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nature structural biology • volume 8 number 2 • february 2001 101

Sequence-specific binding of proteins toDNA is required for essential processesthat range from control of transcription tothe assembly of immunoglobin genes.Many of the proteins are noncatalytic,exerting their effects by binding at appro-priate locations and in some cases chang-ing the local DNA conformation.However, other proteins such as poly-merases, nucleases, glycosylases, methyl-transferases (MTases) and variousintegrases and recombinases have to rec-ognize specific nucleotide sequences whileat the same time bringing catalytic sidechains into play on these samenucleotides. All catalytically active pro-teins balance the requirements for recog-nition against those for catalysis, but forenzymes that act on specific DNAsequences, this balancing act is particular-ly demanding. DNA MTases, which sharethe core structure of the great majority ofS-adenosyl-L-methionine (AdoMet)-dependent MTases, have had to adapt toact on their huge DNA substrates.

On page 121 of this issue of NatureStructural Biology, Goedecke et al.1 presentthe structure of a ternary complexbetween an adenine-N6-specific DNAMTase, M•TaqI, and its two substrates —the specific DNA and a nonreactiveAdoMet analog. The structure of the bina-ry M•TaqI–AdoMet complex was solved in1994 (ref. 2), and was followed by thestructures of equivalent binary complexesof three other DNA MTases that act onexocyclic amino groups — PvuII3 (gener-ating N4-methyl cytosine) and DpnM4

and RsrI5 (both generating N6-methyladenine). Despite considerable effort, nospecific complexes between these enzymesand their DNA substrates had been struc-turally characterized before the currentreport by Goedecke et al.1.

The situation has been quite differentfor the DNA MTases that modify a ringcarbon thereby generating 5-methyl-cytosine. These MTases form a covalentbond between a conserved cysteine andthe target cytosine as a reaction interme-diate6 and suicide substrates allowed trap-

ping of this intermediate (when the pro-ton on the carbon to be methylated isreplaced by a fluorine atom, a poor leavinggroup, the reaction cycle is frozen with thecysteine–cytosine bond intact). The struc-tures of DNA–protein complexes forM•HhaI7 and M•HaeIII8 were originallyobtained in this way, and they were thefirst to reveal how any DNA MTase solvesthe problem of fitting a DNA substrateinto a small catalytic pocket. As describedbelow, there were reasons to believe thatthe DNA amino-methylating MTases (N-MTases) used the same basic appoach,but proving this has taken until now. Asurprise is that M•TaqI is not exactly likeM•HhaI or M•HaeIII in its interactionswith the DNA substrate.

Three MTase-DNA complexesM•TaqI catalyzes a reaction between twosubstrates that appear, at first glance, to beseparated by an unpromisingly large dis-tance from each other — ∼ 15 Å (ref. 2).AdoMet binds in a pocket within a corestructure that varies remarkably littleamong MTases acting on glycine or cate-chol and those acting on macromole-cules9,10. This bound AdoMet must reactwith its target adenine base, which in B-form DNA is buried by base pairing andstacking interactions. Rather than sub-stantially distorting the DNA, the targetadenine is swung completely out of thehelix by torsional rotation of its flankingsugar-phosphate backbone bonds andoccupies the active site pocket of M•TaqI(Fig. 1a). This process is called base flip-ping11,12.

DNA base flipping was initially discov-ered in the trapped complex betweenM•HhaI and DNA containing the suicidesubstrate 5-fluorocytosine (Fig. 1b)7. Theoverall sequence similarity of all cytosine-C5 DNA MTases13 suggested that base flip-ping might be characteristic of theseMTases. It was exciting and reassuringwhen the structure of DNA–M•HaeIII alsorevealed a flipped cytosine (Fig. 1c)8.While none of the structurally character-ized DNA N-MTases have previously been

cocrystallized with their DNA substrates,docking analyses with B-DNA revealedthat AdoMet is far from the target adenineor cytosine, but that by flipping the targetbase out of the helix the two reactantscould be brought into close proximity.The long-awaited experimental test ofthese in silico predictions, provided byGoedecke et al.1, is very satisfying becauseit confirms the universality of base flip-ping among DNA MTases.

Based on results from docking and bio-chemical studies (see below), it wasexpected that M•TaqI would cause a baseflip. It was not expected, however, that thethree available MTase–DNA structureswould reveal three different means of pre-serving the B-like structure of the DNA.All covalent bonds remain intact duringbase flipping, but the base pairing hydro-gen bonds are broken and the stackinginteractions with adjacent bases are lost.

M•HhaI inserts an amino acid side chain(Gln 237; dark blue in Fig. 1b) into thespace left by the flipped cytosine (green) torestore stacking interactions with theneighboring base pairs as well as hydrogenbonding to the ‘orphaned’ guanine (cyan).M•HaeIII also inserts a side chain (Ile 221;dark blue in Fig. 1c) into the DNA helix,but the side chain opens a gap in the DNAso that the partner guanine re-pairs withan adjacent cytosine. As a consequence ofthe altered pairing the outer guanine is leftwithout a complementary base but formsone hydrogen bond with a sugar oxygen onthe opposite strand (Fig. 1c).

In M•TaqI, the amino acid correspond-ing to Gln 237 of M•HhaI and Ile 221 ofM•HaeIII is Pro 393 (dark blue in Fig. 1a).Pro 393 does not protrude into the DNAhelix, but makes a van der Waals contact tothe methyl group of the orphaned thymine(cyan), which is shifted toward the centerof the helix and partially fills the space leftby the flipped adenine (green). Thus theDNA-stabilizing strategy generated by baseflipping is fulfilled by varying combina-tions of inserted protein side chains(M•HhaI, M•HaeIII) and/or movement ofthe orphaned base (M•HaeIII, M•TaqI).

A Taq attack displaces basesRobert M. Blumenthal and Xiaodong Cheng

The cocrystal structure of TaqI DNA methyltransferase in complex with its specific DNA substrate adds to thegrowing list of structurally confirmed DNA base-flipping enzymes, and provides a basis for the generalmechanism of AdoMet-dependent DNA N-methylation.

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Biochemical evidence for baseflippingBiochemical evidence had suggested baseflipping by M•TaqI14 (and by other amino-MTases15 and E. coli uracil-DNA glycosy-lase16). This evidence was obtainedthrough a fluorescence-based assay todetect conformational alterations in DNA,in which 2-aminopurine replaces a base inthe substrate DNA (for M•TaqI the targetadenine is replaced). When fully stackedin double stranded (ds)DNA, the fluores-cence of 2-aminopurine is quenched, andremoval of this base from the stackingenvironment enhances its fluorescence.This assay can be used to detect base flip-ping, but the results should be interpretedwith caution. In some cases, large protein-dependent changes in 2-aminopurine flu-orescence have been observed for DNAs inwhich the fluorophore replaced sites otherthan that of the flipped nucleotide or itspartner17,18. In some other cases, little orno change was observed for complexes

that carried the DNA substitution at theflipping/methylation site18,19. Changes in2-aminopurine fluorescence indicate con-formational or environmental changesthat lead to 2-aminopurine unstacking —base flipping is just one possible explana-tion for the increased fluorescence31.

We would add that for M•TaqI, the evi-dence provided by the fluorescence-basedassay14 was supported by other methods.First, when the target adenine wasreplaced by 5-iodouracil a photochemicalcrosslink was formed between DNA andM•TaqI, and formation of this crosslinkwas reduced by a mutation in theAdoMet-proximal motif IV (describedbelow)20. Second, the target adenine wasreplaced by thymine, and an M•TaqI-dependent enhancement of permanganatereactivity with that particular thyminewas found21 — this indicates that expo-sure of the target thymine to solvent wasselectively increased, consistent with thepossibility of base flipping. Thus for

102 nature structural biology • volume 8 number 2 • february 2001

M•TaqI, there were good reasons to expectthat the cocrystal structure would revealbase flipping.

How is DNA base flipping initiated?There are still mysteries associated withbase flipping; chief among these are how itis initiated and how it relates to recogni-tion of the substrate sequence. However,one thing is clear: despite the name, thebase itself has little or nothing to do with‘base flipping’. In a complex betweenM•HhaI and a DNA substrate having anabasic (apurinic/apyrimidinic) site at theposition of the target cytosine, the struc-ture reveals that the enzyme still rotates thedeoxyribose to the ‘flipped out’ position22.A similar conformation was also observedfor the flipped-out abasic (product) site infour glycosylase–DNA complexes: uracilDNA glycosylase23, mismatch-specificuracil glycosylase24, alkyladenine glycosyl-ase25 and alkylation glycosylase26. It seemspretty clear that the phosphate-sugar back-

b

a

c

Fig. 1 Three MTase–DNA complex structures. The DNA is represented as a magenta stick model,with the flipped nucleotide in green, and the orphaned nucleotide in cyan. The methyl donor orits analogs are represented as gold balls. The enzyme is represented as silver ribbons, with theamino acid in dark blue balls interacting with DNA from the major groove. a, In M•TaqI, Pro 393forms a van der Waals contact with the methyl group of the orphaned thymine (middle). Theflipped adenine is anchored through hydrogen bonds to its Watson-Crick pairing edge with thebackbone carbonyl oxygen atom of Pro 106 and side chain atoms of Asn 105 (right). For clarity,Tyr 108 and Val 21, above and below the plane of the adenine ring, are not shown. The adenineis oriented in a similar way as the flipped cytosine in M•HhaI (below) to demonstrate that therespective exocyclic amino groups (four o’clock position in each case) have similar patterns ofhydrogen bonding. b, In M•HhaI, the Gln 237 side chain penetrates into the cavity left by theflipped cytosine, and forms backbone and side chain hydrogen bonds with the Watson-Crickpairing edge of the orphaned guanine (middle). The flipped cytosine is covalently linked (yel-low) through its C6 carbon atom to the sulfhydryl of Cys 81, and is hydrogen bonded via itsWatson-Crick pairing edge to the backbone oxygen of Phe 79 and side chain atoms of Glu 119and Arg 165 (right). c, In M•HaeIII, Ile 221 juts between the stacked bases and the partner gua-nine re-pairs with a cytosine adjacent to the flipped base. This re-pairing displaces a guaninethat then forms one hydrogen bond (dotted line) with a sugar oxygen on the opposite strand.

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bone is targeted for rotation by base-flip-ping enzymes12, and that the base is merelycarried along for the ride.

This indifference to the identity of thebase is consistent with the fact that base flip-ping by M•HhaI proceeds with most anybase at the target position22,27,28. In fact, thisproperty is what made the 2-aminopurinefluorescence assays possible (see above).Indifference toward the identity of theflipped base might suggest that DNAMTases are nonspecific with respect to thetarget base, but recognition of the partnerbase can still occur (such as thethymine–Pro 393 interaction in M•TaqI).

The cocrystal structure of M•TaqI doesnot shed much light on the initiation ofbase flipping. One might imagine that theflipping starts with Pro 393 pushing in thesoon-to-be-orphaned thymine while Gly 295 and Arg 353 push the neighboringphosphates (see Fig. 2 in ref. 1). If this isindeed the case, the initiation processwould be unique to M•TaqI since neitherM•HhaI nor M•HaeIII distorts the DNA bypushing a nucleotide in towards the DNAhelical axis. To understand how base flip-ping is initiated, the structure of the pre-cursor to base flipping — for example, acomplex between a DNA MTase and anoncognate DNA — would be very helpful.

Mechanism of DNA N-methylationThe catalytic mechanism proposed byGoedecke et al.1 confirms earlier predic-tions. Focusing on the amino group(NH2) that becomes methylated, it wassuggested earlier3 that the free rotation ofthis group along the C–N bond was hin-dered and its pKa altered by formation of apair of hydrogen bonds, one of which is toa MTase backbone carbonyl (see Fig. 6c inref. 3). This particular carbonyl is expect-ed to be fairly immobile relative to mostbackbone carbonyls because it is flankedby two prolines32 in the conservedSer/Asn/Asp-Pro-Pro-Tyr/Phe motif IV(Asn-Pro-Pro-Tyr in M•TaqI). The secondproton of the target amino group makes ahydrogen bond with the side chain of thefirst residue in the conserved motif.Together, these two hydrogen bonds mayincrease the nitrogen electron density andfacilitate a nucleophilic attack by theAdoMet methylsulfonium group.

However, Goedecke et al.1 provide animportant insight that docking studieswere too imprecise to reveal. Both the Pro-Pro carbonyl and the Asn Oδ1 are out ofthe plane of the constrained adenine base,so that in the complex the adenine amino

group is not coplanar with the purine rings.This would deconjugate the nitrogen lonepair while at the same time positioning itfor an in-line attack from AdoMet.

The M•TaqI–DNA structure also illus-trates how a conserved catalytic pocketcan be altered to catalyze distinct chemicalreactions — in this case the conservedAdoMet-dependent MTase pocket beingadapted to direct attack by AdoMet in theDNA N-MTases and to an additional acti-vating sulfhydryl attack in the DNA C-MTases. The conserved Asn-Pro-Pro-Tyr motif IV in M•TaqI is spatially equiva-lent to the conserved Pro-Cys motif IV inMTases that generate 5-methylcytosine(see Fig. 3 in ref. 9). M•TaqI and the otherDNA N-MTases catalyze a direct attack byAdoMet, using motif IV to position thetarget amino group (right side of Fig. 1a).In contrast, the 5-methylcytosine MTasesuse motif IV to attack C6 of cytosine inorder to indirectly activate C5 for methy-lation6 (right side of Fig. 1b).

Loose endsThe M•TaqI structure has answered morequestions about catalysis of N-methyla-tion than about the sequence recognitionand base flipping processes. Together withearlier structures, the M•TaqI–DNA struc-ture reveals that DNA MTases use a varietyof ways to stabilize flipped target bases andthey may use a variety of mechanisms toinitiate the flipping. Whatever thesemechanisms might entail, they appear tobe extremely rapid — a delay of <4 ms wasfound between protein binding and baseflipping by M•EcoRI29 and these twoevents could not be kinetically separatedin M•HhaI30. Because technical considera-tions required the use of nonphysiologi-cally short DNA substrates in thesestudies, initial binding of the DNA wasessentially equivalent to binding of thespecific site. It thus remains to be deter-mined whether base flipping is a simplelinear function of binding occupancy on alonger piece of DNA. If full recognition isnot a prerequisite for base flipping, doesbase flipping increase the residence timeof MTases at some sequences during one-dimensional diffusion search along theDNA, thereby improving recognition effi-ciency? While these basic questionsremain open, the M•TaqI–DNA structurepresented by Goedecke et al.1 is a very wel-come contribution and has brought ourunderstanding of DNA N-MTases out ofthe realm of guess work and into the realworld.

AcknowledgmentsWe thank E. Weinhold for providing coordinates ofthe M•TaqI–DNA complex.

Robert M. Blumenthal is in the Departmentof Microbiology and Immunology, MedicalCollege of Ohio, 3055 Arlington Avenue,Toledo, Ohio 43614-5806, USA, andXiaodong Cheng is in the Department ofBiochemistry, Emory University School ofMedicine, 1510 Clifton Road, Atlanta,Georgia 30322, USA. Correspondenceshould be addressed to R.M.B. email: rblumenthal@mco.edu or X.C. email:xcheng@emory.edu

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22. O’Gara, M., Horton, J.R., Roberts, R.J. & Cheng, X.Nature Struct. Biol. 5, 872–877 (1998).

23. Parikh, S.S. et al. EMBO J. 17, 5214–5226 (1998).24. Barrett, T. E. et al. Cell 92, 117–129 (1998).25. Lau, A. Y., Scharet, O. D., Samson, L., Verdine, G. L.

& Ellenberger, T. Cell 95, 249–258 (1998).26. Hollis, T., Ichikawa, Y. & Ellenberger T. EMBO J. 19,

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