Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface
© Chittori et al.; licensee BioMed Central Ltd. 2012
Received: 17 June 2012
Accepted: 24 September 2012
Published: 2 October 2012
Bacteria such as Escherichia coli and Salmonella typhimurium can utilize acetate as the sole source of carbon and energy. Acetate kinase (AckA) and phosphotransacetylase (Pta), key enzymes of acetate utilization pathway, regulate flux of metabolites in glycolysis, gluconeogenesis, TCA cycle, glyoxylate bypass and fatty acid metabolism.
Here we report kinetic characterization of S. typhimurium AckA (St AckA) and structures of its unliganded (Form-I, 2.70 Å resolution) and citrate-bound (Form-II, 1.90 Å resolution) forms. The enzyme showed broad substrate specificity with k cat /K m in the order of acetate > propionate > formate. Further, the K m for acetyl-phosphate was significantly lower than for acetate and the enzyme could catalyze the reverse reaction (i.e. ATP synthesis) more efficiently. ATP and Mg2+ could be substituted by other nucleoside 5′-triphosphates (GTP, UTP and CTP) and divalent cations (Mn2+ and Co2+), respectively. Form-I St AckA represents the first structural report of an unliganded AckA. St AckA protomer consists of two domains with characteristic βββαβαβα topology of ASKHA superfamily of proteins. These domains adopt an intermediate conformation compared to that of open and closed forms of ligand-bound Methanosarcina thermophila AckA (Mt AckA). Spectroscopic and structural analyses of StAckA further suggested occurrence of inter-domain motion upon ligand-binding. Unexpectedly, Form-II St AckA structure showed a drastic change in the conformation of residues 230–300 compared to that of Form-I. Further investigation revealed electron density corresponding to a citrate molecule in a pocket located at the dimeric interface of Form-II St AckA. Interestingly, a similar dimeric interface pocket lined with largely conserved residues could be identified in Form-I St AckA as well as in other enzymes homologous to AckA suggesting that ligand binding at this pocket may influence the function of these enzymes.
The biochemical and structural characterization of St AckA reported here provides insights into the biochemical specificity, overall fold, thermal stability, molecular basis of ligand binding and inter-domain motion in AckA family of enzymes. Dramatic conformational differences observed between unliganded and citrate-bound forms of St AckA led to identification of a putative ligand-binding pocket at the dimeric interface of St AckA with implications for enzymatic function.
KeywordsAcetate metabolism AckA-Pta pathway Acetate and Sugar Kinases/Heat shock cognate (Hsc) 70/Actin (ASKHA) superfamily Conformational rearrangement Enzyme regulation
Bacteria respond to frequent changes in their environment by activating metabolic pathways that allow conversion of available nutrients into metabolites of central pathways. Utilization of acetate as a source of carbon and energy requires its initial activation to acetyl-CoA [1–3]. Sequential activities of acetate kinase (AckA, EC 126.96.36.199) and phosphotransacetylase (Pta, EC 188.8.131.52) result in the interconversion of ATP, acetate and CoA to ADP, acetyl-CoA and orthophosphate via acetyl-phosphate [4, 5]. In addition to being an important pathway for carbon flow, the AckA-Pta activity might control the cellular concentration of acetyl-CoA and acetyl-phosphate, which serve as important metabolic intermediates. Acetyl-CoA plays a central role in carbon metabolism [2, 3], while acetyl-phosphate acts as a global signal that regulates the function of several proteins involved in flagella biosynthesis and assembly, biofilm development, colonic acid biosynthesis and type-I pilus assembly [6, 7]. Studies on AckA from several organisms have shown that the enzyme is also important for xylose metabolism, phosphoryl transfer to enzyme-I of the phosphoenolpyruvate: glucose phosphotransferase system, periplasmic binding proteins and response regulator proteins of two-component systems [8–11].
Enzymes catalyzing transfer of phosphate group include wide-spread protein folds responsible for several indispensable cellular roles including signal transduction, molecular regulation and metabolic functions . Acetate kinase catalyzes reversible transfer of a γ-phosphate from ATP to acetate in the presence of a divalent metal ion . Similarly, propionate and butyrate kinases utilize propionate and butyrate, respectively, as preferred substrates for phosphoryl transfer from ATP to acceptor ligands [13, 14]. These enzymes are hereafter referred to as acetokinase family of enzymes (Pfam: PF00871; SCOP: 53080). Extensive structural and functional studies have been carried out for AckA from the archean Methanosarcina thermophila[15, 16]. An earlier study on AckA from E. coli suggested that in addition to its cognate substrate acetate, it could also phosphorylate analogous short-chain fatty acids (SCFAs) such as propionate and butyrate . However, in another study, AckAs from E. coli and S. typhimurium, which share 98% sequence identity, were found to be inactive with respect to propionate and butyrate . In the present study, we report the biochemical characterization and structures of S. typhimurium AckA (StAckA, NCBI accession: NP_461279.1, residues: 400, molecular mass: 43.3 kDa) in two crystal forms at 2.70 Å (apo, Form-I) and 1.90 Å (citrate-bound, Form-II) resolutions. Sequence and structure-based comparisons with homologous enzymes were carried out with the view of understanding their biochemical specificity, overall fold, stability, active site geometry, domain motion and plausible regulation.
Kinetic constants of St AckA catalyzed reaction
K m (mM)
V max (μmol min-1 mg-1)
k cat (s-1)
kca t/K m (s-1 mM-1)
13.5 ± 0.3
1180 ± 20
880 ± 105
68 ± 15
0.085 ± 0.010
1160 ± 10
870 ± 120
10240 ± 80
1.2 ± 0.1
1560 ± 18
1180 ± 75
985 ± 62
0.070 ± 0.005
1550 ± 10
1170 ± 85
16860 ± 50
11.2 ± 0.1
1250 ± 12
940 ± 85
85 ± 10
0.075 ± 0.004
1230 ± 40
900 ± 135
11350 ± 50
0.28 ± 0.04
2350 ± 30
1764 ± 25
6300 ± 45
0.100 ± 0.003
2340 ± 20
1750 ± 65
17645 ± 10
K m (mM)
0.070 ± 0.005
0.078 ± 0.027
0.0960 ± 0.058
0.088 ± 0.042
V max (μmol min-1 mg-1)
1560 ± 18
1475 ± 25
1185 ± 22
950 ± 30
1.0 ± 0.2
1.10 ± 0.6
2.30 ± 0.3
3.50 ± 1.0
V max (μmol min-1 mg-1)
1560 ± 18
1590 ± 30
250 ± 25
70 ± 40
[I] (mM) e
63 ± 15
75 ± 20
7 ± 1.8
5 ± 2.2
3 ± 1.3
1 ± 0.5
V app (μmol min-1 mg-1) f
1400 ± 80
1415 ± 65
900 ± 70
650 ± 85
340 ± 50
175 ± 95
Circular dichroism (CD) spectra of St AckA in the presence of various ligands were recorded using a JASCO J715 spectropolarimeter. The protein concentration was kept at 0.5 mg ml-1 in 5 mM HEPES-NaOH pH 7.5 and 20 mM NaCl in a cell with a path length of 0.1 mm. Thermal denaturation was monitored by recording the CD profile at a suitable wavelength from 20 to 95°C with a rate of 1°C min-1 rise in temperature in a peltier controlled cell holder (JASCO). To study the effect of ligand binding on thermal stability, protein samples were preincubated for 1 h with the selected ligand (at a concentration close to their K m values) prior to denaturation studies using CD.
The intrinsic fluorescence of AckA was examined using a Hitachi F-200 fluorimeter and a 1 cm path length cuvette with ~1 μM enzyme in a total volume of 250 μl buffer containing 50 mM HEPES-NaOH pH 7.5 and 200 mM NaCl. Enzyme was titrated with the selected ligand (at a concentration close to their K m values) and the fluorescence spectra were measured after an incubation time of 10 min.
Structure refinement and validation: ab-initio model building of residues 230–300 in Form-II St AckA
Structure refinement and validation statistics
Resolution range (Å) a
No. of atoms
Protein / Water / EDO / CIT b
11748 / 204 / 16 / -
5838 / 442 / 16 / 13
R-factors (%) c
Rwork / Rfree
22.1 / 28.3
18.9 / 22.4
Correlation coefficient (%) d
Wilson B-factor (Å2)
Average B-factor (Å2)
Protein / Water / EDO / CIT
44.7 / 10.4 / 45.8 / -
36.1 / 44.2 / 56.4 / 33.9
Bond length (Å)
Bond angle (°)
Dihedral angle (°)
Chiral-center restraints (Å3)
General planes (Å)
Coordinate error: Luzzati (Å)
Residues in Ramachandran map (% / number)
Most favoured region
89.1 / 1,228
90.9 / 610
10.9 / 150
8.8 / 59
Generously allowed region
0 / 0
0.3 / 2
0 / 0
0 / 0
Sequence and structural analyses
Sequence homologs of St AckA were identified in the Swiss-Prot database . DALI  server was used for the identification of homologous structures. Multiple sequence alignment was achieved using ClustalW  and a graphical representation of the alignment as well as superposition of the secondary structures was obtained using ESPript . The Protein Interfaces, Surfaces and Assemblies (PISA)  and Protorp  servers were used for the analysis of dimeric interfaces. HingeProt  and ElNeMo  servers were used to analyze plausible conformational dynamics. Computed Atlas of Surface Topography of proteins (CASTp)  server was used for locating potential ligand-binding cavities. Ligands were modeled at the active site of St AckA by comparison with the ligand bound structure of Mt AckA (PDB:1TUY) , and energy minimized using the CNS program . Molecular figures were created with PyMOL (http://www.pymol.org/).
The atomic coordinates and structure factors for the apo (Form-I, PDB:3SLC) and citrate-bound (Form-II, PDB:3SK3) forms of StAckA have been deposited with RCSB.
Acetokinase family of enzymes in prokaryotes
Enzymatic specificity of the recombinant St AckA
The biochemical investigations were further extended for assessment of nucleotide analogs as phosphoryl donors in St AckA catalyzed reaction. These kinetic assays showed that apart from ATP and GTP, consistent with reports from Fox & Roseman , St AckA could also utilize pyrimidine bases such as UTP and CTP with comparable affinities (Table 1). Activity of St AckA was found to be completely abolished in the presence of EDTA (5 times Mg2+ concentration) or in the absence of suitable divalent ions, suggesting that divalent cations are essential for the catalysis. In addition to MgCl2 (V max = 100%), the enzyme could be activated by MnCl2 (V max = 100%), CoCl2 (V max = 15%) and to a minor extent by NiCl2 (V max = 5%) (Table 1). However, several other divalent (CaCl2, FeCl2, CuCl2, ZnCl2, CdCl2 and HgCl2) and monovalent (LiCl or CsCl) ions failed to activate the enzyme. A divalent metal-ion ratio of 1:1 with ATP appeared to be optimal while a large excess (>25 times) of Mg2+ relative to ATP was found to reduce the catalytic rate, which might suggest that free Mg2+ could inhibit the binding of catalytically competent ATP-Mg2+ complex to the enzyme.
Crystal structure of Form-I St AckA
The four subunits of St AckA present in the ASU are further organized as two dimers resembling the dimeric structure of the archeal enzymes . The two dimers of the asymmetric unit could be superposed with Cα rmsd of 0.50 Å for 706 target pairs suggesting that the organization of the protomers in the two dimers are essentially identical. The subunits of a dimer are related by nearly perfect non-crystallographic two-fold symmetries (Figure 3C). The accessible surface area (ASA) of an St AckA monomer was found to be 17,920 Å2 and upon dimerization approximately 3,061 Å2 (17% of total ASA) per subunit gets buried. Several segments of domain-II (αIg, αIh, αIIa, αIIb, αII1 and 3IIf and f*) contribute to the dimeric interface. A total of approximately 81 residues (20% of total surface residues), of which 23% are polar, 53% are non-polar and 24% are charged, contribute to the interactions at the interface leading to approximately 23 hydrogen bonds and 8 salt bridges. There are also a few water-mediated hydrogen bonds between the two subunits of the dimer. This analysis indicates a stable dimeric interface.
Active site pocket and specificity determinants
A cleft between the two domains forms the active site pocket of St AckA. Structural comparison with the ligand-bound Mt AckA structures [15, 16] allowed identification of residues likely to be important for acetate (Val93, Ala181, Leu122, Pro234 and Arg243), nucleotide (Arg91, His123, His182, Gly212, Asn213, Gly214, Arg243, Asp285, Arg287, Gly333, Ile334 and Asn337) and metal-ion (Asn10, Lys17, Asp150, Glu387) binding by St AckA. These residues are also conserved in other members of acetokinase family (Figure 1), indicating their shared ligand binding modes and catalytic mechanisms.
Similarly, modeling of nucleotides was carried out based on the acetate-AlF3-ADP bound structure of Mt AckA . The analysis revealed that the enzyme interacts with the nucleotide base mainly by hydrophobic interactions (Figure 4B). Absence of directional ionic interactions with nucleotides could account for the broad nucleotide specificity of the enzyme. Although it is likely that AckA is primarily an ATP-dependent enzyme, the broad specificity will allow other nucleotides also to support acetate utilization.
Ligand-induced conformational changes in St AckA
Crystal structure of Form-II St AckA
The three conformationally distinct subunits (subunits of Form-I and A- and B-subunits of Form-II) also show variations in the degree of domain closure. B-subunit of Form-II represents the most closed state while A-subunit represents a conformation between those of Form-I and B-subunit of Form-II (data not shown). Despite the large conformational differences in the variable segment and inter-domain closure, structures of other segments are largely retained (Figures 6A and B) and the dimeric nature is preserved in Form-II (Figure 6C). The residues in the variable segment of Form-I are involved in inter-subunit interactions. This leads to reduction in the buried surface area (1,996 Å2 compared to 3,061 Å2 of Form-I) and ionic interactions (hydrogen bonds = 12; salt bridges =13 compared to 23 and 10, respectively, of Form-I) of the dimeric interface between the subunits (ASA of Form-II St AckA monomer: 17,235 Å2) of Form-II. As the residues of the variable segment are also involved in the formation of active site pocket, Form-II structure is not suitable for binding nucleotides and therefore may represent an inhibited state of the enzyme.
Identification of a putative dimeric interface pocket
Structural features of the dimeric interface pocket identified in acetokinase family of enzymes
RMSD (Å2) / Cαaligneda
0 / 797
0.59 / 706
St AckA-II-AB b
1.44 / 579
1.78 / 676
1.46 / 764
1.74 / 708
1.45 / 732
St TdcD-AA' c
1.19 / 744
2.37 / 604
unpublished results d
Implications to SCFA metabolism
Acetate kinase is ubiquitously present in bacteria and archea  and appears to be absent in humans . As AckA is involved at the junction of carbohydrate and fatty acid metabolism, it might be a suitable target for development of inhibitors . We have earlier structurally and biochemically characterized Salmonella typhimurium propionate kinase (St TdcD) and demonstrated that the enzyme is specific to propionate although could utilize acetate at a 10 times lower rate [13, 35]. In the present study, we report structural and mechanistic investigations of St AckA. Among the SCFAs tested, acetate was the preferred substrate although the enzyme showed significant activity with formate as well as propionate (Table 1), which is consistent with the physiological function of the enzyme in acetate metabolism. On the other hand, affinity for various nucleotides were comparable (Table 1). Modeling studies revealed that interactions with the nucleotide occur mainly through the base moiety with minor contribution from the phosphates, which is in agreement with the comparable K m obtained for ADP and ATP for St AckA (Table 1). The observed broad specificity of St AckA is suggestive of its primitive origin which might have been crucial for the survival of ancestral cells that functioned with limited resources.
Interestingly, St AckA could catalyze the reverse reaction (ATP formation) more efficiently when compared to the forward reaction (acetyl-phosphate synthesis) (Table 1). This could serve as a major source of energy during anaerobic growth of S. typhimurium. The structure of ADP-AlF3-acetate complex of Mt AckA [15, 16] reveals that the phosphate is likely to bind at a deeper site in the active site pocket with acetyl moiety occupying an exterior site. The phosphate is likely to form significant interactions with the protein and contribute to the higher affinity for acetyl-phosphate when compared to acetate (Table 1).
Diversification of AckA fold
DALI search  revealed significant similarities of St AckA with over 100 non-redundant (90% sequence identity cut-off) structures deposited in the PDB. These structurally similar domains include not only kinases but also several other proteins with diverse functions such as transcriptional regulator ROK family homolog of E. coli MLC protein (2GUP/3.9 Å/11%), O-sialoglycoprotein endopeptidase (2IVN/4.2 Å/14%), actin (3B63/4.6 Å/11%), cell division protein FtsA (1E4G/4.1 Å/11%), plasmid segregation protein ParM (3IKY/4.2 Å/10%), diol dehydratase-reactivating factor large subunit (2D0O/4.6 Å/10%), activator of 2-hydroxyglutaryl-CoA dehydratase (1HUX/4.3 Å/15%), glycerol dehydratase reactivase α-subunit (1NBW/4.6 Å/12%), heat shock 70 kDa protein (3FZF/5.4 Å/10%), rod shape-determining protein MreB (1JCF/4.0 Å/10%), ethanolamine utilization protein EutJ (3H1Q/3.8 Å/14%) and a few other proteins of unknown function (corresponding PDB code, rmsd of Cα atoms upon superposition with St AckA, and sequence identity with St AckA are shown in parentheses). This remarkable structural and functional versatility is comparable to that of the well-known TIM-barrel proteins and is consistent with biochemical studies that suggest emergence of AckA fold early in evolution.
Although no overall sequence similarity between Acetate and Sugar Kinases/Heat shock cognate (Hsc) 70/Actin (ASKHA) superfamily could be detected, these proteins typically bind ATP and contain a duplicated core with βββαβαβα topology that harbors five highly conserved motifs ( Adenosine, Phosphate-1, Phosphate-2, Connect-1 and Connect-2)  (Figure 3). The N- and C- terminal domains of ASKHA superfamily of proteins could be further divided into two subdomains. The N- and C-terminal conserved subdomains conform to the βββαβαβα topology while variable subdomains are constituted by insertions (Figures 3A and B) that may account for the functional diversity of these proteins. Among acetokinase family, a characteristic insertion corresponding to residues 150–180 of St AckA is present before αI3 of domain-I (Figures 3A and B). This segment contains a few α- and 310-helices, which form part of the dimer interface. Another unique insertion (residues 354–377 of St AckA) in acetate and propionate kinases is found between αII2 and βII5 of domain-II. In St AckA, the insertion consists of an additional β-strand (βIIa) that extends the central β-sheet, an α-helix (αIIg) and two 310 helices (3IIf and 3IIf*). This insertion is not found in butyrate kinase. Also, the sequence of the inserted segment is not well conserved between acetate and propionate kinases. As residues from this region interact with the base of the nucleotide, the insertion may be significant for mechanistic differences within the acetokinase family of enzymes.
Molecular basis of thermal stability in acetokinases
Availability of several acetokinase structures from mesophilic (Form-I St AckA; S. typhimurium propionate kinase (St TdcD), PDB:2EIY; Francisella tularensis acetate/propionate kinase (Ft TdcD), PDB:3KHY and Mycobacterium avium acetate kinase (Ma AckA), PDB:3P4I) as well as thermophilic (Mt AckA, PDB:1 G99; Thermotoga maritima acetate kinase (Tm AckA), PDB:2IIR and Tm Buk2, PDB:1SAZ) organisms in PDB allows analysis of features that might contribute to the enhanced stability of AckA homologs found in thermophiles. Analysis of amino acid composition of these proteins revealed that the protein surfaces in thermophilic AckA homologs have a larger number of charged residues and a smaller number of polar residues when compared to mesophilic counterparts. Solvent exposed surface of thermophilic Mt AckA contains 23% polar, 40% non-polar and 37% charged residues compared to 30% polar, 39% non-polar and 31% charged residues, respectively, of mesophilic St AckA. The increase in charged residues on the surface of the thermophilic proteins results in enhanced intra-subunit ionic interactions (salt bridges: St AckA = 12; Mt AckA = 23). Also, an excess of hydrogen bonds (St AckA = 23; Mt AckA = 32) and salt-bridges (St AckA = 8; Mt AckA = 19) in the dimeric interface provides additional stability to the thermophilic enzymes. Thus, the thermophilic proteins of acetokinase family seem to achieve stability by a large number of intra- and inter-subunit ionic interactions.
Domain motion associated with ligand binding
Superposition of Form-I St AckA with protomers of Mt AckA structure (PDB:1TUY) revealed that St AckA is in a conformation intermediate to that of the open and closed states of Methanosarcina enzyme (Figure 5A). In order to gain insights on plausible domain motion, St AckA and Mt AckA were subjected to normal mode analysis using the ELastic NEtwork MOdel (ELNEMO) server. The analysis revealed conformations of St AckA that were similar to both the open (Cα rmsd: 1.15 Å) and closed (Cα rmsd: 1.23 Å) states of Mt AckA subunits, and in conjunction with fluorescence studies (Figure 5B), suggests that St AckA is also compatible with the inter-domain movements as observed in Mt AckA. It is possible that the structure of Form-I St AckA protomer represents an intermediate state in which the active site is accessible to the solvent and ligands. The closed form may represent the active site geometry required for catalysis. The open form may facilitate expulsion of product by reducing the interactions that stabilize the bound ligands.
Implication of dimeric interface pocket for the function of St AckA
The most intriguing result of the present investigations is the rearrangement and partial disorder observed in a large segment (residues 230–300) of the Form-II polypeptide (Figures 6A and B). Despite the disordered nature, modeled residues of the variable segment possess significant electron density (Additional file 1 Figure S1) and show well restrained stereochemistry . Examination of the electron density revealed the presence of a citrate molecule bound at the dimeric interface (Figures 6C and 7) and led to the identification of a putative ligand binding pocket in acetokinase family of enzymes (Figure 8 and Additional file 2: Figure S2). AckA is an important enzyme that could play a key role in controlling the flux of metabolites in several pathways including glycolysis, gluconeogenesis, TCA cycle, glyoxylate bypass and fatty acid metabolism [2, 3, 6–8, 10, 11]. Examination of the thermal stability of St AckA incubated with 10 mM citrate showed an increase in Tm (55°C) by 10°C consistent with the binding of the ligand. However, at this concentration of citrate, no change in the activity of St AckA was observed. Therefore, it is possible that some other metabolite of these pathways bind at the putative dimeric interface pocket and regulate the enzyme activity. In this regard, some of the metabolites of TCA cycle and their analogs were tested for inhibition of St AckA, of which malate was found to inhibit the enzyme maximally (Table 1). Further investigations on the nature of inhibition and similar studies with other members of acetokinase family enzymes might reveal the physiological significance of such a ligand-binding pocket.
Biochemical studies on St AckA suggested that the preferred substrate of the enzyme is acetate. The enzyme showed significant catalytic rates with formate and propionate but did not utilize butyrate as a substrate. The kinetic characterization further revealed broad specificity of the enzyme with respect to nucleotides and metal ions. Structure of Form-I St AckA determined in the present study represents the first report of an unliganded as well as mesophilic AckA. Biophysical studies of St AckA and comparison with other AckA homologs provided insights into the mechanism of ligand binding, domain motion and thermal stability in AckA family of enzymes. In Form-II St AckA, we observed completely unexpected conformational differences in a large segment of the polypeptide between the two forms. This lead to the serendipitous identification of a conserved ligand binding pocket at the dimeric interface of St AckA and its homologs that could form a basis for further mechanistic investigations of this family of enzymes.
- St AckA:
Salmonella typhimurium acetate kinase
- ASKHA :
Acetate and sugar kinases/heat shock cognate (Hsc) 70/Actin.
The authors would like to thank James and Babu of X-ray facility at the Molecular Biophysics Unit, Indian Institute of Science (IISc), and Dr. Hassan Belrhali and Dr. Babu Manjasetty of beamline BM14 at European Synchrotron Radiation Facility (ESRF), France for the assistance during X-ray diffraction data collection. We thank Chhavi Mathur for critical reading of the manuscript. This work was supported by the Department of Science and Technology (DST) [grant number SR/SO/BB-47/2009 (to MRN and HSS)] and Department of Biotechnology (DBT) [grant number BT/PR10912/BRB/10/630/2008 (to MRN and HSS)], Government of India; the Council for Scientific and Industrial Research (CSIR), Government of India, and IISc fellowships to SC.
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