroline Carboxylate

Reductase. Geometry optimization and calculation of torsional bond angles were performed

using the HyperChem software package employing the Polak-Ribiere (conjugate gradient)

method. Red indicates oxygen atoms; light blue, carbon atoms; dark blue, nitrogen atoms;

yellow, sulfur atoms; white, protons. Numbering of each of the rings (including the proline and

thiazolidine rings) corresponds to the conventional numbering of a pyrrole ring, with N as 1 and

the carbon adjacent to the carboxylate as 2.

Figure 2. Conversion of γ-glutamate semialdehyde to pyrroline carboxylate, and the

P5CR-catalyzed production of proline.

Figure 3. Inhibition of NADP+-dependent oxidation of thiaproline by L-glutamate and L-

proline. P5CR activity was measured exactly as described in Materials and Methods.

Glutamate and proline solutions were prepared in the same buffer as the enzyme assay (300 mM

Tris-HCl) and were adjusted to pH 7.2 directly before performing the assay. ■ indicates L-

proline; ♦ indicates L-glutamate.

Figure 4. Amino acid sequence homology between β-hydroxyacid dehydrogenases and

pyrroline carboxylate reductases. Sequences taken from NCBI databases were used for pair-

wise alignment to the rat hydroxyisobutyrate dehydrogenase sequence using either BLAST or

tBLASTn. Shown in black boxes are conserved residues, both identical and semiconserved,

which appear in at least 50% of all of the sequences. Arrows and text indicate functional

domains previously established for several of the β-hydroxyacid dehydrogenases. Blue boxes

indicate the motif GXXGXG in the catalytic domain. Red boxes indicate the invariant catalytic

lysine residue previously proposed in the β- hydroxyacid dehydrogenases. Stars indicate the

position of residues that were mutated in the E. coli P5CR during the present study. AE000357,

AE000157, and AE000394 represent loci in the E. coli genome coding for the corresponding

tartronate semialdehyde reductase sequences. HIBADH, hydroxyisobutyrate dehydrogenase;

RN, Rattus norvegicus, PA, Pseudomonas aeruginosa; AT, Arabidopsis thaliana; GM, Glycine

max; PS, Pisum sativum; EC, Escherichia coli; BS, Bacillus subtilis; PA, Pseudomonas

aeruginosa; HS, Homo sapiens.

Figure 5. CD Spectral Comparison of Hydroxyisobutyrate Dehydrogenase and Pyrroline

Carboxylate Reductase. Rat β-hydroxyisobutyrate dehydrogenase (HIBADH) was purified as

previously described (21). Each protein was analyzed by CD spectrapolarimetry exactly as

described in Materials and Methods. Spectra shown are averaged from five successive

measurements.

Figure 6. Effect of Iodoacetamide and Tetranitromethane on Wild-Type P5CR. Treatment

with iodoacetamide and tetranitromethane and enzyme assay were performed exactly as

described in Materials and methods. IAA, iodoacetamide. TNM, tetranitromethane.

Table 1. Kinetic Parameters of Wild-Type and Mutant P5CRs.

Enzyme

Km NADP+ (mM)

Km T4C (mM)

Vmax (mmol/min/mg)

Kcat (Vmax/

nmole of enzyme)

Kcat/Km

NADP+

Kcat/Km

T4C

Wild-Type

0.18

0.30

1.70

11.97

66.510

39.90

Thr122Ala 0.24 3.73 0.67 1.74 7.27 0.47

Thr122Ser 0.67 2.53 1.11 3.71 5.54 1.47

Tyr35Phe 0.27 0.58 8.40 116.67 432.10 201.15

Tyr178Phe 0.33 0.91 4.61 80.88 245.08 88.87

Tyr201Phe 0.83 0.89 10.86 434.40 523.37 488.09

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6