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Journal of Bacteriology, January 2001, p. 680-686, Vol. 183, No. 2
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.2.680-686.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Urkinase: Structure of Acetate Kinase, a Member of the ASKHA
Superfamily of Phosphotransferases
Kathryn A.
Buss,1
David R.
Cooper,1
Cheryl
Ingram-Smith,2
James G.
Ferry,2
David Avram
Sanders,1 and
Miriam
S.
Hasson1,*
Department of Biological Sciences, Purdue
University, West Lafayette, Indiana 47907,1
and Department of Biochemistry and Molecular Biology, Eberly
College of Science, The Pennsylvania State University, University
Park, Pennsylvania 16802-45002
Received 27 September 2000/Accepted 25 October 2000
 |
ABSTRACT |
Acetate kinase, an enzyme widely distributed in the
Bacteria and Archaea domains, catalyzes the
phosphorylation of acetate. We have determined the three-dimensional
structure of Methanosarcina thermophila acetate kinase
bound to ADP through crystallography. As we previously predicted,
acetate kinase contains a core fold that is topologically identical to
that of the ADP-binding domains of glycerol kinase, hexokinase, the
70-kDa heat shock cognate (Hsc70), and actin. Numerous charged
active-site residues are conserved within acetate kinases, but few are
conserved within the phosphotransferase superfamily. The identity of
the points of insertion of polypeptide segments into the core
fold of the superfamily members indicates that the insertions existed
in the common ancestor of the phosphotransferases. Another remarkable shared feature is the unusual, epsilon conformation of the residue that
directly precedes a conserved glycine residue (Gly-331 in acetate
kinase) that binds the 
-phosphate of ADP. Structural, biochemical,
and geochemical considerations indicate that an acetate kinase may be
the ancestral enzyme of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases.
| |
INTRODUCTION |
Phosphoryl transfer is the most
common enzymatic function encoded by the yeast genome
(12), and the reaction is catalyzed by central regulatory
enzymes, such as protein kinases, ATPases, and GTPases
(7). A number of aspects of the mechanism of
enzyme-catalyzed phosphoryl transfer are still incompletely understood
and are a source of ongoing controversy (34). However,
X-ray crystallographic studies of phosphotransferases are making a
critical contribution to our understanding of this central reaction.
They also ground evolutionary analyses of these enzymes (7, 23,
29).
Acetate kinase, discovered in 1944 by Lipmann (32) and
isolated in 1954 by Ochoa et al. (41), is the prototypic
carboxylate kinase and one of the earliest phosphoryltransfer enzymes
to be recognized. Acetate kinase is widespread in both anaerobic and aerobic microbes of the Bacteria and Archaea
domains and a central player in a major link in the global carbon
cycle, the anaerobic decomposition of organic matter to methane, in
which it performs a dual role (14). In the first step of
methane production by microbial consortia, fermentative anaerobes from
the Bacteria domain degrade complex organic matter to
acetate. Acetate kinase catalyzes the final reaction in this process,
conversion of acetyl phosphate and ADP into acetate and ATP. Anaerobes
from the Archaea domain then convert the acetate into
methane and carbon dioxide. In this second process, acetate kinase
catalyzes the first reaction, activation of acetate to acetyl phosphate.
Acetyl phosphate is not only a precursor of important metabolic
intermediates, such as acetyl coenzyme A (acetyl-CoA), but also a
potential regulator of bacterial signal-transduction pathways. Bacterial responses to changes in environmental conditions are most
commonly evoked through two-component regulatory systems consisting of
a sensor kinase that autophosphorylates on a histidine residue and a
response regulator (39). The response regulator is an
enzyme that catalyzes the transfer of phosphate from the histidine
residue of the sensor protein to its own active site asparate residue
(42, 43). The active conformation of the response
regulator for its regulatory function is the phosphoenzyme intermediate. It has been demonstrated that the response regulators can
directly utilize acetyl phosphate but not ATP as a phosphoryl donor
(13, 33). A number of studies have indicated that cellular levels of acetyl phosphate may regulate the in vivo function of response regulators through modulation of their phosphorylation state
(6, 13, 21, 35, 36, 40, 44, 51).
One incompletely elucidated issue concerning the mechanism and
evolution of acetate kinase is whether there are one or more covalent
phosphoenzyme intermediates formed during catalysis by acetate kinase.
In the presence of either ATP or acetyl-phosphate, Escherichia coli acetate kinase becomes phosphorylated on
the side chain of one or more of its glutamate residues
(49). The phosphoenzyme is relatively stable and can be
isolated. The rate of phosphoenzyme formation is comparable to the rate
of the overall reaction (19). The isolated
phosphoenzyme is able to transfer its phosphoryl group to
either of the normal substrates, ADP and acetate (2-4,
19), as well as to the active site of Enzyme I of the
phosphotransferase system (18). This evidence argues that
the acyl-phosphate form of the enzyme is a covalent intermediate in
catalysis. However, it has been demonstrated that the phosphoryl group
is transferred by E. coli acetate kinase with inversion of
configuration (5). Such data are typically taken as
evidence for a direct, in-line transfer of phosphate from substrate to product without an enzyme-linked covalent intermediate
(28). Possible resolutions to the conflict in data have
been discussed (10, 47, 48), but additional detailed
structural and modern biochemical studies are required.
An additional issue is the evolutionary relationship between acetate
kinase and other phosphotransferases. The only other enzymes that are
identified as similar to the acetate kinases by sequence
comparison programs are the propionate and butyrate kinases (10,
20, 50). However, we have postulated, through secondary-structure prediction based upon comparative sequence analysis, that acetate kinase would possess a common topology with that
of glycerol kinase, hexokinase, actin, and the 70-kDa heat shock
cognate (Hsc70) (10).
In order to address these biological and biochemical questions, we have
solved the structure of Methanosarcina thermophila acetate kinase by crystallography. The view of the active site of
acetate kinase identifies residues for which roles in catalysis can be
postulated. In addition, study of the structure has provided ideas
about the early appearance of acetate kinase in evolution.
| |
MATERIALS AND METHODS |
Purification and crystallization.
Expression and
purification of homogeneous acetate kinase from M. thermophila (1, 31, 37), as well as conditions for the crystallization of the native enzyme bound to ATP
(10), have been described previously. Selenomethionyl
crystals, also space group C2, required incubation at 20°C for a
minimum of 3 weeks, followed by transfer to 37°C.
Data collection and model building.
Selenomethionyl data
were collected at Advanced Photon Source beamline BM14D. The multiple
isomorphous replacement (MIR) data were collected at 277K and the
multiwavelength anomalous diffraction (MAD) data were collected at
100K. All data were processed with DENZO/SCALEPACK (38).
Programs in the CCP4 suite (11) were used for phasing and
phase refinement. Patterson maps were used to locate heavy atoms in
MIR. To locate selenium atoms in MAD, a map was calculated with MIR
phases and the anomalous difference from the peak MAD wavelength
(0.9794 Å). Initial phases and positions of the MIR and MAD solutions
were refined in the CCP4 program MLPHARE. Multicrystal density
modification was performed using DMMULTI. The model was built using the
program O (25). Refinement was carried out using XPLOR
(8) followed by CNS (version 1.0) (9). Model
quality was checked using Procheck (30).
Noncrystallographic symmetry information was used in phase and model refinement.
Coordinates.
The coordinates and structure factors are
deposited in the Protein Data Bank as 1G99.
| |
RESULTS AND DISCUSSION |
Architecture of acetate kinase.
The structure of M. thermophila acetate kinase was solved through the combination
of two crystallographic methods (Tables 1 and 2). Electron
density maps produced independently through either MIR or MAD
using selenomethionine-substituted protein were incomplete.
Multicrystal density modification was performed using the initial
phases from both techniques and treating each domain as an independent
group. This treatment significantly improved the quality of the
electron density maps, allowing 96% of the structure to be built into
the native-protein map during the first round of model building.
The overall structure of the acetate kinase dimer resembles a bird with
its wings spread (Fig.
1A). The body of
the bird is
formed by the C-terminal domains of the monomers and
contains
the dimer interface, while the wings are composed of the
N-terminal
domains. The two monomers in the dimer are
related by a noncrystallographic
twofold rotation axis. Each monomer
consists of two domains, each
consisting of a central
-sheet
surrounded by
-helices. The fold
of the N-terminal domain consists
of an eight-stranded
-sheet
and eight helices. The C-terminal domain
is composed of a seven-stranded
-sheet, eleven helices, and an
additional small two-stranded
-sheet. The nucleotide-binding site is
located in the cleft between
the domains (Fig.
1B).
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FIG. 1.
Structure of acetate kinase. The structure of the
acetate kinase dimer (A) and a view with a 90° rotation around a
horizontal axis (B) are shown. The two monomers of the dimer are shown
in green and blue. The C-terminal domains, at the center, form the
dimer interface. The ADP and sulfate molecules in the active site
(between the N and C domains) are shown in space-filling models. The
structure contains 801 of the 816 residues in the dimer, with the
missing residues located at solvent-exposed regions following the
C-terminal helix. (C) Stereoview of monomer A of acetate kinase,
numbered every 20 residues.
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|
As we had predicted despite the absence of sequence identity
(
10), the fold of acetate kinase (Fig.
2) contains a core that
is
identical to that of the glycerol kinase/hexokinase/actin/Hsc70
superfamily (
15-17,
23,
24,
26). Henceforth this family
will
be referred to as the ASKHA (acetate and sugar
kinases/Hsc70/actin)
superfamily of phosphotransferases. The
ASKHA core consists of
a duplicated
secondary
structure with insertions of subdomains
between particular elements of
the
-sheet. As has been noted
before, the C-terminal
-helix of
each of these domains should
properly be considered a part of the other
domain (
15). The
alpha-carbon positions of 66 pairs of
structurally equivalent
amino acid residues within the C-terminal
domains of acetate kinase
and Hsc70 can be superimposed with a root
mean square deviation
of 2.08 Å (Fig.
3).
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FIG. 2.
Topology diagram of acetate kinase. Secondary structures
conserved in the ASKHA family (the duplicated
core) are rendered gray, and the inserts are shown in white. In
standard nomenclature, the subdomains are
denoted IA (left) and IIA (right). In acetate kinase, the core strands in domain IA are numbered 1 to 5, whereas those in domain IIA
are numbered 1' to 5'.
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FIG. 3.
Stereoview of the superposition of the C-terminal
domains of acetate kinase and of Hsc 70. The conserved ASHKA core is
colored yellow for acetate kinase (with the remainder dark gray) and
red for Hsc 70 (with the remainder white). The graphics program O was
used to calculate the superposition matrix. The terminal helix, which
extends into the N-terminal domain, is not shown.
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|
Similar architectural plans of related enzymes.
A detailed
analysis of the secondary structure of acetate kinase is central to an
understanding of this diverse family of proteins. Acetate kinase
contains subdomains inserted between the third strand of each of the
cores and the first -helix (the sites of
subdomains IB and IIB in actin and Hsc70) (Fig. 2). In domain I, this
insertion consists of a pair of -strands that extend the sheet. Our
analysis of the sequences of the E. coli acetate and
propionate kinases and those of the butyrate kinases of various species
predicts that these strands would be either absent or profoundly
shortened in the structures of those proteins. An insertion in domain
II (subdomain IIB) largely forms the dimer interface as is true for the
analogous insertions in the other ASKHA polypeptides (15-17, 23,
24, 26). In acetate kinase it is associated with subdomain IC,
which is inserted before 3 of domain I. An insertion at this site is
unique to acetate kinase among the ASKHA family.
Acetate kinase, similarly to glycerol kinase and hexokinase, contains
an insertion between
4 and
2. It consists of an additional
-strand that extends the subdomain IA
-sheet and an additional
-helix. Between
2' and
5' are inserted a
-strand, which
forms
the edge of the
-sheet, an
-helix, and a
-strand that
borders
5'. This insertion is unique to the acetate kinases. Our
structural
prediction indicates that the elements inserted between
2' and
5' will not be present in the butyrate
kinases.
In the crystal, the active-site clefts in the two monomers of the
acetate kinase dimer (monomers A and B) are closed to different
extents. In addition, there is a sulfate ion in the active site
resulting from the crystallization conditions. Nevertheless, we
can
examine some aspects of the active site that are revelatory
of the
mechanism and evolution of the ASKHA phosphotransferases.
Although the
crystals were grown in the presence of ATP, only
two phosphates can be
observed in the electron density. The
-phosphate
of ADP appears to
point away from the active site, perhaps resulting
from the binding of
a sulfate ion in the active site, which repels
the
-phosphate from a
site it would normally occupy. We propose
that the sulfate ion occupies
the site of the phosphate of acetyl
phosphate. The sulfate ion binds to
the side chains of arginine-91,
histidine-123, histidine-180, and
arginine-241 and the amide proton
of glycine-212 (Fig.
4A); all are conserved within the acetate
kinase-butyrate kinase family.
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FIG. 4.
Stereoviews of the active site of acetate kinase.
Conserved ASKHA secondary structures are pink and purple, and inserted
secondary-structural elements are gray. Loops in the N-terminal domain
are green, and those in the C-terminal domain are blue. (A) The binding
site. It is likely that the sulfate occupies the position where the
phosphate of acetyl phosphate would bind. No magnesium ion is apparent
in our current structure despite the inclusion of 750 µM
MgCl2 in the crystallization conditions. (B) The proposed
site of acetate binding. VOIDOO (27) was used to locate
solvent-accessible cavities. The cavity shown could easily accommodate
the methyl group of acetate or acetyl phosphate, positioning the
phosphate roughly where the sulfate is located. As shown, the center of
the cavity is 4.2 Å away from the sulfate.
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|
Design of the active site.
The adenine base of the nucleotide
is bound in a hydrophobic pocket consisting of the aliphatic chains of
arginine-285, isoleucine-332, and isoleucine-339. Arginine-285 is
conserved throughout the acetate kinase family (the guanidinium group
makes an electrostatic interaction with the carboxylate of the
conserved aspartate-283), whereas the isoleucines can be substituted
with other aliphatic residues in other family members. The isoleucine
residues are from the same part of the polypeptide chain, a turn of a
helix that follows 4' and 2', that forms the hydrophobic
nucleotide base binding pocket in glycerol kinase, actin, and Hsc70.
There are no single hydrogen bonds between the adenine and the protein.
The adenine amino group is exposed to solvent. The lack of specific
contacts with the base may explain the lack of specificity for a
particular nucleotide triphosphate as the phosphoryl donor. The ribose
ring is bound by phenylalanine-284 and the 2' hydroxyl by the
carboxylate of the absolutely conserved aspartate-283.
The
-phosphate is bound by the amide of glycine-331 (Fig.
4A); a
similar interaction is seen with equivalent glycine residues
in the
other family members (G-411, G-302, and G-339 in glycerol
kinase,
actin, and Hsc70, respectively [
15-17,
23,
24,
26]).
Remarkably, this glycine is preceded by an alanine residue that
is in
the epsilon conformation (
= 75.4°,
= 175.3°).
This unusual
conformation is also found in the residue that precedes
the
-phosphate-binding
glycine residues and initiates a turn of a
helix in all of the
ASKHA members. It is striking that the conformation
of these residues,
which has not been noted in previous publications,
has been conserved
over the course of the evolution of this
superfamily.
The
-phosphate is bound by histidine-208 and the amides of
asparagine-211 and glycine-212 (in monomer B), which are part
of a loop
between
1' and
2' that corresponds to a loop with
a similar role
in the other members of the ASKHA family. It is
intriguing that the
backbone carbonyl of asparagine-211 interacts
through a water molecule
with arginine-241, which binds the sulfate
ion. Perhaps the binding of
nucleotide is communicated through
aspargine-211 to orient the
conserved arginine-241 in the acetyl-phosphate
binding
site.
Two components of the interaction between the protein and the
nucleotide that are observed in other ASKHA phosphotransferases
but are
absent in our structure are (i) the interaction between
the loop
between
1 and
2 and the
-phosphate of ATP and (ii)
the
conserved magnesium binding site. However, a movement of the
loop of
approximately 3 Å, similar to those observed in the other
ASKHA
phosphotransferases, would close the cleft between the two
domains in
monomer A and would position the amide protons of the
residues in
the loop, the
-amino group of lysine-14, and the
carbonyl group
of asparagine-7 (an aspartate residue in the other
ASKHA
phosphotransferases that coordinates the nucleotide-bound
magnesium
ion) in the active
site.
Aspartate-148, which is in a loop following
5, is likely to
participate in magnesium ion coordination as do the carbonyl-possessing
side chains of residues at identical sites in the sequence of
the other
ASKHA phosphotransferases. Interestingly, it has been
suggested that the aspartate residues at this position in glycerol
kinase and hexokinase (aspartate-245 and aspartate-211,
respectively)
also function as the catalytic bases for sugar-substrate
deprotonation
(
23,
24). In acetate kinase, following
aspartate-148, there
is a helical insert (domain IC) which is unique to
acetate kinase
and which projects away from the core polypeptide fold.
This insert
forms essentially a closed loop that positions the
absolutely
conserved histidine-180 adjacent to aspartate-148. As
discussed
above, histidine-180 is bound to the sulfate ion that we
propose
occupies the acetyl phosphate-binding site. It appears that
during
the course of the evolution of the kinases, two functions, one
in catalysis and the other in magnesium ion binding, which are
carried
out by two different residues that are spatially adjacent
in acetate
kinase, were imposed on a single residue in glycerol
kinase and
hexokinase.
Glutamate-384 is absolutely conserved among the acetate and butyrate
kinases, is essential for function (
45), and is probably
the site of phosphorylation that has been detected previously.
In our
structure it lies at the N-terminal end of
3'. The side
chain
carboxylate points towards the active site but is 5.9 Å
from the
sulfate ion and 6.5 Å from the
-phosphate (Fig.
4A).
However, as we
have noted above,
3' is in fact a part of the
N-terminal domain, and
cleft closure would bring glutamate-384
into the active site, where it
could participate directly in
catalysis.
Acetyl phosphate binding site.
Our structure also permits us
to model the acetate and acetyl phosphate binding site. We predict that
the methyl group of acetate will be bound between the side chains of
valine-93, phenylalanine-179, and methionine-228 and the cyclopentyl
ring of proline-232 (Fig. 4B). These residues are virtually completely
conserved in the acetate kinases but differ in the butyrate kinases.
Interestingly, valine-93, which lies at the base of the proposed
acetate-binding pocket is replaced with an alanine residue in the
propionate kinases of E. coli and Salmonella
enterica serovar Typhimurium. We suggest that this substitution
creates the space for the additional methylene group in propionate as
compared to acetate and is largely responsible for the altered
substrate specificity of the propionate kinases. The orientation of the
sulfate ion ligands suggests that arginine-241 will be directly
involved in acetate binding and that arginine-91, histidine-123, and
histidine-180 will be involved in binding to the phosphate moiety of
acetyl phosphate. The results of site-directed mutagenesis and chemical
rescue experiments support the essential roles of arginine-91 and
arginine-241 in substrate binding, most probably to acetate and acetyl
phosphate (46).
Acetate kinase, an ancient enzyme.
The ASKHA
phosphotransferase family has undergone extensive divergent evolution.
Nevertheless, a number of elements appear to have been conserved: (i) a
two-domain structure containing duplicated core secondary structure
elements, (ii) residues that bind the catalytic magnesium ion and the
nucleotide -phosphate (the unusual conformation of the residue
preceding the glycine that binds the -phosphate and the following
turn of a helix are also conserved), and (iii) points of insertion of
secondary-structure elements into the core fold.
The last item suggests a scenario for the evolution of the ASKHA
enzymes. The common ancestor of these enzymes was a protein
containing
a duplication of the core
a fold that had an
insertion between
3 and
1, considering the universality of
insertions
at this position. Extending this analysis, we note that the
kinases
all possess inserted sequences between
4 and
2, whereas
the
ATPases in the ASKHA family do not. The superfamily probably
originally
evolved to transfer phosphoryl groups to substrates rather
than
to hydrolyze nucleotide triphosphates; therefore, this insertion
was present in the common ancestor of the ASKHA enzymes and deleted
during the evolution of the ATPases. The butyrate kinases provide
an
example of the deletion of sequences inserted into the core,
for they
have unquestionably evolved comparatively recently (as
indicated by
their limited phylogenetic distribution and high
sequence identity)
from the acetate kinases and have eliminated
certain peripheral
secondary-structure elements. Acetate kinase
also has an insertion
between
5 and
3, which brings into proximity
two conserved
residues (histidine-180 and aspartate-148) whose
functions during
further evolution of the enzymes were essentially
incorporated into a
single residue in glycerol kinase and
hexokinase.
We hypothesize that the structure of acetate kinase that we have
determined represents the best approximation of the common
ancestor of the ASKHA superfamily. This hypothesis is consistent
with
the biochemistry of acetate kinase and the posited role of
acetate
in the early stages of the evolution of life. It possesses
properties
associated with "primitive" enzymes; the
Km
of
M. thermophila acetate kinase for its substrates (2.8 mM
for ATP and 22 mM for
acetate) is quite high compared to that of the
other ASKHA enzymes,
and it lacks specificity for ATP relative to other
nucleotide
triphosphates (
1).
Short-chain carboxylic acids were among the most common organic
molecules in prebiotic and early biotic environments. Acetic
acid has
the interesting property of being capable of diffusing
relatively
freely across membranes; the retention of acetate as
a biosynthetic
precursor within a cell would require its phosphorylation.
This also
activates the acetate for biosynthetic reactions. Acetyl
phosphate and
CoA form acetyl-CoA in a reaction now catalyzed
enzymatically by a
phosphotransacetylase. Acetyl-CoA is the common
precursor of fatty acid
synthesis, so it is plausible that early
cellular growth relied on
retention and activation of acetate
through
phosphorylation.
Another scenario of the role of acetate kinase in the early stages of
the evolution of life depends upon the chemoautotrophic
theory of the
origin of life. Early organisms fed through fixation
of CO or
CO
2 at volcanic or hydrothermal sites with the formation
of
thioacetic acid in an analogous process to that carried out
by the
enzyme acetyl-CoA synthetase (
22). If early organisms
could synthesize acetyl phosphate from such thioesters, including
acetyl-CoA itself, then ATP synthesis might have proceeded through
the
acetate kinase reaction. The secreted acetic acid could then
be taken
up by another early organism through acetate kinase-mediated
phosphorylation in a primitive form of the metabolic cooperation
observed between microbial species to the present
day.
| |
ACKNOWLEDGMENTS |
Kathryn A. Buss and David R. Cooper contributed equally to this work.
We thank our colleagues in the Markey Structural Group at Purdue.
This work was supported by an NIH Biophysics Training Grant to K.A.B.
and D.R.C. an American Cancer Society grant to D.C., a Department
of Energy-Basic Energy Sciences grant to J.G.F., an NSF CAREER awards
to D.A.S. and M.S.H., a March of Dimes and David and Lucille Packard
Foundation Fellowship to M.S.H., and an NIH Cancer Center Support at
Purdue University. The diffraction and computing facilities shared by
the Structural Biology group at Purdue have been developed and
supported by grants from NIH, NSF, the Lucille P. Markey Foundation,
the Keck Foundation, and the office of the university executive vice
president for academic affairs. Use of the Advanced Photon Source was
supported by the U.S. Department of Energy, Basic Energy Sciences, and
the Office of Energy Research. Use of the BioCARS Sector 14 was
supported by the National Institutes of Health, National Center for
Research Resources.
| |
FOOTNOTES |
*
Corresponding author. Mailing address: Dept. of
Biological Sciences, 1392 Lilly Hall of Life Sciences, Purdue
University, West Lafayette, IN 47907-1392. Phone: (765) 496-2928. Fax: (765) 496-1189. E-mail:
mhasson{at}bragg.bio.purdue.edu.
| |
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Journal of Bacteriology, January 2001, p. 680-686, Vol. 183, No. 2
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.2.680-686.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
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Abstract
Introduction
