Phosphate chains of NTP molecules and their analogs are colored by atoms: oxygen atoms in red, phosphorus in orange. The K+ ion is shown as a purple sphere, Na+ ion is shown as a blue sphere, Mg2+ …
The color scheme is as in Figure 1. (A) Superposition of the ATP phosphate chain conformations observed in the MD simulations in the presence of K+ ions (shown in purple); Na+ ions (shown in blue) …
Radial distributions are shown for all atoms of the ATP phosphate chain. (A) Atom names are in accordance with the CHARMM naming scheme (Vanommeslaeghe et al., 2010) and the recent IUPAC …
(A) Probability distribution functions for cations around the phosphate chain. We have plotted the number of atoms inside the area centered on phosphorus atoms of the ATP phosphate chain as a …
Distances to the AG and BG binding sites (RAG and RBG) were calculated as averages of the distances to the two corresponding oxygen atoms (see Figure 2 in the main text). The distances to the oxygen …
(A) Conformations of Mg-ATP complexes with one and two K+ ions bound as inferred from MD simulations; left structure, no K+ ion bound in the AG site; right structure, a K+ ion is bound in the AG …
Data from MD simulations with restraints on the positions of K+ ions (see the text and Supplementary file 1C). The top graph shows free energy calculated from normalized probabilities of ATP …
Each left panel shows the PA-PG distance (upper trace) and the PB-O3B-PG angle (bottom trace) in the course of MD simulations. Thin gray lines show actual values measured from each frame of the MD …
Black vertical lines indicate borders between independent simulations, thick colored lines show moving averages of distances measured during MD simulations. Oxygen atoms are labeled as in Figure 1D. …
A,B, Changes of the distance value upon MD simulations of βγ-coordinated Mg-ATP complexes with no additional monovalent cations (A) and with K+ ions (B) provided as examples. (C) Autocorrelation …
A, B, Changes of the angle value upon MD simulations of βγ-coordinated Mg-ATP complexes with no additional monovalent cations (A) and with K+ ions (B) provided as examples. (C) Autocorrelation …
Heat maps for systems with monovalent cations include only conformations of Mg-ATP complexes with at least one cation present within 4 Å radius. The color intensity is proportional to the …
Heat maps for systems with monovalent cations include only conformations of Mg-GTP complexes with at least one cation present within 4 Å area, and with Mg2+ in βγ coordination. The color intensity …
PDB entries for structures of P-loop NTPases were extracted from InterPro database entry IPR027417 ‘P-loop containing nucleoside triphosphate hydrolase’ and filtered to contain only those X-ray …
The color scheme is as in Figure 1; dark blue spheres indicate positions of positively charged side-chain nitrogen atoms of Lys and Arg residues, P-loop regions are shown as cartoons in grey. (A) …
Each of the proteins shown has both Asn residues that were shown to be associated with binding of monovalent cations in related proteins (Ash et al., 2012). Switch I, including the K-loop, and its …
(A) Inactive dimer of the full-length MnmE in the GTP-bound form (the structure (PDB: 3GEI) was resolved with non-hydrolyzable GTP analogs). The P-loop domain is shown in grey, the K-loop is not …
(A) Inactive Era in the GDP-bound form [PDB: 3IEU] (Tu et al., 2009) in two projections. (B) Active Era in complex with nucleotides 1506–1542 of 16S rRNA and a non-hydrolyzable analog of GTP [PDB: …
(A) Cation-dependent RadA recombinase from Methanococcus voltae [PDB: 2F1H] (Qian et al., 2006). (B) Cation-independent RecA recombinase from E. coli [PDB: 3CMX] (Chen et al., 2008). The protein …
(A) Superposition of the GTP-binding sites of the inactive, monomeric G-domain of MnmE (the 2GJ8W system, blue) and the active K+-bound dimer of G-domains (the 2GJ8K system, red); representative …
Distances between phosphate chain oxygen atoms and surrounding amino acid residues were measured in the course of 100-ns MD simulations. (A) inactive monomer without a full-fledged K-loop (the 3GEI …
Plotted are data for the active dimer of G-domains with K+ ions bound (the 2GJ8K system, red and magenta for individual monomers) and inactive, monomeric G-domain of MnmE with the K+ ion replaced by …
The color scheme is as in Figure 1, except that Al and F atoms in the GDP-AlF4- complexes are colored grey and cyan, respectively. (A) Superposition of the K+-bound (solid structure) and Na+-bound …
Added cation | Conformation of the triphosphate chain of Mg-ATP* | |||||
---|---|---|---|---|---|---|
βγ-coordination | βγ-coordination, ‘curled’ phosphate chain | αβγ-coordination | ||||
PA-PG distance, Å | PB-O3B-PG angle | PA-PG distance, Å | PB-O3B-PG angle | PA-PG distance, Å | PB-O3B-PG angle | |
None | 5.46 ± 0.34 | 122.3 ± 3.5 | N/A | 4.76 ± 0.18 | 124.9 ± 3.3 | |
K+ | 4.91 ± 0.24 | 122.0 ± 3.3 | N/A | 4.32 ± 0.24 | 128.0 ± 3.5 | |
Na+ | 4.69 ± 0.22 | 122.9 ± 3.2 | 4.60 ± 0.22 | 124.0 ± 3.3 | 4.26 ± 0.37 | 127.7 ± 3.6 |
NH4+ | 4.85 ± 0.22 | 122.3 ± 3.3 | 4.56 ± 0.21 | 124.6 ± 3.3 | 4.22 ± 0.16 | 127.8 ± 3. |
*The conformations of the Mg-ATP complex were determined as described in the text. Mean values and standard deviations of PA-PG distance (in Å) and the PB-O3B-PG angle (in degrees) were measured over the respective parts of the simulations. Simulation periods corresponding to βγ and αβγ conformations were identified by tracking distances between Mg2+ and non-bridging oxygen atoms of the phosphate chain (Figure 4—figure supplement 1); simulation periods corresponding to the ‘curled’ conformation were identified from PA-PG distance tracks and visual inspection of the phosphate chain shape (Figure 4). Data for the αβγ coordination of the Mg-ATP complex and conformations with curled phosphate chain were calculated from simulations 1–4 in Supplementary file 1C; characterization of the βγ-coordination was based on simulations 5–8 in Supplementary file 1C, see Supplementary file 1E for further details.
Superfamily | Family | Activating charge | Activation mechanism |
---|---|---|---|
Kinase-GTPase division, TRAFAC class | |||
Classic translation factor GTPases | EF-G/EF-2 | K+ | Functional interaction with ribosomal RNA/other protein(s)/other domain(s) of the same protein (Hwang and Inouye, 2001;Moreau et al., 2008; Tomar et al., 2011; Achila et al., 2012;Fasano et al., 1982; Ebel et al., 1992; Dubnoff and Maitra, 1972;Kuhle and Ficner, 2014; Manikas et al., 2016; Daigle and Brown, 2004; Foucher et al., 2012;Rafay et al., 2012; Pérez-Arellano et al., 2013; Villarroya et al., 2008) |
EF-Tu/EF-1A | K+ | ||
EIF2G | K+ | ||
ERF3 | K+ | ||
IF-2 | K+ | ||
LepA | K+ | ||
OBG-HflX-like GTPases | HflX | K+ | |
OBG | K+ | ||
NOG | K+ | ||
YchF/OLA1 | K+ | ||
YlqF/YawG GTPases | NOG2 | K+ | |
RsgA | K+ | ||
TrmE-Era-EngA-EngB-Septin-like GTPases | EngA (Der) | K+ | |
EngB | K+ | ||
Era | K+ | ||
FeoB | K+ | Dimerization (e.g. mRNA-associated in the case of MnmE) (Chappie et al., 2010; Koenig et al., 2008; Gasper et al., 2009) | |
MnmE | K+ | ||
Septin | Arg finger | ||
Toc34-like | Arg finger | ||
Dynamin-like GTPases | hGBP | Arg finger | |
Dynamin | K+/Na+ | ||
Extended Ras | Ras family | Arg finger | Interaction with a specialized activating protein or domain(Bos et al., 2007; Cherfils and Zeghouf, 2013) |
Gα subunits | Arg finger | ||
Myosin/kinesin | Myosin | Arg finger | |
Kinesin | Arg finger | ||
ASCE division, RecA/F1-like class | |||
DNA-repair and recombination ATPases | RecA | Lys finger | DNA/RNA-dependent oligomerization(Chen et al., 2008) |
RadA | K+ | ||
Rho helicases | Rho | Arg finger | Interaction with the neighboring subunit within a conformationally coupled hexamer (Komoriya et al., 2012; Walker, 1998;Senior et al., 2002; Skordalakes and Berger, 2006) |
T3SS ATPases | YscN | Arg finger | |
Flil | Arg finger | ||
F-/V-type ATPases | V-type A | Arg finger | |
F-type β | |||
V-type B | |||
F-type α |
Protein | PDB entry | Bound NTP analog | Occupation of the AG site | Phosphate chain shape | |||
---|---|---|---|---|---|---|---|
Cation | Distance to the closest O atom of PA, Å* | Distance to the closest O atom of PG, Å*,† | PA-PG distance, Å* | PB-O3B-PG angle, degrees† | |||
TRAFAC class NTPases | |||||||
GTPase MnmE(TrmE) | 2gj8 | GDP AlF4- | K+ | 2.8 | 2.6 | 5.4 | 136.3 |
2gja | GDP AlF4- | NH4+ | 2.9 | 2.5 | 5.4 | 136.9 | |
2gj9 | GDP AlF4- | Rb+ | 2.9 | 2.8 | 5.5 | 131.6 | |
GTPase FeoB | 3ss8 | GDP AlF4- | K+ | 2.8 | 2.6 | 5.4 | 144.9 |
Dynamin-like proteins | 2x2e | GDP AlF4- | Na+ | 4.0 | 2.5 | 5.3 | 131.2 |
2x2f | GDP AlF4- | Na+ | 4.1 | 2.6 | 5.3 | 133.6 | |
3w6p | GDP AlF4- | Na+ | 4 | 2.4 | 5.5 | 135.3 | |
3t34 | GDP AlF4- | Na+ | 3.8 | 2.4 | 5.6 | 149.3 | |
GTPase Era | 3r9w | GNP | H2O‡ | 3 | 3.4 | 5.1 | 129.2 |
Eukaryotic translation initiation factor eIF5B | 4ncn | GTP | Na+ | 2.4 | 2.4 | 5.0 | 126.6 |
4tmv | GSP | Na+ | 2.4 | 2.8 (S)§ | 4.9 | 126.3 | |
4tmw | GTP | Na+ | 2.4 | 2.4 | 4.9 | 125.9 | |
4tmz | GSP | K+ | 2.7 | 3.3 (S)§ | 4.9 | 122.1 | |
RecA/F1-like class NTPases | |||||||
DNA recombinase RadA | 3ew9 | ANP | K+ | 6.2 | 3.3 | 5.1 | 124.5 |
2f1h | ANP | K+ | 6.6 | 3.5 | 5.3 | 125.3 | |
2fpm | ANP | K+ | 5.9 | 2.6 | 5.1 | 124.2 | |
1xu4 | ANP | K+ | 6.1 | 2.7 | 5.2 | 125.0 |
*The values were measured directly in the respective protein structures displayed in PyMOL.
† If the γ-phosphate was replaced by an AlF4- complex, the distance was measured to the closest F atom
‡ While GTPase Era has been shown to be K+-dependent (Rafay et al., 2012; Meier et al., 2000), the crystallization solution contained no K+, only Na+, so that the likely cation-binding site is occupied by a water molecule, which forms hydrogen bonds with K+ ligands.
§ Non-hydrolyzable GTP analog GDP-monothiophosphate (GSP) contains a sulfur atom in the place of the O1G atom of γ-phosphate; this atom in involved in coordination of monovalent cations in respective structures.
(A) Monovalent cation requirements of P-loop GTPases and ATPases. (B) Properties of monovalent cations and their interactions with the Mg2+-ATP complex. (C) Molecular dynamics simulations performed in this work. (D) Values of dihedral angles of the phosphate chains of Mg-ATP in the presence of K+ ions. (E) Lifetimes of the βγ-conformation of Mg-ATP complex during MD simulations. (F) Characteristics of the triphosphate chain for different interactions between the Mg2+ ion and ATP. (G) Comparison of the PA-PG distance measurements of the βγ-coordinated Mg-ATP complexes. (H) Comparison of the PA-PG distance measurements of the αβγ-coordinated Mg-ATP complexes. (I) Comparison of the PA-PG distance measurements for the αβγ-coordinated and ‘curled’ βγ-coordinated Mg-ATP complexes in different systems. (J) Comparison of the PB-O3B-PG angle measurements for the βγ-coordinated Mg-ATP complexes. (K) Comparison of the PB-O3B-PG angle measurements for the αβγ-coordinated Mg-ATP complexes. (L) Comparison of the PA-PG distance measurements for the αβγ-coordinated and ‘curled’ βγ-coordinated Mg-ATP complexes.