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Tiêu đề Si-face stereospecificity at C5 of coenzyme F420 for F420H2 oxidase from methanogenic Archaea as determined by mass spectrometry
Tác giả Henning Seedorf, Jörg Kahnt, Antonio J. Pierik, Rudolf K. Thauer
Trường học Max Planck Institute for Terrestrial Microbiology
Chuyên ngành Biology
Thể loại báo cáo khoa học
Năm xuất bản 2005
Thành phố Marburg
Định dạng
Số trang 6
Dung lượng 151,18 KB

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Nội dung

All F420-dependent enzymes analysed to date in this respect have been shown to be Si-face stereospecific at C5 of F420 [6].. All the coenzyme F420-dependent enzymes investigated to date h

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oxidase from methanogenic Archaea as determined by

mass spectrometry

Henning Seedorf1, Jo¨rg Kahnt1, Antonio J Pierik2and Rudolf K Thauer1

1 Max Planck Institute for Terrestrial Microbiology, Marburg, Germany

2 Fachbereich Biologie, Philipps-Universita¨t, Marburg, Germany

Methanogenic Archaea fluoresce greenish yellow when

irradiated with UVA light The fluorescence is due to

coenzyme F420, a

7,8-didemethyl-8-hydroxy-5-deaza-riboflavin derivative (Fig 1) The coenzyme, which is

generally present in 1 mm intracellular concentrations

[1], functions as a redox mediator in methanogenesis,

in NADP+ reduction and in glucose-6-phosphate

dehydrogenation [2] With respect to its redox

proper-ties, F420 is much more similar to pyridine nucleotides

than to flavins [3] Both F420 and NAD(P) transfer

hydride anions and not single electrons In the reduced

form, both F420 and NAD(P) have a prochiral centre,

F420 at C5 and NAD(P) at C4 They differ

function-ally, mainly in that the redox potential of the

F420⁄ F420H2 pair (E¢ ¼)360 mV) is 40 mV more

negative than that of the NAD(P)+⁄ NAD(P)H pair (E¢ ¼)320 mV) [5]

All F420-dependent enzymes analysed to date in this respect have been shown to be Si-face stereospecific at C5 of F420 [6] This is surprising because NAD(P)-dependent enzymes can be Si-face or Re-face specific [7] and some flavoenzymes, whose apoproteins catalyse the reduction of synthetic 8-hydroxy-5-deaza-FAD, have been shown to be Si-face stereospecific with respect to C5 of the synthetic deazaflavin and others

to be Re-face stereospecific [7,8] In case of the pyridine-nucleotide-dependent enzymes the redox potential (E) of the electron acceptor reduced by NAD(P)H is thought to be an important factor deter-mining the stereospecificity of these enzymes [9,10]

Keywords

coenzyme F 420 ; 5-deazaflavins;

F420H2oxidase; methanogenic Archaea;

stereospecificity

Correspondence

R K Thauer, Max Planck-Institute for

Terrestrial Microbiology,

Karl-von-Frisch-Strasse, D-35043 Marburg, Germany

Fax: +49 642 117 8109

Tel: +49 642 117 8101

E-mail: thauer@staff.uni-marburg.de

(Received 4 July 2005, revised 17 August

2005, accepted 23 August 2005)

doi:10.1111/j.1742-4658.2005.04931.x

Coenzyme F420 is a 5-deazaflavin Upon reduction, 1,5 dihydro-coenzyme

F420 is formed with a prochiral centre at C5 All the coenzyme

F420-dependent enzymes investigated to date have been shown to be Si-face stereospecific with respect to C5 of the deazaflavin, despite most F420 -dependent enzymes being unrelated phylogenetically In this study, we report that the recently discovered F420H2 oxidase from methanogenic Archaea is also Si-face stereospecific The enzyme was found to catalyse the oxidation of (5S)-[5-2H1]F420H2 with O2 to [5-1H]F420 rather than to [5-2H]F420 as determined by MALDI-TOF MS (5S)-[5-2H1]F420H2 was generated by stereospecific enzymatic reduction of F420 with (14a-2H2 )-[14a-2H2] methylenetetrahydromethanopterin

Abbreviations

Adf, F420-specific alcohol dehydrogenase; F420, coenzyme F420; Fgd, F420-dependent glucose-6-phosphate dehydrogenase; Fno, F420H2: NADP + oxidoreductase; Fpo, F 420 H 2 dehydrogenase complex; FprA, F 420 H 2 oxidase; Frd, F 420 -dependent formate dehydrogenase; Frh,

F 420 -reducing hydrogenase; H 4 MPT, tetrahydromethanopterin; Mer, F 420 -dependent methylenetetrahydromethanopterin reductase;

methylene-H4MPT, methylenetetrahydromethanopterin; Mtd, F420-dependent methylenetetrahydromethanopterin dehydrogenase; TFA, trifluoroacetic acid.

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Redox potentials (E) of the electron acceptor more

neg-ative than )200 mV generally promote Si-face

stereo-specificity and redox potentials more positive than

)200 mV promote Re-face stereospecificity at C4

of NAD(P) Thus the NADP-dependent

glucose-6-phos-phate dehydrogenase is Si-face specific (E ¼

)330 mV) and the NAD-dependent malate

dehydro-genase is Re-face specific (E ¼)170 mV) Most

eth-anol dehydrogenases are Re-face specific (E ¼

200 mV), but the enzyme from Drosophila melanogaster

is Si-face specific For recent literature on the subject see

Berk et al [11]

The following eight F420-dependent enzymes have

been analysed and shown to be Si-face specific: F420

-reducing hydrogenase (Frh) [12,13]; F420-dependent

formate dehydrogenase (Frd) [14]; F420-specific alcohol

dehydrogenase (Adf) [6]; F420-dependent

methylene-tetrahydromethanopterin dehydrogenase (Mtd) [15,16];

F420-dependent methylenetetrahydromethanopterin

reductase (Mer) [15]; F420H2 dehydrogenase complex

(Fpo) [15]; F420H2: NADP+ oxidoreductase (Fno)

[17,18]; and F420-dependent glucose-6-phosphate

de-hydrogenase (Fgd) [6] Adf, Mer and Fgd form a

fam-ily, as do the F420-binding subunits FpoF, FrhB and

FrdB The two families, Mtd and Fno are not

phylo-genetically related The eight enzymes catalyse redox

reactions with electron acceptors ranging in redox

potential (E¢) from )414 mV (2H+

⁄ H2) to )165 mV (methanophenazine ox⁄ red) [19] The Si-face

stereospe-cificity of F420-dependent enzymes thus appears to be

independent of their phylogenetic origin and of the

thermodynamics of the reactions catalysed by them

Recently a novel F420-dependent enzyme, F420H2

oxidase (FprA), was discovered in methanogenic

Arch-aea [20] FprA catalyses the oxidation of 2 F420H2with

O2 to 2 F420and 2 H2O The 45 kDa protein contains

1 FMN per mol and harbours a binuclear iron centre

indicated by the sequence motif H-X-E-X-D-X63

-H-X18-D-X62-H FprA is not phylogenetically related

to any of the other F420-dependent enzymes and cata-lyses a reaction with a redox potential difference

of +1.27 V (F420H2 oxidation with O2) We therefore investigated the stereospecificity of this enzyme and found it to be Si-face specific at C5 of F420 The method used was based, in principle, on the technique for determining the hydride transfer stereospecificity of nicotinamide adenine dinucleotide-linked oxidoreduc-tases by MS [21]

Results

The following findings are important for the under-standing of the results shown in Fig 2: (a) [5-1H]F420 and [5-2H]F420 can be identified and the relative amounts present in a mixture quantitated using MALDI-TOF-MS; (b) F420H2 auto-oxidizes nonstereo-specifically to F420 in the matrix used for MALDI-TOF-MS; (c) F420 is stereospecifically reduced to

F420H2 with methylenetetrahydromethanopterin (methylene-H4MPT) in the presence of F420-dependent methylene-H4MPT dehydrogenase (Mtd), which has been shown to be Si-face specific at C5 of F420[15,16]; and (d) F420 is chemically reduced to F420H2 with NaBH4in a nonstereospecific reaction

In Fig 2A three MALDI-TOF mass spectra of a control experiment are shown: the spectrum of [5-1H]F420 (Fig 2Aa); the spectrum of [5-1H2]F420H2 generated from [5-1H]F420 by Mtd-catalysed reduction with [14a-1H2]methylene-H4MPT (Fig 2Ab); and the spectrum of [5-1H]F420 generated from [5-1H2]F420H2

by FprA catalysed oxidation (Fig 2Ac) As seen from the normalized 1 Da separated stick spectra (insets, black) all three mass spectra are almost identical to the stick spectrum (insets, white) calculated for [5-1H]F420 from its elemental composition considering the isotope composition of the elements: 98.9% 12C, 1.1% 13C; 99.63% 14N, 0.37% 15N; 99.99% 1H, 0.01% 2H; and 99.76% 16O, 0.24%17O and18O

The experiment shown in Fig 2B differs from that

in Fig 2A only in that in the first step F420 was enzy-matically reduced with [14a-2H2] methylene-H4MPT yielding (5S)-[5-2H1]F420H2 FprA catalysed oxidation

of (5S)-[5-2H1]F420H2 yielded only[5–1H]F420 as indica-ted by the mass spectrum (Fig 2Bc), which was identi-cal to that identi-calculated for [5-1H]F420 (Fig 2Ba) This result can only be explained if FprA is Si-face specific with respect to C5 of F420 In contrast, auto-oxidation

of (5S)-[5-2H1]F420H2 yielded a 1 : 2 mixture of [5-1H]F420 and [5-2H]F420, as indicated by the relative intensities of the 772 and 773 Da mass peaks

Fig 1 Structure of reduced coenzyme F 420 (F 420 H 2 ) F 420 ¼

N-(N-L -lactyl- L -glutamyl)- L -glutamic acid phosphodiester of

7,8-didemethyl-8-hydroxy-5-deazariboflavin.

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(Fig 2Bb, stick spectrum, black) For comparison the

relative intensities calculated for a 1 : 1 mixture are

given (Fig 2Bb, stick spectrum, white) The [5-1H]F420

to [5-2H]F420 ratio of 1 : 2 can be explained assuming

a deuterium isotope effect of  2 for the

auto-oxida-tion reacauto-oxida-tion

As a control, F420 was reduced with NaB2H4

(NaBD4) yielding a mixture of (5S)-[5-2H1]F420H2 and

(5R)-[5-2H1]F420H2 The FprA-catalysed oxidation of

the mixture yielded a 1 : 1 mixture of [5-1H]F420 and

[5-2H]F420as revealed by the relative intensities of the

772 and 773 Da mass peaks (Fig 2Cc) The results are

consistent with FprA catalyzing the oxidation of

(5S)-[5-2H1]F420H2to [5-1H]F420 and the oxidation of

(5R)-[5-2H1]F420H2 to [5-2H]F420 as to be expected for a

Si-face-specific enzyme The finding that the 775 Da

mass peak in Fig 2Cb was much lower than in

Fig 2Bb is probably due to the fact that reduction

of F420 with NaBD4 (Fig 2C) was not complete

and therefore after auto-oxidation the F420 analysed

contained less2H

Discussion

In the Introduction it was pointed out that all F420

-dependent enzymes investigated have been shown to be

Si-face specific at C5 of F420, despite four of these

enzymes being unrelated phylogenetically The finding

that F420H2oxidase (FprA) is also Si-face specific brings

to five the number of Si-face-specific F420-dependent

enzymes that are not related phylogenetically There is only a 6.25% probability that this is by chance

To date, the crystal structures of four F420-dependent enzymes have been resolved: F420H2:NADP oxido-reductase, with and without F420 bound [22];

F420-dependent alcohol dehydrogenase with F420bound [23]; Mer, with and without F420 bound [24,25]; and Mtd without F420bound [26] A common F420-binding

Fig 2 MALDI-TOF-MS analysis of F420and F420H2for the

deter-mination of the stereospecificity of F420H2 oxidase (FprA) The

insets show normalized 1 Da separated stick spectra obtained from

the measured data (black) aligned to simulated spectra (white) For

better visibility in the structures deuterium is abbreviated by D

rather than by 2 H and hydrogen by H rather than 1 H Mtd,

Si-face-specific F420-dependent methylenetetrahydromethanopterin

de-hydrogenase (A) Experiment with nonlabelled substrates showing

that the mass spectrum of [5- 1 H 2 ]F 420 H 2 (b), owing to

auto-oxida-tion of F 420 H 2 , is identical to that of [5-1H]F 420 (a, c) The simulated

stick spectra (white) are for [5- 1 H]F420 (B) Experiment with

specif-ically 2 H-labelled substrates showing that the mass spectrum of

F 420 formed from (5S)-[5-2H 1 ]F 420 H 2 by FprA-catalysed oxidation (c)

is identical to the spectrum of [5- 1 H]F420 (a) The simulated stick

spectrum (b, white) of (5S)-[5- 2 H1]F420H2 is for a 1 : 1 mixture of

[5-1H]F 420 and [5-2H]F 420 The other two (a, c) are for [5-1H]F 420 (C)

Experiment with NaB 2 H4-reduced [5- 1 H]F420showing that the mass

spectrum of F420formed from reduced F420by FprA-catalysed

oxi-dation corresponds to that of a mixture of [5- 1 H]F 420 and [5- 2 H]F 420

(c) The simulated stick spectrum of reduced F420(b, white) and

that of the FprA oxidation product (c, white) are for a 1 : 1 mixture

of [5- 1 H]F 420 and [5- 2 H]F 420

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motif explaining the Si-face specificity of these enzymes

was not found It therefore has to be considered that

Si-face specificity may be an intrinsic property of F420

rather than of the F420-dependent enzymes An example

of the stereospecificity of a dehydrogenase being

dicta-ted by the structure of its substrate has recently been

published There are several phylogenetically unrelated

methylenetetrahydromethanopterin dehydrogenases

and methylenetetrahydrofolate dehydrogenases that are

all Re-face specific at the carbon of the methylene group

[27,28] It has been calculated that the transition state

conformation of methylenetetrahydromethanopterin

and methylenetetrahydrofolate for the dehydrogenation

from the Re-face is energetically favoured [28]

How-ever, in the case of F420, there are no centres of

asym-metry in the near neighbourhood of C5 that could

interact with the reactant or the product, or affect the

transition state(s) and by that induce an intrinsic

ener-getic difference in the reaction profiles involving the Si

versus the Re side of F420 The nearest asymmetry

cen-tres are in the N10 side chain It is therefore difficult

to envisage how the Si-face stereospecificity of F420

-dependent enzymes could be dictated by the structure

of F420

Experimental procedures

Isotopes, coenzymes and enzymes

Deuterium oxide (2H2O) and deuterated formaldehyde

(2H2CO) were from Euriso-Top (Saarbru¨cken, Germany)

and sodium borodeuteride (NaB2H4) was from Fluka

(Tauf-kirchen, Germany) Coenzyme F420 and

tetrahydrometha-nopterin (H4MPT) were purified from Methanothermobacter

marburgensis(DSMZ 2133) [29] [14a-1H2]methylene-H4MPT

was prepared by spontaneous reaction of H4MPT and

1

H2CO and [14a-2H2]methylene-H4MPT by spontaneous

reaction of H4MPT and2H2CO [30] FprA from M

marbur-gensis [20] and Mtd from Methanopyrus kandleri [26] were

produced heterologously in Escherichia coli and purified to

specific activities of 100 and 4000 UÆmg)1, respectively

(1 U¼ 1 lmolÆmin)1) Protein was determined with the

Rot-Nanoquant-Microassay from Roth (Karlsruhe, Germany)

using bovine serum albumin as standard

Assay to determine the stereospecificity of F420H2

oxidase

The assay is described in Fig 2B The 1.2 mL assay

mix-ture at 30C contained 60 lm H4MPT, 140 lm2H2CO and

55 lm F420 in oxic 120 mm potassium phosphate pH 6

Reduction of F420to (5S)-[2H1]F420H2with [14a-2H2

]methy-lene-H4MPT (spontaneously generated from H4MPT and

2H2CO) was started by the addition of 120 U Mtd (Si-face specific) and was completed after 5 min Subsequently,

60 U FprA were added, which catalysed the oxidation of

F420H2 with O2 as the electron acceptor Samples of the assay were taken before and 5 min after the addition of Mtd and 5 min after the addition of FprA and analysed by MALDI-TOF-MS

In the control experiment described in Fig 2A, the 1.2 mL assay mixture contained 140 lm 1H2CO instead of

140 lm2H2CO

In the control experiment described in Fig 2C, the 1.2 mL assay did not contain H4MPT, H2CO or Mtd Instead, F420 was reduced with NaB2H4 to a mixture of (5S)-[5-2H1]F420H2 and (5R)-[5-2H1]F420H2 This step was carried out under anaerobic conditions

Analysis of F420and F420H2by MALDI-TOF-MS

Samples (25 lL) of the 1.2 mL assay mixtures were applied

to a small ZipTips (Millipore Corp, Bedford, MA, USA) column previously equilibrated with 0.1% (v⁄ v) trifluoro-acetic acid (TFA) The column was then washed with 0.1% (v⁄ v) TFA to remove salts and was then eluted with 84% (v⁄ v) acetonitrile ⁄ 0.1% (v ⁄ v) TFA The eluate was dried by vacuum centrifugation and the dried pellet dissolved in

10 lL 0.1% (v⁄ v) TFA and subsequently supplemented with 10 lL of a saturated solution of a-cyano-4-hydroxy-cinnamic acid in 70% (v⁄ v) acetonitrile ⁄ 0.1% (v ⁄ v) TFA Aliquots were air dried and analysed by MALDI-TOF-MS The mass spectra were collected in the reflector negative-ion mode For each spectrum, at least 150 single shots were summed The spectra were determined with a Voyager DE

RP from PE Biosystems

The natural isotopic distribution in F420 was calculated

by the isotope pattern calculator provided by the University

of Sheffield at the ChemPuter site (http://www.shef.ac.uk/ chemistry/chemputer/) All calculations of simulated data were carried out in excel 2000 and transformed into stick spectra separated by 1 Da [31]

Acknowledgements

This work was supported by the Max Planck Society and by the Fonds der Chemischen Industrie Henning Seedorf thanks the Deutsche Forschungsgemeinschaft for a graduate fellowship We are indebted to Christ-oph Hagemeier for providing purified F420-dependent Mtd from Methanopyrus kandleri

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