Structural and enzymatic characterization of the choline kinase LicA from Streptococcus pneumoniae

Article abstract of DOI:10.1371/journal.pone.0120467

LicA plays a key role in the cell-wall phosphorylcholine biosynthesis of Streptococcus pneumonia. Here we determined the crystal structures of apo-form LicA at 1.94 ? and two complex forms LicA-choline and LicA-AMP-MES, at 2.01 and 1.45 ? resolution, respectively. The overall structure adopts a canonical protein kinase-like fold, with the active site located in the crevice of the N- and C- terminal domains. The three structures present distinct poses of the active site, which undergoes an open-closed-open conformational change upon substrate binding and product release. The structure analyses combined with mutageneses and enzymatic assays enabled us to figure out the key residues for the choline kinase activity of LicA. In addition, structural comparison revealed the loop between helices α7 and α8 might modulate the substrate specificity and catalytic activity. These findings shed light on the structure and mechanism of the prokaryotic choline kinase LicA, and might direct the rational design of novel anti-pneumococcal drugs.

Full text of DOI:10.1371/journal.pone.0120467

RESEARCH ARTICLE
Structural and Enzymatic Characterization of
the Choline Kinase LicA from Streptococcus
pneumoniae
Lei Wang1, Yong-Liang Jiang1*, Jing-Ren Zhang2, Cong-Zhao Zhou1, Yuxing Chen1*
1 Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University
of Science and Technology of China, Hefei, Anhui, 230026, People’s Republic of China, 2 Center for
Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, 100084, People’s Republic of
China
a11111
* jyl@mail.ustc.edu.cn (YLJ); cyxing@ustc.edu.cn (YC)
Abstract
LicA plays a key role in the cell-wall phosphorylcholine biosynthesis of Streptococcus
pneumonia. Here we determined the crystal structures of apo-form LicA at 1.94 Å and two
complex forms LicA-choline and LicA-AMP-MES, at 2.01 and 1.45 Å resolution, respective-
ly. The overall structure adopts a canonical protein kinase-like fold, with the active site locat-
ed in the crevice of the N- and C- terminal domains. The three structures present distinct
poses of the active site, which undergoes an open-closed-open conformational change
upon substrate binding and product release. The structure analyses combined with muta-
geneses and enzymatic assays enabled us to figure out the key residues for the choline ki-
nase activity of LicA. In addition, structural comparison revealed the loop between helices
α7 and α8 might modulate the substrate specificity and catalytic activity. These findings
shed light on the structure and mechanism of the prokaryotic choline kinase LicA, and might
direct the rational design of novel anti-pneumococcal drugs.
OPEN ACCESS
Citation: Wang L, Jiang Y-L, Zhang J-R, Zhou C-Z,
Chen Y (2015) Structural and Enzymatic
Characterization of the Choline Kinase LicA from
Streptococcus pneumoniae. PLoS ONE 10(3):
e0120467. doi:10.1371/journal.pone.0120467
Academic Editor: Young-Hwa Song, University of
Luebeck, GERMANY
Received: November 6, 2014
Accepted: January 22, 2015
Published: March 17, 2015
Copyright: © 2015 Wang et al. This is an open
access article distributed under the terms of the
Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any
medium, provided the original author and source are
credited.
Introduction
The Gram-positive pathogen Streptococcus pneumoniae, is a major cause of human pneumo-
nia, meningitis, bacteremia, otitis media and sinusitis [1, 2]. The cell wall of S. pneumoniae is
essential for the bacterial survival and infection. The major components of pneumococcal cell
wall are the teichoic acid and lipoteichoic acid to which abundant choline is attached in the
form of phosphorylcholine [3–5]. It has been proved that lack of choline or its replacement
with ethanolamine in pneumococci led to the inhibition of bacterial autolysis, the attenuation
of genetic transformation and the formation of long chains [6, 7]. Moreover, recent studies
have suggested that pneumococcal phosphorylcholine can interact with the host cell by binding
to the platelet-activating factor receptor and the C-reactive protein [8]. In addition, a series of
choline-binding proteins (CBPs), which are non-covalent linked to the phosphorylcholine of
cell wall, are involved in bacterial growth, cell division and pathogenesis. For example, N-
Data Availability Statement: All structure files are
available from the Protein Data Bank database
(accession numbers 4R77, 4R78, 4R7B).
Funding: This work was supported by the National
Natural Science Foundation of China (Grant No.
31470739, 31270781, 31400628 and U1332114:
http://www.nsfc.gov.cn/) and the Research Fund for
the Doctoral Program of Higher Education (Grant No.
20123402110004: http://www.cutech.edu.cn/cn/kyjj/
gdxxbsdkyjj/A010301index_1.htm). The funders had
no role in study design, data collection and analysis,
decision to publish, or preparation of the manuscript.
PLOS ONE | DOI:10.1371/journal.pone.0120467 March 17, 2015
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Pneumococcal Choline Kinase LicA
Competing Interests: The authors have declared
that no competing interests exist.
acetylmuramoyl-L-alanine amidase LytA, a major autolysin of cell wall, is important for the
cell division and virulence factor release [9], whereas the major surface adhesion choline-
binding protein A (CbpA) enables the pneumococcal resistance to host defense by binding to
human complement factor H [10].
A gene operon termed lic (lipo-polysaccharide core) has been identified for the phosphoryl-
choline metabolism pathway of S. pneumoniae [11]. It contains two transcriptional units lic1
and lic2, in which lic1 consists of five genes licA, licB, licC, tarI, and tarJ, whereas lic2 contains
three genes licD1, licD2 and tacF. The encoded proteins govern the phosphorylcholine metabo-
lism, in which the choline transmembrane transporter LicB firstly acquires choline from exter-
nal environment. Afterwards, the choline kinase LicA phosphorylates choline in the cytoplasm
to form phosphocholine [12], which is further activated into CDP-choline by the phosphocho-
line cytidylyl transferase LicC [13]. Two phosphocholine transferases LicD1 and LicD2 catalyze
the transfer of phosphocholine moiety from CDP-choline to the precursor of teichoic acid,
which is synthesized by the cytidylyl transferase TarI and alcohol dehydrogenase TarJ [14].
The mature teichoic acid is flipped across the cytoplasmic membrane by the transmembrane
teichoic acid flippase TacF and finally integrated into the cell wall [15]. Therefore, the choline
kinase LicA is crucial due to its role in initiating phosphorylcholine metabolism pathway [16].
The choline kinases (EC 2.7.1.32) exist in almost all species [17]. To date, several crystal
structures of choline kinases have been solved, such as Caenorhabditis elegans CKA-2 (PDB
1NW1) [17], Homo sapiens hCKα2 (PDB 2CKO) [18], Plasmodium falciparum PF14_0020
(PDB 3FI8) [19], Plasmodium knowlesi PKH_134520 (PDB 3C5I) [20], Cryptosporidium par-
vum CGD3_2030 (PDB 3MES) [21] and Mesorhizobium loti NP_106042.1 (PDB 3DXQ) [22].
They all share a similar overall structure and a conserved catalytic core. The kinetic characteri-
zation and complex structures of human hCKα2 suggest a two-step double-displacement
mechanism [18, 23, 24]. A conserved residue Asp306 stabilizes the phospho-enzyme interme-
diate, followed by the transfer of the phosphate to choline to produce phosphocholine [24].
However, the structure and catalytic mechanism of prokaryotic choline kinases
remain unknown.
Here we determined the crystal structures of apo-form LicA at 1.94 Å (apo-LicA) and two
complex forms with choline (LicA-choline) and AMP/MES (LicA-AMP-MES) at 2.01 Å and
1.45 Å, respectively. Three structures presented the snapshots of the conformational change in
the active site upon substrate binding and products release. Structural analysis combined with
mutageneses and enzymatic assays enabled us to assign the key residues for the choline kinase
activity of LicA. Structural comparison of LicA with its human homolog revealed that insertion
or deletion of an active-site loop differs the activity of eukaryotic and prokaryotic choline ki-
nases. These findings provide insights into the catalysis of prokaryotic choline kinases, and also
might direct the rational design of new anti-pneumococcal drugs.
Materials and Methods
Overexpression and purification of LicA and mutants
The gene encoding the 289-residue LicA of S. pneumoniae R6 was initially cloned into the
pET28a expression vector (Novagen) with an N-terminal 6×His tag. The recombinant plasmid
was transformed into E. coli BL21 (DE3) cells by heat shock. The cells were grown at 37°C in
LB medium containing 30 μg/mL kanamycin until OD600nm reached about 0.8. Expression of
proteins was induced with 0.2 mM isopropyl β-D-thiogalactopyranoside (IPTG) overnight at
16°C. The selenomethionine-substituted LicA protein (SeMet-LicA) was expressed in M9 min-
imal medium supplemented with 25 mg/L selenomethionine and other essential amino acids at
50 mg/L. Cells were harvested by centrifugation and resuspended in a lysis buffer (20 mM Tris-
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Pneumococcal Choline Kinase LicA
HCl, pH 7.5, and 100 mM NaCl). After sonication and centrifugation, the supernatant contain-
ing target protein was loaded onto a Ni-NTA column (GE Healthcare) and washed with the
wash buffer (20 mM Tris-HCl, pH7.5, 100 mM NaCl, and 20 mM imidazole). The LicA protein
was eluted with 500 mM imidazole and further loaded onto a Superdex 200 column (GE
Healthcare) equilibrated with the buffer of 20 mM Tris-HCl, pH 7.5, 100 mM NaCl. Purified
LicA proteins were concentrated to 30 mg/mL for crystallization and 1 mg/mL for enzymatic
assays. Protein samples for enzymatic activity assays were stored at -80°C.
Site-directed mutagenesis was performed by using the QuickChange site-directed mutagen-
esis kit (Stratagene, La Jolla, CA) with the plasmid encoding the wild-type LicA as the template.
The mutant proteins were expressed, purified and stored in the same manner as the wild-
type protein.
Crystallization, data collection and processing
Both native and SeMet-LicA proteins were concentrated to 30 mg/mL by ultrafiltration (Milli-
pore Amicon) for crystallization. All crystals were grown at 16°C using the hanging drop
vapor-diffusion method. The apo-LicA crystals were grown in a reservoir solution containing
0.1 M HEPES, pH 7.5, 1.2 M sodium citrate and 4% glycerol (v/v). The LicA-choline complex
crystals were obtained by soaking the apo-LicA crystals with 10 mM choline overnight while
LicA-AMP-MES complex crystals were grown in the reservoir solution of 0.1 M 2-(N-
morpholino)ethanesulfonic acid (MES), pH 6.5, 30% polyethylene glycol 6000 (w/v) by the ad-
dition of AMP to the final concentration of 10 mM. All crystals were transferred to cryoprotec-
tant (reservoir solution added with 30% glycerol (v/v)) and flash-cooled with liquid nitrogen.
The diffraction data were collected at 100 K in a liquid nitrogen stream using beam line 17U
with a Q315r CCD (ADSC, MAR research, Germany) at the Shanghai Synchrotron Radiation
Facility (SSRF). The diffraction data were integrated and scaled using the program HKL2000
[25].
Structure determination and refinement
The structure of LicA was determined by the single-wavelength anomalous diffraction (SAD)
method using the SeMet-LicA crystals at a resolution of 2.6 Å. The selenium atoms were locat-
ed using the SHELXD program of IPCAS [26]. The phase was calculated by OASIS [27] and
further improved with the programs RESOLVE and Buccaneer [28, 29]. The model was built
by Autobuild in PHENIX [30]. Afterwards, the initial model was subjected to the molecular re-
placement against the native data of the apo-form and two complex-forms using MOLREP
[31]. All structures were refined with the program REFMAC5 from CCP4i [32] and rebuilt in-
teractively using the program COOT [33]. The final structures were evaluated with the pro-
grams MOLPROBITY [34] and PROCHECK [35]. Data collection and refinement statistics
were given in Table 1. All structure figures were prepared with the program PyMoL [36].
Enzymatic assays
The choline kinase activity of LicA and mutants were measured by high performance liquid
chromatography (HPLC) assays [23]. The reaction mixture in a final volume of 50 μL con-
tained 20 mM Tris-HCl, pH 8.0, 100 mM NaCl, 2 mM MgCl2, 2 mM ATP and choline at vary-
ing concentrations. The reaction was triggered by the addition of 50 nM LicA and was lasted
for 10 min at 37°C. Then the reaction was terminated by boiling at 100°C for 10 min. Each
sample was centrifuged at 12,000 × g for 10 min, then 40 μL supernatant was applied to the
HPLC system (Agilent 1200 Series). The buffer of 100 mM K2HPO4/KH2PO4, pH 6.5 was used
as the mobile phase to equilibrate the column (Eclipse XDB-C18 column, 5 μm, 4.6 × 250 mm;
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Pneumococcal Choline Kinase LicA
Table 1. Crystal parameters, data collection and structure refinement statistics.
Data Processing
SeMet-LicA
apo-LicA
LicA-AMP-MES
LicA-Choline
Data collection
Space group
P212121
P212121
P212121
P212121
Unit cell (Å), (°)
70.00, 96.96, 97.92, 90.00 69.35, 96.47, 97.59, 90.00 62.34, 62.86, 68.75, 90.00 70.39, 96.69, 98.60, 90.00
No. of molecules per asymmetric unit
Resolution range (Å)
Unique reflections
Completeness (%)
<I/σ(I)>
2
2
1
2
50.00–2.60
21,083 (2,064)a
99.8 (100)
11.9 (5.9)
16.4 (66.6)
9.5 (9.7)
50.00–1.94
47,710 (4,732)
97.2 (97.8)
20.3 (2.8)
6.2 (52.9)
3.0 (3.0)
50.00–1.45
47,856 (4,723)
98.5 (98.8)
12.3 (2.0)
8.5 (65.1)
3.6 (3.6)
50.00–2.01
44,656 (4,354)
98.2 (98.0)
16.4 (3.4)
9.4 (57.1)
3.4 (3.4)
Rmergeb (%)
Average redundancy
Structure refinement
Resolution range (Å)
R-factorc/R-freed (%)
Number of protein atoms
Number of water atoms
RMSDe bond lengths (Å)
RMSD bond angles (°)
Mean B factors (Å2)
Ramachandran plotf (%)
Most favored (%)
50.00–1.94
21.6/26.2
4,587
46.39–1.45
19.3/21.4
2,341
50.00–2.01
20.0/23.7
4,679
289
328
312
0.010
0.006
0.010
1.107
1.042
1.138
39.2
19.4
36.2
94.8
5.2
96.8
3.2
95.8
4.2
Additional allowed (%)
Outliers (%)
0
0
0
PDB entry
4R77
4R78
4R7B
aThe values in parentheses refer to statistics in the highest bin.
bRmerge = ∑hkl∑i|Ii(hkl)-<I(hkl)>|/∑hkl∑iIi(hkl), where Ii(hkl) is the intensity of an observation and <I(hkl)> is the mean value for its unique reflection;
Summations are over all reflections.
cR-factor = ∑h||Fo(h)|-|Fc(h)||/∑h|Fo(h)||, where |Fo| and |Fc| are the observed and calculated structure-factor amplitudes, respectively.
dR-free was calculated with 5% of the data excluded from the refinement.
eRoot-mean square-deviation from ideal values.
fCategories were defined by Molprobity.
doi:10.1371/journal.pone.0120467.t001
Agilent) and the components were separated at a flow rate of 1 mL/min. The product ADP was
monitored with the absorption at 254 nm and was assigned based on the retention time of the
standards. All the measurements were done in triplicate. The final enzymatic kinetic parame-
ters were calculated based on the yield of ADP by nonlinear fitting to the Michaelis-Menten
equation with the program GraphPad Prism.
Results and Discussion
Overall structure
Each asymmetric unit contains two molecules of LicA. The interface between the two mole-
cules is about 650 Å2, which is not large enough to maintain a stable dimer. In fact, LicA exists
as a monomer in solution, which was confirmed by gel-filtration chromatography (S1 Fig.).
The overall structures of two molecules are very similar with a root-mean-square deviation
(RMSD) of 0.4 Å over 280 Cα atoms, thus we took molecule A for further structural analyses.
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Pneumococcal Choline Kinase LicA
Fig 1. Overall structure of LicA. (A) apo-LicA (blue). The secondary structure elements are labeled sequentially. (B) LicA-choline complex structure
(orange). The substrate choline is shown as green sticks, with the Fo-Fc electron-density omit map contoured at 3.0 sigma. (C) LicA-AMP-MES complex
structure (magenta). The AMP and MES molecules are shown as yellow sticks, with the Fo-Fc electron-density omit map contoured at 3.0 sigma. (D)
Superposition of overall structures between LicA (blue) and H. sapiens hCKα2 (gray). The loopα7-α8 from hCKα2 is labeled in red.
doi:10.1371/journal.pone.0120467.g001
The structure of LicA adopts a protein kinase-like fold which comprises of an N-terminal
domain (residues 1–92) and a C-terminal domain (residues 93–283) (Fig. 1A). The N-terminal
domain contains two helices (α1 and α2), which sandwich a twisted five-strand antiparallel β-
sheet (β1-β5). The C-terminal domain consists of eight α-helices (α3-α10) surrounding five
short β-strands (β6-β10). The N- and C-terminal domains form a catalytic crevice that harbors
several conserved motifs: the ATP-binding motif [18, 37] in the loop (the so-called P-loop, resi-
dues Gly26-Asn31) connecting β1 and β2, the phosphotransferase Brenner’s motif [(CS)
HNDhX3N] [38] in the loop (Ser172-Asn181) between β7 and β8 and choline kinase motif
[(ILV)X2ID(FWY)E(YF)X3NX3(FYW)DX6E] [17] in the region of β9, β10 and α7 (Leu190-
Glu213). These motifs were reported to be indispensable for the catalysis [18].
In the complex structure of LicA-choline, a molecule of choline is located at the active site
of the C-terminal domain (Fig. 1B), whereas in the complex structure of LicA-AMP-MES, an
AMP molecule and an MES molecule occupy the active site (Fig. 1C). The MES molecule,
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Pneumococcal Choline Kinase LicA
which should be introduced from the crystallization buffer, occupies the corresponding posi-
tion of choline in LicA-choline, whereas the AMP molecule is stabilized by the N-terminal do-
main. The Fo-Fc omit map at 3 σ revealed poor density of the ribose-phosphate moiety of
AMP, as reflected by its low occupancy. The physiological substrate and product of LicA are
ATP and ADP, respectively, both of which are larger than the molecule of AMP. Thus the
AMP molecule could only partially occupy the active-site pocket with a relatively lower binding
affinity, which was further indicated by the fewer hydrogen bonds of LicA-AMP, compared to
ADP binding to hCKa2 (PDB 2CKP) [18].
Structural homology search using DALI [39] indicated that the overall structure of LicA re-
sembles the members of the choline kinase family, although LicA only shares a sequence identi-
ty of less than 25% with the members of known structure. The closest member is the putative
choline kinase NP_106042.1 from M. loti (PDB 3DXQ, Z-score = 26.4, RMSD = 3.0 Å over 268
Cα atoms) [22], whose biochemical information has not been elucidated. Other similar struc-
tures include P. knowlesi choline kinase PKH_134520 (PDB 3C5I, Z-score = 25.1, RMSD = 2.5
Å over 272 Cα atoms) [20] and H. sapiens choline kinase hCKα2 (PDB 2CKO, Z-score = 24.8,
RMSD = 2.6 Å over 275 Cα atoms) [18]. Superposition of the LicA structure against that of
human hCKα2 revealed that they share a similar overall structure, despite that hCKα2 contains
a more flexible N-terminal loop and two longer helices (corresponding to α5 and α9 in LicA)
(Fig. 1D). The most significant difference is the variations of the loopα7-α8 in the active site.
The loopα7-α8 of LicA has only 5 residues, but the corresponding loop of hCKα2 possesses 21
residues, which forms a long hairpin-like structure and extends to the top of the choline-
binding pocket (Fig. 1D, in red). In previous reports, this loop was proposed to modulate the
access of the substrate choline [17, 18]. Thus the deletion of loopα7-α8 might differ the catalytic
activity of LicA from that of hCKα2.
The active site
In the LicA-choline structure, four aromatic residues, Tyr197, Trp251, Trp254 and Tyr268 to-
gether with Val178 form a hydrophobic pocket to accommodate the quaternary amine moiety
of choline (Fig. 2A). Glu213 at the rim of the pocket makes a charge charge interaction with
the positively charged quaternary amine of choline. In addition, residues Thr29 (mediated by a
water molecule) and Asp176 form two hydrogen bonds with the hydroxyl moiety of choline.
The corresponding residues Ser121 and Asp306 in hCKα2 are proved to be essential for cataly-
sis [18].
In the LicA-AMP-MES structure, the MES molecule presents in the same place as choline in
the structure of LicA-choline (Fig. 2B). The morpholine ring of MES is stabilized by residues
Tyr197, Glu213, Trp251, Trp254 and Tyr268, whereas the sulfonic acid moiety forms hydrogen
bonds with Gln31, Lys45 and Asp176. The AMP molecule is located at the N-terminal domain.
The adenine ring of AMP makes hydrophobic interactions with residues Ile43, Tyr90 and I183,
and also forms hydrogen bonds with the main chains of Glu89 and Ile91. The ribose moiety
makes hydrogen bonds with the side chain of Thr96 and the main chain of Glu180, respective-
ly, whereas the α-phosphate moiety interacts with Asn32, Asn181 and Asp194.
Comparison between the active site of LicA-AMP-MES and that of hCKα2-ADP (PDB
2CKP) [18] showed that the AMP molecule in LicA could be well superimposed to the product
ADP in hCKα2-ADP (Fig. 2C). AMP adopts a same conformation as ADP, and both of which
share a similar binding pattern. However, the ribose of AMP in LicA makes hydrogen bond
with side chain of Thr96, and the α-phosphate moiety interacts with Asn32, Asn181 and
Asp194, whereas the ribose of ADP in hCKa2 makes hydrogen bond with the main chain of
Arg213, the α-phosphate moiety interacts with Arg146, Asn311 and Asp330, and the β-
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Pneumococcal Choline Kinase LicA
Fig 2. The active site. (A) The choline-binding site of LicA. The binding residues and choline are shown as orange and green sticks, respectively. The
secondary structure elements are shown as semi-transparent cartoon. The hydrogen bonds and polar interactions are indicated as dashed lines. (B) The
AMP- and MES-binding sites of LicA. The binding residues are shown as magenta sticks whereas the AMP and MES molecules are shown as yellow sticks.
(C) Superposition between LicA-AMP-MES (magenta) and human hCKα2-ADP (cyan). (D) Structural comparison of the choline-binding sites of LicA-choline
(yellow), LicA-AMP-MES (magenta) and hCKα2-phosphocholine (gray).
doi:10.1371/journal.pone.0120467.g002
phosphate moiety interacts with Arg177 and Asn122. For the choline-binding pocket
(Fig. 2D), the choline or MES molecule in LicA could be well aligned to the phosphocholine in
hCKα2-phosphocholine (PDB 2CKQ) [18]. The key hydrophobic residues involved in stabiliz-
ing the quaternary amine of choline or the morpholine ring of MES in LicA are structurally
conserved in hCKα2-phosphocholine. However, in hCKα2, the residue Tyr354 in the long
hairpin-like loopα7-α8 interacts with the quaternary amine of phosphocholine (Fig. 2D), but
this interaction is missing in LicA due to the fact that the corresponding loopα7-α8 is much
shorter (Fig. 1D). In addition, the phosphate moiety of phosphocholine in hCKα2 is stabilized
by Ser121 and Asp306, whereas the corresponding residues Thr29 and Asp176 in LicA interact
with choline. Moreover, in the structure of LicA-AMP-MES, only Asp176 stabilizes the sulfon-
ic acid moiety of MES, with Thr29 on the P-loop flipping away from the active-site pocket. The
similar binding patterns suggest that AMP and MES in LicA-AMP-MES might mimic the na-
tive products ADP and phosphocholine, respectively. On the other hand, the differences of the
active site between LicA and hCKα2 revealed the species specificity which might guide the de-
sign of inhibitors against choline kinases.
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Pneumococcal Choline Kinase LicA
Fig 3. Conformational changes in the active site. (A) Comparison between apo-LicA (blue) and LicA-choline (orange) with P-loop shown as cartoon. The
choline molecule and the interacting residues are shown as sticks. The hydrogen bonds are indicated as dashed lines. (B) Comparison between LicA-choline
(orange) and LicA-AMP-MES (magenta). The choline molecule is shown as green sticks while AMP and MES are shown as yellow sticks. The 18° rotation of
the N-terminal domain is indicated as black arrow.
doi:10.1371/journal.pone.0120467.g003
The conformational changes during catalysis
Superposition of the LicA-choline complex structure against the apo-LicA structure revealed
an RMSD of 0.4 Å over 278 Cα atoms indicating slight conformational changes of the overall
structure. However, drastic differences were found in the active site. Upon the binding of the
substrate choline, Thr29 forms a water-mediated hydrogen bond with choline, resulting in a
shift of the P-loop about 4 Å towards the choline molecule. The residue Asn30 in the P-loop
also moves to the active site and makes a hydrogen bond with Glu196 to further stabilize the P-
loop (Fig. 3A). Therefore, the active-site pocket undergoes a change from an open to a closed
conformation upon choline binding.
The human hCKα2-phosphocholine structure revealed a closed conformation with the P-
loop closure and 16° rotation of the two domains, upon phosphocholine binding [18]. Similar
to hCKα2, the N-terminal domain of LicA-AMP-MES rotates approximately 18° towards the
C-terminal domain comparing to apo-LicA by the program DynDom [40], making N- and C-
terminal domains much closer to each other. Structural comparison between the two complex
structures LicA-choline and LicA-AMP-MES yields an RMSD of 1.4 Å over 273 Cα atoms. The
P-loop in LicA-choline is close to the active site and the residue Thr29 of P-loop interacts with
choline, whereas the P-loop in LicA-AMP-MES is far away from the active site and adopts a
conformation similar to that in apo-LicA structure. In addition, the N-terminal domain in
LicA-AMP-MES also shows a rotation of about 18° towards the C-terminal domain comparing
to LicA-choline structure (Fig. 3B). Therefore, based on the three structures of LicA and two
complex structures of hCKα2, we propose a catalytic cycle of choline kinases (S2 Fig.). In the
apo-form state, the enzyme adopts an open conformation (1), with the P-loop protruding out-
wards from a wider active-site pocket. Upon the binding of substrate choline, the P-loop shifts
towards the active site to stabilize the substrate, resulting in a closed conformation (2). Binding
of the second substrate ATP triggers the catalytic reaction which might lead to domain rotation
in addition to P-loop closure (3). When the products are formed, the P-loop is kicked away
from the active site (4), accompanied with the release of the products (5) and turnover of
the enzyme.
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Pneumococcal Choline Kinase LicA
Fig 4. Enzymatic activities of wild-type LicA and mutants. (A) Effect of magnesium or EDTA on LicA
activity. (B) The relative enzymatic activities of the wild-type LicA and mutants. One-way ANOVA with a post
hoc Dunnett test is used for the comparison of statistical significance. The P values of <0.05, 0.01 and 0.001
are indicated with *, ** and ***, respectively.
doi:10.1371/journal.pone.0120467.g004
Choline kinase activity of LicA
The choline kinase activity was tested by HPLC assays. LicA showed an optimal activity at pH
8.0 in the presence of Mg2+. Despite no metal observed in the three structures, we propose that
the activity of LicA is dependent on Mg2+, as deprivation of metal ions using ethylenediamine-
tetraacetic acid (EDTA) drastically diminished its activity by 6 fold (Fig. 4A). Similar case has
also been found in ChoKα1, that the metal Mg2+ was found in the substrate-binding pocket to
stabilize the phosphate group of ADP [23]. The wild-type LicA has Km and kcat values of 0.15
0.05 mM and 5.1 0.7 s-1, respectively, resulting in the activity (kcat/Km) of 33.3 s-1mM-1. Mu-
tation of the conserved Asp176 to alanine decreased the relative activity to about 14% of the
wild-type suggesting Asp176 is critical for catalysis (Fig. 4B). The corresponding residue
Asp306 in hCKα2 makes a critical hydrogen bond with the inorganic phosphate anion to stabi-
lize the phosphor-enzyme intermediate [24]. In addition, mutation of the choline-binding resi-
due Thr29 to alanine decreased the relative activity to about 10% of the wild-type. However,
Fig 5. Multiple-sequence alignment of eukaryotic and prokaryotic choline kinases. The alignment is generated with the programs Multalin [46] and
Espript [47]. Secondary structure elements of LicA and hCKα2 are indicated on the top and bottom of the sequences, respectively. The loopα7-α8 that differs
the eukaryotic choline kinases from that of prokaryotes is indicted by a red line on the top of the sequence. The conserved tyrosine residue in the loopα7-α8 is
labeled by a green box.
doi:10.1371/journal.pone.0120467.g005
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Pneumococcal Choline Kinase LicA
the T29S mutant retained the full activity, supporting the importance of the hydroxyl group at
this position. In addition, other conserved residues, such as Asn181, Asp194 and Glu196 are
also important for catalysis, which were also found in hCKα2 [18]. Site-directed mutageneses
together with enzymatic assays indicate that LicA might also adopt the two-step double-
displacement mechanism [24].
The human choline kinase hCKα2 has an activity (kcat/Km) of 848 s-1mM-1, which is 25-fold
higher than that of LicA (33.3 s-1mM-1) [18, 41–44]. Structural comparison revealed the
loopα7-α8 at the choline-binding pocket might attribute to the different enzymatic activities. As
a prokaryotic choline kinase, LicA has a very short loopα7-α8 of 5 residues, resulting in a rela-
tively open choline-binding pocket, whereas the corresponding loop in hCKα2 is about 21-
residue long, which extends to active site and covers the choline-binding pocket (Fig. 1D). In
addition, an additional residue Tyr354 on loopα7-α8 stacks the quaternary amine of phospho-
choline in hCKα2 (Fig. 2D). This tyrosine residue is exclusively conserved in eukaryotic choline
kinases, but it is absent in prokaryotes (Fig. 5). Thus an insertion in the loopα7-α8 of the eukary-
otic hCKα2 contributes to the high catalytic activity, maybe via increasing the binding affinity
of the substrate choline. The higher activity of eukaryotic choline kinases is also consistent with
the requirement of higher amount of phosphocholine, involved in the phosphatidylcholine bio-
synthesis for membrane phospholipid [45]. Multiple-sequence alignment revealed that the lon-
ger loopα7-α8 is a common feature in eukaryotic choline kinases, but this loop is much shorter
in prokaryotic choline kinases (Fig. 5). Therefore, the loopα7-α8 at the choline-binding pocket
plays an important role in substrate specificity and catalytic activity of choline kinases, and the
variation of the loop length might differ the prokaryotic choline kinases from their orthologs
in eukaryotes.
Supporting Information
S1 Fig. The gel filtration data showing the monomeric state of LicA. The standard curve was
inserted as an inlet.
(TIF)
S2 Fig. A schematic diagram depicting the catalytic cycle of choline kinases.
(TIF)
Acknowledgments
We thank the staff at the Shanghai Synchrotron Radiation Facility (SSRF) for the assistance of
data collection. We are grateful to all the developers of the CCP4 suite, ESPript, PHENIX and
PyMOL.
Author Contributions
Conceived and designed the experiments: YLJ YC. Performed the experiments: LW. Analyzed
the data: LW YLJ CZZ YC. Wrote the paper: LW YLJ YC CZZ JRZ.
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