Phylogeny of mRNA capping enzymes.
ABSTRACT The m7GpppN cap structure of eukaryotic mRNA is formed cotranscriptionally by the sequential action of three enzymes: RNA triphosphatase, RNA guanylyltransferase, and RNA (guanine-7)-methyltransferase. A multifunctional polypeptide containing all three active sites is encoded by vaccinia virus. In contrast, fungi and Chlorella virus encode monofunctional guanylyltransferase polypeptides that lack triphosphatase and methyltransferase activities. Transguanylylation is a two-stage reaction involving a covalent enzyme-GMP intermediate. The active site is composed of six protein motifs that are conserved in order and spacing among yeast and DNA virus capping enzymes. We performed a structure-function analysis of the six motifs by targeted mutagenesis of Ceg1, the Saccharomyces cerevisiae guanylyltransferase. Essential acidic, basic, and aromatic functional groups were identified. The structural basis for covalent catalysis was illuminated by comparing the mutational results with the crystal structure of the Chlorella virus capping enzyme. The results also allowed us to identify the capping enzyme of Caenorhabditis elegans. The 573-amino acid nematode protein consists of a C-terminal guanylyltransferase domain, which is homologous to Ceg1 and is strictly conserved with respect to all 16 amino acids that are essential for Ceg1 function, and an N-terminal phosphatase domain that bears no resemblance to the vaccinia triphosphatase domain but, instead, has strong similarity to the superfamily of protein phosphatases that act via a covalent phosphocysteine intermediate.
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ABSTRACT: Vaccinia virus capping enzyme is a heterodimer of D1 (844 aa) and D12 (287 aa) polypeptides that executes all three steps in m(7)GpppRNA synthesis. The D1 subunit comprises an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module and a C-terminal guanine-N7-methyltransferase (MTase) module. The D12 subunit binds and allosterically stimulates the MTase module. Crystal structures of the complete D1⋅D12 heterodimer disclose the TPase and GTase as members of the triphosphate tunnel metalloenzyme and covalent nucleotidyltransferase superfamilies, respectively, albeit with distinctive active site features. An extensive TPase-GTase interface clamps the GTase nucleotidyltransferase and OB-fold domains in a closed conformation around GTP. Mutagenesis confirms the importance of the TPase-GTase interface for GTase activity. The D1⋅D12 structure complements and rationalizes four decades of biochemical studies of this enzyme, which was the first capping enzyme to be purified and characterized, and provides new insights into the origins of the capping systems of other large DNA viruses.Structure 03/2014; 22(3):452-465. · 6.79 Impact Factor
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ABSTRACT: The nuclear pore complex proteins SonA and SonB, the orthologs of mammalian RAE1 and NUP98, respectively, were identified in Aspergillus nidulans as cold-sensitive suppressors of a temperature-sensitive allele of the essential mitotic NIMA kinase (nimA1). Subsequent analyses found that sonB1 mutants exhibit temperature-dependent DNA damage sensitivity. To understand this pathway further we performed a genetic screen to isolate additional conditional DNA damage-sensitive suppressors of nimA1. We identified two new alleles of SonA and four intragenic nimA mutations that suppress the temperature sensitivity of the nimA1 mutant. In addition, we identified SonC, a previously unstudied binuclear Zn cluster protein involved with NIMA and the DNA damage response. Like sonA and sonB, sonC is an essential gene. SonC localizes to nuclei and partially disperses during mitosis. When the nucleolar organizer region (NOR) undergoes mitotic condensation and removal from the nucleolus, nuclear SonC and histone H1 localize in a mutually exclusive manner with H1 being removed from the NOR region and SonC being absent from the end of the chromosome beyond the NOR. This region of chromatin is adjacent to a cluster of nuclear pore complexes to which NIMA localizes last during its progression around the nuclear envelope during initiation of mitosis. The results genetically extend the NIMA regulatory system to include a protein with selective large-scale chromatin location observed during mitosis. The data suggest a model in which NIMA and SonC, its new chromatin-associated suppressor, might help to orchestrate global chromatin states during mitosis and the DNA damage response.Genetics 11/2013; · 4.87 Impact Factor
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ABSTRACT: Rotaviruses and orbiviruses are non-turreted Reoviridae members. The rotavirus VP3 protein is a multifunctional capping enzyme and antagonist of the interferon-induced cellular oligoadenylate synthetase-ribonuclease L pathway. Despite mediating important processes, VP3 is the sole protein component of the rotavirus virion whose structure remains unknown. In the current study, we used sequence alignment and homology modeling to identify features common to non-turreted Reoviridae capping enzymes and to predict the domain organization, structure, and active sites of rotavirus VP3. Our results suggest that orbivirus and rotavirus capping enzymes share a domain arrangement similar to that of the bluetongue virus capping enzyme. Sequence alignments revealed conserved motifs and suggested that rotavirus and orbivirus capping enzymes contain a variable N-terminal domain, a central guanine-N7-methyltransferase domain that contains an additional inserted domain, and a C-terminal guanylyltransferase and RNA 5'-triphosphatase domain. Sequence conservation and homology modeling suggested that the insertion in the guanine-N7-methyltransferase domain is a ribose-2'-O-methyltransferase domain for most rotavirus species. Our analyses permitted putative identification of rotavirus VP3 active-site residues, including those that form the ribose-2'-O-methyltransferase catalytic tetrad, interact with S-adenosyl-L-methionine, and contribute to autoguanylation. Previous reports have indicated that group A rotavirus VP3 contains a C-terminal 2H-phosphodiesterase domain that can cleave 2'-5' oligoadenylates, thereby preventing ribonuclease L activation. Our results suggest that a C-terminal phosphodiesterase domain is present in the capping enzymes from two additional rotavirus species. Together, these findings provide insight into a poorly understood area of rotavirus biology and are a springboard for future biochemical and structural studies of VP3.Journal of Virology 06/2014; · 4.65 Impact Factor
Proc. Natl. Acad. Sci. USA
Vol. 94, pp. 9573–9578, September 1997
Phylogeny of mRNA capping enzymes
SHUANG PING WANG, LIANG DENG, C. KIONG HO, AND STEWART SHUMAN*
Molecular Biology Program, Sloan–Kettering Institute, New York, NY 10021
Communicated by Kenneth I. Berns, Cornell University Medical College, New York, NY, July 7, 1997 (received for review May 14, 1997)
mRNA is formed cotranscriptionally by the sequential action
of three enzymes: RNA triphosphatase, RNA guanylyltrans-
ferase, and RNA (guanine-7)-methyltransferase. A multifunc-
tional polypeptide containing all three active sites is encoded
by vaccinia virus. In contrast, fungi and Chlorella virus encode
monofunctional guanylyltransferase polypeptides that lack
triphosphatase and methyltransferase activities. Transguany-
lylation is a two-stage reaction involving a covalent enzyme-
GMP intermediate. The active site is composed of six protein
motifs that are conserved in order and spacing among yeast
and DNA virus capping enzymes. We performed a structure–
function analysis of the six motifs by targeted mutagenesis of
Ceg1, the Saccharomyces cerevisiae guanylyltransferase. Essen-
tial acidic, basic, and aromatic functional groups were iden-
tified. The structural basis for covalent catalysis was illumi-
nated by comparing the mutational results with the crystal
structure of the Chlorella virus capping enzyme. The results
also allowed us to identify the capping enzyme of Caenorhab-
ditis elegans. The 573-amino acid nematode protein consists of
a C-terminal guanylyltransferase domain, which is homolo-
gous to Ceg1 and is strictly conserved with respect to all 16
amino acids that are essential for Ceg1 function, and an
N-terminal phosphatase domain that bears no resemblance to
the vaccinia triphosphatase domain but, instead, has strong
similarity to the superfamily of protein phosphatases that act
via a covalent phosphocysteine intermediate.
The m7GpppN cap structure of eukaryotic
mRNA capping occurs by a series of three enzymatic reactions
in which the 5?-triphosphate terminus of a primary transcript
is first cleaved to a diphosphate by RNA triphosphatase, then
capped with GMP by RNA guanylyltransferase, and methyl-
ated at the N7 position of guanine by RNA (guanine-7)-
methyltransferase (1). To date, only the guanylyltransferase
reaction mechanism has been dissected in detail. Transfer of
GMP from GTP to the 5?-diphosphate terminus of RNA
occurs in a two-stage reaction involving a covalent enzyme–
GMP intermediate (2). The GMP is linked to the enzyme
through a phosphoamide (P–N) bond to the ?-amino group of
a lysine residue. This structure is analogous to the enzyme
(-Lys)-AMP intermediate formed when DNA ligase reacts
The GTP-dependent capping enzymes and ATP-dependent
ligases make up a superfamily of covalent nucleotidyltrans-
ferases (3). The guanylate or adenylate moiety is covalently
bound to an invariant lysine residue within a conserved KxDG
element (motif I in Fig. 1). Five other sequence motifs are
conserved in the same order and with similar spacing in the
capping enzymes and ligases (motifs III, IIIa, IV, V, and VI in
Fig. 1). The amino acid sequence similarity between the
capping enzymes and polynucleotide ligases is limited to these
segments, suggesting a common core structure in which the six
motifs are brought together at the enzyme’s active site. This
prediction has been borne out by the recent reports of the
crystal structures of bacteriophage T7 DNA ligase with bound
ATP and Chlorella virus capping enzyme with bound GTP (4,
The guanylyltransferases of Saccharomyces cerevisiae (Ceg1;
459 amino acids), Schizosaccharomyces pombe (Pce1; 402
amino acids), Candida albicans (Cgt1; 449 amino acids), and
Chlorella virus PBCV-1 (330 amino acids) are monofunctional
polypeptides that catalyze GMP transfer to RNA but do not
catalyze cap methylation or ?-phosphate cleavage (6–9). In
budding yeast, the triphosphatase and methyltransferase func-
tions are encoded separately (6). In contrast, the vaccinia virus
capping enzyme is a multifunctional protein that catalyzes all
three capping reactions (10). The triphosphatase, guanylyl-
transferase, and methyltransferase catalytic domains are ar-
rayed in a modular fashion within a single 844-amino acid
polypeptide (Fig. 2) (11–16). This trifunctional domain struc-
ture also applies to the capping enzyme of African swine fever
We are interested in the evolution of the RNA capping
machinery and are focusing on four questions. What structural
features are essential for the guanylyltransferase, methyltrans-
ferase, and triphosphatase activities? To what extent are these
features conserved? How do the essential structural elements
illuminate the reaction mechanisms? How have the physical
and functional organizations of the component activities di-
verged from viral to cellular systems? This analysis requires
that the essential structural features be defined by mutagenesis
and that genes encoding the capping proteins be identified
from a wide variety of sources. In practice, the results of
mutational analyses can be helpful in genomics-based identi-
fication of novel gene family members—i.e., the predictive
value of initial protein sequence searches can be enhanced by
visual screening for specific essential residues. For example,
mutagenesis of the vaccinia capping enzyme helped us to
identify the S. cerevisiae ABD1 gene encoding the cellular cap
methyltransferase (18). Abd1 is a 436-amino acid monomeric
protein that is similar in size and sequence to the C-terminal
methyltransferase domain of the vaccinia enzyme. In turn,
mutagenesis of Abd1 led to the identification of the cap
methyltransferase of Caenorhabditis elegans (19).
In this study, we have performed an extensive structure–
function analysis of Ceg1, the RNA guanylyltransferase of S.
cerevisiae. The guanylyltransferase activity of Ceg1 is essential
for cell viability (20–22). Hence, mutational effects on Ceg1
function in vivo can be evaluated by simple exchange of mutant
CEG1 alleles for the wild-type gene. After locating essential
amino acids by alanine scanning, we determined by conserva-
tive replacements the essential features of individual amino
acid side chains. Consideration of the results in light of the
crystal structure of the Chlorella virus capping enzyme (5)
elucidates the mechanism of catalysis and the basis for nucle-
The publication costs of this article were defrayed in part by page charge
payment. This article must therefore be hereby marked ‘‘advertisement’’ in
accordance with 18 U.S.C. §1734 solely to indicate this fact.
© 1997 by The National Academy of Sciences 0027-8424?97?949573-6$2.00?0
PNAS is available online at http:??www.pnas.org.
*To whom reprint requests should be addressed at: Molecular Biology
Program, Sloan–Kettering Institute, 1275 York Avenue, New York,
NY 10021. e-mail: email@example.com.
otide binding. Moreover, insights gained from the mutational
capping enzyme of C. elegans. The nematode polypeptide is
remarkable in that it includes a phosphatase domain that bears
no resemblance to the vaccinia triphosphatase domain but,
instead, has strong similarity to the superfamily of protein
phosphatases that act via a covalent phosphocysteine inter-
METHODS AND MATERIALS
Site-Directed Mutagenesis. Missense mutations in the
CEG1 gene were programmed by synthetic oligonucleotides
using the two-stage PCR-based overlap extension strategy. An
NdeI–BamHI restriction fragment of each PCR-amplified
CEG1 gene was inserted into pET16b. The presence of the
desired mutation was confirmed in every case by dideoxy
sequencing. Restriction fragments of each CEG1 mutant were
exchanged with the corresponding segment in the yeast plas-
mid pGYCE-358 (CEN TRP1 CEG1). Expression of CEG1 in
this context is driven by its natural promoter. We sequenced
the entire CEG1 insert in each pGYCE plasmid to exclude the
occurrence of PCR-generated mutations outside the targeted
Test of CEG1 Function by Plasmid Shuffle. Strain YBS2
(MATa ura3 trp1 lys2 leu2 ceg1::hisG pGYCE-360), which is
deleted at the chromosomal CEG1 locus, is viable when it
maintains an extrachromosomal copy of CEG1 on a CEN
URA3 plasmid (pGYCE-360) (20). YBS2 was transformed
with pGYCE-358 plasmids bearing mutant alleles of CEG1.
Trp?transformants were selected on medium lacking trypto-
phan. Individual colonies were patched on medium lacking
tryptophan. Cells from each patch were then streaked on
medium containing 0.75 mg?ml fluoroorotic acid (FOA). The
plates were incubated at 25°C and 30°C. Mutations scored as
lethal were those that did not support colony formation after
7 days. Individual colonies of the viable CEG1 alleles were
picked from the FOA plate and patched to yeast extract?
peptone?dextrose (YPD). Two isolates of each mutant were
tested for growth on YPD agar at 25°C and 37°C.
RESULTS AND DISCUSSION
Alanine-Substitution Mutations Define Essential Residues.
Amino acid residues essential for Ceg1 function were identi-
fied by alanine-scanning mutagenesis of the six conserved
of functional domains within RNA guanylyltransferases is illustrated
in cartoon form. ASFV, African swine fever virus.
Phylogeny of RNA Guanylyltransferases. The organization
function in vivo
Effect of alanine-substitution mutations on CEG1
Motif Mutation Growth
YBS2 was transformed with CEN TRP1 plasmids containing the
indicated mutant alleles. Trp?transformants were selected and then
streaked on medium containing fluoroorotic acid (FOA) (0.75 mg?
ml). The plates were incubated at 25°C and 30°C. Lethal mutations
were those that formed no colonies after 7 days. All other alleles
supported colony formation in 3 days. Individual colonies were picked
from the FOA plate and patched to yeast extract?peptone?dextrose
(YPD). Two isolates of each mutant were tested for growth on YPD
agar at 37°C. Mutants that formed colonies at both temperatures were
scored as two-plus (??). Temperature-sensitive (ts) mutants were
those that did not form colonies after 7 days at 37°C.
motifs I, III, IIIa, IV, V, and VI, are conserved in guanylyltransferases and ATP-dependent DNA ligases as shown. The amino acid sequences are
aligned for capping enzymes (CE) encoded by S. cerevisiae (Sce), Sc. pombe (Spo), C. albicans (Cal), Chlorella virus PBCV-1 (ChV), African swine
fever virus (ASF), vaccinia virus (Vac), Shope fibroma virus (SFV), and molluscum contagiosum virus (MCV). Grouped below the capping enzymes
are aligned sequences for the DNA ligases (Lig) of vaccinia, Sc. pombe, human ligase I (Hu1), and human ligase 3 (Hu3). The numbers of amino
acid residues separating the motifs are indicated. Residues in the yeast capping enzyme Ceg1 that were found by mutational analysis to be essential
for function are shown in shaded boxes. Where these residues are conserved in other family members, they are also shaded. Ceg1 residues judged
to be nonessential (i.e., tolerant of alanine substitution) are denoted by dots. Ceg1 positions at which alanine replacement caused a
temperature-sensitive growth defect are denoted by ?.
Conserved sequence elements define a superfamily of covalent nucleotidyltransferases. Six collinear sequence elements, designated
9574Biochemistry: Wang et al.Proc. Natl. Acad. Sci. USA 94 (1997)
motifs that define the covalent nucleotidyltransferase super-
family. We reported previously that alanine substitutions at
Lys-70 and Gly-73 (motif I), Asp-130 and Glu-132 (motif III),
Asp-225 and Gly-226 (motif IV), and Lys-249 and Asp-257
(motif V) were lethal (7, 20). Here, we introduced alanine
mutations at 22 new positions within motifs I, IIIa, V, and VI.
The CEG1-Ala alleles were tested for in vivo function using the
plasmid shuffle procedure (Table 1). Eight of the mutations
were lethal: these were at positions Arg-75 (motif I), Phe-151
and Asp-152 (motif IIIa), Lys-247 (motif V), Trp-363, Arg-369,
Asp-371, and Lys-372 (motif VI). Thirteen of the mutations
had no apparent effect on cell growth. One mutation, Y65A,
conferred a temperature-sensitive (ts) growth phenotype.
The results of alanine scanning at 39 residues of the con-
served motifs are summarized in Fig. 1. Nineteen nonessential
amino acids are denoted by dots above the yeast sequence.
Four positions at which alanine replacement resulted in ts
growth are denoted by ?. The 16 essential amino acids are
shown in shaded boxes.
Structure–Function Relationships at Essential Residues.
Alanine substitution eliminates the side chain beyond the
?-carbon. This mutational approach provides an indication of
the essentiality of the side chain for protein function but does
not reveal the properties of the missing side chain that are
important. This issue can be addressed by introducing conser-
vative substitutions for the essential residues. For example,
replacement of Lys-70 by arginine, histidine, or threonine is
lethal, implying a strict requirement for lysine as the active site
nucleophile in GMP transfer from GTP to RNA (20–22). In
the present study, we tested 20 conservative substitutions at 13
essential positions. These included 6 acidic, 5 basic, and 2
aromatic amino acids. (The two essential glycines were not
analyzed further.) Instructive results were obtained for each
position, as shown in Table 2.
Among the acidic residues, we found that Asp-130 in motif
III, Asp-257 in motif V, and Asp-371 in motif VI could be
replaced by glutamate, but not by asparagine. Similarly, Glu-
132 could be replaced by aspartate, but not by glutamine. We
surmise that at each of these positions an acidic side chain is
essential for Ceg1 function. Asp-225 of motif IV was strictly
essential. Substitution by either asparagine or glutamate was
lethal. This is noteworthy, because the equivalent position is a
Glu in the vaccinia capping enzyme and the DNA ligases (Fig.
1). Context-dependent steric constraints may account for the
failure of the bulkier Glu residue to replace Asp-225. At
Asp-152 of motif IIIa, a glutamate substitution was viable,
whereas replacement by asparagine resulted in a ts growth
phenotype. The fact that D152N cells grew normally at 25°C
indicates that an acidic side chain is not essential. Asp-152 may
engage in hydrogen bonding, a capacity shared with Glu and
Asn, but not with Ala.
Four of the essential basic residues were intolerant of
conservative substitutions. Lysine mutations were lethal at
Arg-75 in motif I and Arg-369 in motif VI. Similarly, Lys-247
and Lys-249 of motif V could not be substituted by arginine.
Only Lys-372 in motif VI was tolerant of replacement by
arginine. A requirement for an aromatic residue was evident
at Phe-151 of motif IIIa. A F151Y mutant was viable, whereas
replacement by leucine was lethal. Trp-363 of motif VI could
be replaced by phenylalanine.
Mechanistic Implications. Insights into substrate binding
and catalysis emerge when the Ceg1 mutational findings are
interpreted in light of the crystal structure of PBCV-1 capping
enzyme, which has been solved with GTP bound at the active
site and with GMP bound covalently (5).
The ?-amino group of the active site Lys in motif I is
positioned near the ?-phosphate of GTP in the crystal struc-
ture, as one might expect (Fig. 3). It is likely that formation of
the enzyme–GMP intermediate proceeds through a pentaco-
ordinate phosphorane transition state in which the active site
lysine and the ?-phosphate are positioned apically. The
PBCV-1 enzyme structure reveals a large conformational
change in the GTP-bound enzyme, from an ‘‘open’’ to a
‘‘closed’’ state, that reorients the phosphates for in-line attack
by the lysine (5). Adoption of the closed conformation brings
motif VI into direct contact with the ?- and ?-phosphates of
GTP and also moves the essential Asp at the end of motif V
(Asp-257 in Ceg1) close to the ?-phosphate. Motif VI makes
several key contacts (Fig. 3). The motif VI Arg residue
(Arg-369 in Ceg1) interacts with the ?-phosphate and also
hydrogen bonds to the essential Asp side chain situated nearby
in motif VI (Asp-371 in Ceg1). A requirement for bidentate
hydrogen bonding by Arg-369 would explain why lysine sub-
stitution at this position is lethal. The essential Lys of motif VI
(Lys-372 in Ceg1) contacts the ?-phosphate of GTP. As noted
above, Arg can functionally substitute for Lys at this position.
Effect of conservative substitutions on CEG1 function
See Table 1 for definitions.
GTP at the capping enzyme active site. The figure shows the inter-
actions of essential amino acids with GTP in the context of the closed
conformation of the PBCV-1 capping enzyme–GTP cocrystal (5). The
they reside—e.g., the active site lysine nucleophile is Lys (I).
Interactions between essential amino acid side chains and
Biochemistry: Wang et al.Proc. Natl. Acad. Sci. USA 94 (1997) 9575
Contacts with the ?-phosphate of GTP are made by the two
essential basic residues in motif V. The first lysine of the KxK
sequence (Lys-247 in Ceg1) is hydrogen-bonded to the ?-
phosphate in the open conformation; this contact is attenuated
during the conformational change. In the closed form of the
enzyme, the distal Lys of motif V (Lys-249 in Ceg1) hydrogen
bonds with the ?-phosphate (this residue is denoted as Lys? in
Fig. 3). In the covalent enzyme–GMP intermediate, the ?-
phosphate oxygens interact with both positively charged side
chains and a divalent cation (5). We hypothesize that the two
lysines and the divalent cation enhance catalysis by stabilizing
the equatorial phosphate oxygens in the transition state.
The essential Asp residue of motif IV (Asp-225 in Ceg1)
hydrogen bonds to the active site lysine residue (Fig. 3). We
speculate that this side chain acts as a general base to withdraw
a proton from the -NH2of lysine during formation of the P–N
bond to GMP. The phosphoamide bond should, in principle,
be stabilized when the amide nitrogen is unprotonated. The
Asp chain would donate a proton back to the Lys, leaving the
group as the 5? diphosphate of RNA attacks the enzyme–GMP
intermediate to form the cap structure.
analogs of Arg-87, Glu-131, and Phe-146) make direct contact
with the nucleoside moiety of GTP in the PBCV-1 enzyme
structure (5). The Arg residue of motif I hydrogen bonds with
the ribose 3? OH (Fig. 3). In addition, this Arg side chain
hydrogen bonds with the essential Asp of motif III. (The Asp
contacts by Arg-87 would explain why lysine substitution is
lethal. It would also explain why the Arg of motif I is
enzymes of yeast, African swine fever virus, and PBCV-1 and
in the DNA ligases. This Arg is conspicuously not conserved
in motif I of the poxvirus-encoded capping enzymes (where it
is a Pro or Gly) and neither is the Asp in motif III (Fig. 1). The
absence of Arg implies either that the vaccinia capping enzyme
does not require the 3? OH sugar interactions made by other
guanylyltransferases and by DNA ligase (4) or that it achieves
these contacts via divergent structural elements. The essential
Glu side chain of motif III hydrogen bonds with the ribose 2?
OH of GTP, whereas the essential Phe of motif IIIa is stacked
on the guanine base. The mutational effects confirm the
functional importance of these contacts.
Identification of a Capping Enzyme from C. elegans. Gua-
nylyltransferase activities have been isolated from several
higher eukaryotes (23); however, no genes encoding these
enzymes have been identified to date. We found that the
structure–function relationships revealed by the present mu-
tational analysis of Ceg1 conferred predictive power to a
genomics-based search for candidate capping enzymes in
higher eukaryotes. By imposing complete conservation of
residues essential for Ceg1 function, we identified the capping
enzyme from C. elegans. The C. elegans C03D6.3 gene product
is a 573-amino acid (66-kDa) polypeptide derived by concep-
tual translation after computer-modeled joining of 11 exons
distributed over 2.4 kb of genomic DNA (GenBank accession
no. Z75525). This is in good agreement with the sizes of the
and wheat germ (77 kDa)], which were determined by SDS?
PAGE analysis of the covalent enzyme–GMP catalytic inter-
To confirm that this polypeptide is truly the product of a
cDNA clones by reverse transcription–PCR amplification of C.
elegans total RNA using oligonucleotide primers flanking the
were also used to amplify specific cDNAs from a C. elegans
cDNA library. Both approaches led to the isolation of 1.7-kbp
cDNAs. We determined by sequencing several cDNA clones
that the exons were spliced as predicted by the nematode
genome project and that the ORF was continuous. Analysis of
consists of an N-terminal phosphatase domain fused to a
C-terminal guanylyltransferase domain (Fig. 2).
Alignment of the sequence of the C terminus of the C.
elegans protein with the guanylyltransferases encoded by S.
cerevisiae, Sc. pombe, C. albicans, and Chlorella virus PBCV-1
reveals conservation at 75?301 positions (Fig. 4). The nema-
tode protein contains all six defining motifs of the covalent
nucleotidyltransferase superfamily (shaded boxes in Fig. 4).
All 16 residues that we have identified as essential for Ceg1
function are strictly conserved in the C. elegans protein.
Moreover, the amino acids of the Chlorella virus capping
enzyme that contact GTP in the cocrystal (arrowheads in Fig.
4) are conserved in the nematode protein; these include
several amino acids outside of the six motifs.
A Putative RNA Triphosphatase Domain of the C. elegans
Capping Enzyme. The N-terminal portion of the C. elegans
capping enzyme contains the (I?V)HCxAGxGR(S?T)G sig-
nature motif of the dual-specificity protein phosphatase?
protein tyrosine phosphatase enzyme family (Fig. 5). These
proteins catalyze phosphoryl transfer from a protein phospho-
monoester substrate to the thiol of a cysteine on the enzyme
to form a covalent phosphocysteine intermediate (29). The
intermediate is then attacked by water to liberate phosphate.
The cysteine within the signature motif is the active site of
phosphoryl transfer and is thus essential for reaction chemis-
try. The conserved Arg side chain makes bidentate contacts
with the phosphate oxygens and is also critical for phosphatase
enzyme with the baculovirus-encoded protein phosphatase
sequence of the C. elegans C03D6.2 gene product from residues 273 to
573 is aligned with the sequences of the guanylyltransferases of Sc.
pombe (spo), S. cerevisiae (sce), C. albicans (cal), and Chlorella virus
PBCV-1 (chv). Gaps in the sequence are indicated by dashes (-).
Amino acids conserved in all five proteins are denoted by asterisks.
The six nucleotidyltransferase motifs are shown in shaded boxes.
Residues in proximity to the GTP moiety in the PBCV-1 cocrystal are
indicated by arrowheads.
9576Biochemistry: Wang et al.Proc. Natl. Acad. Sci. USA 94 (1997)
(34) is shown in Fig. 5. (Two other predicted C. elegans gene
products with homology to the capping enzyme N terminus are
included in the alignment.) The similarity extends well beyond
the signature motif and includes a conserved aspartate (Asp-
64) located upstream of the putative active site cysteine
(Cys-124). Biochemical and structural studies of several pro-
totypal protein phosphatases have shown that this aspartate
acts as a general acid during formation of the cysteinyl
phosphate intermediate (29, 30). The Asp is situated within a
WxD motif in numerous protein tyrosine phosphatases, and
this is also the case in the nematode protein (Fig. 5). This
extent of conservation makes it likely that the C. elegans
enzyme is a phosphatase. More specifically, we suggest that the
N-terminal domain of the protein is an RNA triphosphatase
that removes the ?-phosphate of triphosphate-terminated
Available biochemical data support the idea that higher
eukaryotes encode a bifunctional capping enzyme with
triphosphatase and guanylyltransferase activities. The guany-
lyltransferases from rat liver and brine shrimp copurify with an
RNA triphosphatase activity (28, 31). In the case of the brine
shrimp protein, Yagi et al. (28) showed that both catalytic
activities reside within a single 73-kDa polypeptide that was
converted by partial proteolysis into catalytically active do-
mains: a 20-kDa triphosphatase module could be separated
from a 44-kDa fragment guanylyltransferase domain. The sizes
of these two active fragments are consistent with those of the
two putative domains of the nematode capping enzyme.
It is noteworthy that the RNA triphosphatase activity of the
rat liver capping enzyme is optimal in the absence of a divalent
cation and that EDTA has no effect on ?-phosphate cleavage
(31, 33). A distinctive characteristic of the protein phospha-
tases to which the C. elegans protein is related is that they do
not require metal cofactors for catalysis (29).
Phylogeny of the Guanylyltransferases. The results of this
study underscore the conserved structural basis for covalent
nucleotidyl transfer by cellular and DNA virus-encoded gua-
nylyltransferases. The guanylyltransferases can now be sub-
grouped according to two criteria: (i) conservation of specific
residues within the six motifs and (ii) sequence similarities
outside the motifs. Based on intra-motif conservation, we
delineate two subgroups: the first consists of the enzymes from
fungi, C. elegans, Chlorella virus, and African swine fever virus,
and the second consists of the poxvirus enzymes (of vaccinia,
Shope fibroma virus, and molluscum contagiosum virus). The
first group contains four essential amino acids (Arg in motif I,
Asp in motif III, Asp in motif IIIa, and Trp in motif VI) that
are replaced by unrelated functional groups in the poxvirus
proteins. The essentiality of these four amino acids for achiev-
ing RNA capping is apparently context dependent. (Three of
the four residues—Arg in motif I, Asp in motif III, and Asp in
motif IIIa—are also conserved in the DNA ligases.)
have placed the enzymes from S. cerevisiae, Sc. pombe, C.
albicans, C. elegans, and Chlorella virus into a discrete sub-
family. A sequence alignment highlights two motifs that are
unique to these capping enzymes, which we have designated
motif P and motif Vc (Fig. 4). Motif P is a proline-containing
segment [FPGx(Q?N)PVS(L?F?I)] located 17–18 amino acids
upstream of the active site lysine. Motif Vc [(K?R)I(I?V)EC]
is situated between motifs V and VI. The alignment in Fig. 4
provides a blueprint for further structure–function analysis of
conserved functional groups in the new motifs and at con-
served positions outside the motifs.
Evolution of the Capping Apparatus. The physical organi-
zations of the component activities of the capping apparatus
have diverged in viral and cellular systems. The poxviruses and
African swine fever virus have collected all three active sites
within a single multidomain polypeptide. Fungi and higher
eukaryotes have segregated the guanylyltransferase and meth-
yltransferase functions to distinct gene products. Yet, it is clear
from the few genes available that the guanylyltransferase and
methyltransferase proteins of fungi and C. elegans are con-
served with respect to the corresponding vaccinia domains. In
general, the cellular proteins are more similar to each other
than to the vaccinia protein, suggesting that the poxviruses
diverged earlier from ancestral nucleotidyl transferase and
Lower and higher eukaryotes differ clearly with respect to
the physical linkage of the guanylyltransferase and triphos-
phatase functions. Yeasts encode a monofunctional guanylyl-
transferase, whereas C. elegans encodes a bifunctional phos-
phatase-guanylyltransferase. As discussed above, biochemical
evidence suggests that bifunctional triphosphatase-guanylyl-
transferase enzymes are present in many higher eukaryotes.
The linear arrangement of N-terminal phosphatase and C-
terminal guanylyltransferase domains in the C. elegans protein
is similar to that of the vaccinia capping enzyme (11, 13, 35).
Yet, the sequences of the vaccinia and C. elegans N-terminal
domains are entirely dissimilar. Moreover, the biochemical
properties of the vaccinia triphosphatase differ from those of
the triphosphatase from higher eukaryotes in one key respect.
The rat liver and brine shrimp triphosphatases require no
divalent cation for activity (in fact, they are inhibited by
divalent cations), whereas the triphosphatase activity of the
vaccinia capping enzyme depends absolutely on a divalent
cation cofactor (13, 31–33). The sequence of the C. elegans
protein implies that ?-phosphate cleavage occurs through a
phosphoenzyme intermediate. Strenuous efforts to detect a
phosphoenzyme intermediate for the vaccinia triphosphatase
have been unsuccessful, which suggests that covalent catalysis
does not apply in this case (S.S., unpublished data). Mutational
analysis of the vaccinia triphosphatase provides additional
evidence for a distinct mechanism. We have pinpointed four
acidic side chains that are essential for catalysis by vaccinia
triphosphatase and are conserved among the poxvirus and
African swine fever virus enzymes (ref. 13; A. Martins, Y. Yu,
and S.S., unpublished data). These acidic residues are likely to
bind the essential metal ion(s). An RNA triphosphatase has
on a divalent cation cofactor (33). We surmise that higher
eukaryotes have diverged from vaccinia and yeast with respect
to mechanism and structure of the triphosphatase component
of the capping machinery.
Note. After this paper was submitted, Takagi et al. (36)
reported that an N-terminal fragment of the C. elegans capping
enzyme polypeptide, from residues 1 to 236, possesses RNA
The amino acid sequence of the C. elegans capping enzyme (Cel CE)
from residues 59 to 171 is aligned with the 167-amino acid baculovirus-
encoded protein phosphatase (Bac PP; GenBank accession no.
M96763) and the sequences of two phosphatase-like C. elegans gene
products: T23G7.5 (GenBank accession no. Z68319) and F54C8.4
(GenBank accession no. Z22178). Gaps in the sequences are indicated
by dashes (-). Amino acids conserved in all four proteins are denoted
by asterisks. The protein phosphatase signature motif is highlighted in
the shaded box. The active site cysteine is in boldface type.
A phosphatase domain in the C. elegans capping enzyme.
Biochemistry: Wang et al.Proc. Natl. Acad. Sci. USA 94 (1997)9577
We thank Dale Wigley, Kjell Hakansson, and Aidan Doherty for
helpful discussions and for providing the coordinates of the PBCV-1
capping enzyme-GTP cocrystal. This work was supported by National
Institutes of Health Grant GM52470.
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