Supporting Information - pnas.org€¦ · Supporting Information ... formed with ATP and in the...
4
Supporting Information Oldham and Chen 10.1073/pnas.1108858108 γ VO 4 α β BeF 3 γ α β α β BeF 3 α β α β VO 4 α β ADP - AlF 4 ADP - BeF 3 ADP - VO 4 AMP-PNP AlF 4 α β AlF 4 α β Fig. S1. Nonweighted 2F o − F c electron density maps contoured at 1.5σ for outward-facing transporter complexes cocrystallized with AMP-PNP, ADP-BeF 3 , ADP-VO 4 , or ADP-AlF 4 . Oldham and Chen www.pnas.org/cgi/doi/10.1073/pnas.1108858108 1 of 4
Transcript of Supporting Information - pnas.org€¦ · Supporting Information ... formed with ATP and in the...
Supporting InformationOldham and Chen 10.1073/pnas.1108858108
γ
VO4
α
β
BeF3
γ
α
β
α
β
BeF3
α
β
α
β
VO4
α
β
ADP - AlF4
ADP - BeF3
ADP - VO4
AMP-PNP
AlF4
α
β
AlF4
α
β
Fig. S1. Nonweighted 2Fo − Fc electron density maps contoured at 1.5σ for outward-facing transporter complexes cocrystallized with AMP-PNP, ADP-BeF3,ADP-VO4, or ADP-AlF4.
Oldham and Chen www.pnas.org/cgi/doi/10.1073/pnas.1108858108 1 of 4
A
B
H192E159
Q82
Walker A
Walker B
switch
β
γ
α
Mg2+
H O2
H O2
K42
S43
H192E159
Q82
Walker A
Walker B
switch
β
γ
α
Mg2+
H O2
H O2
K42
S43
Fig. S2. (A) Stereo view of a superposition of the newly reported structure of the maltose-binding protein ðMBPÞ-MalFGK2 complex formed with AMP-PNP inthe presence of Mg2þ (MalK, red and green; MBP, magenta; MalF, blue; MalG, yellow) with that of the same complex obtained for the E159Q mutant (cyan)formed with ATP and in the presence of EDTA (Protein Data Bank ID code 2R6G). (B) Stereo view of a superposition of the active sites of complexes from Aformed with AMP-PNP (red: MalK, chain A; green: MalK, chain B) or ATP-EDTA (yellow). Motifs and specific residues that interact with the nucleotide or Mg2þ
are indicated with the exception of main-chain interactions for the Walker A motif. The LSSGQ loop is removed for clarity.
Oldham and Chen www.pnas.org/cgi/doi/10.1073/pnas.1108858108 2 of 4
A
α
β
H O2 Q82
S43
E159
ADP - AlF4
BeF3
AlF4
ADP - BeF3
1.5
α
β
Mg2+
S43
Q82
E159
BeF3
α
β
Mg2+
S43
Q82
E159
1.5
Mg2+
α
β
H O2 Q82
S43
E159
AlF4 Mg2+
2.0 2.0
2.3 2.3
2.6 2.6
β
Q82
S43
E159
(H O)2
VO4
ADP - VO4
Q82
α
βS43
E159
Mg2+
γ
Q82
α
S43
E159
Mg2+
γ
α
β
Mg2+
Q82
S43
E159
(H O)2
VO4
α
β
Mg2+
AMP-PNP
2.0
2.7
2.0
2.7
ground state analogs
transition-state analogsB
Fig. S3. Stereo views of the interactions between the nucleotide and E159 to the γ-phosphate analog and/or attacking water for structures of MBP-MalFGK2
complexes formed with (A) AMP-PNP and ADP-BeF3 (ground state) or (B) ADP-VO4 and ADP-AlF4 (transition state). The metal-liganding interactions to theoctahedrally coordinated Mg2þ ion are also shown.
βα
VO4
VO4
αβ
ADP
ADP
βα
VO4
VO4
αβ
ADP
ADP
Fig. S4. Stereo view of theMalK dimer (gray) from theMBP-MalFGK2 complex formedwith ADP-VO4. An anomalous differencemap contoured to 10σ (purplemesh) calculated from diffraction data taken at 7 keV (near the absorption edge for vanadium at 5.5 keV) is shown.
Oldham and Chen www.pnas.org/cgi/doi/10.1073/pnas.1108858108 3 of 4
Table S1. Data collection and refinement statistics
AMP-PNP ADP-VO4 ADP-AlF4 ADP-BeF3 ADP-VO4 (SAD) *
Data collectionSpace group P1 P1 P1 P1 P1Cell dimensions
a, b, c, Å 72.1, 95.8, 110.0 81.8, 97.1, 112.8 81.9, 97.3, 112.3 82.1, 97.3, 112.8 78.7, 96.8, 112.2α, β, γ, ° 86.7, 82.7, 76.4 85.6, 78.7, 72.7 85.8, 79.4, 72.5 85.6, 79.0, 72.3 86.3, 79.7, 74.4
Resolution, Å 20–2.2 20–2.4 20–2.3 20–2.3 20–3.6Rsym, %
† 5.4 (34.2) 6.9 (47.6) 5.4 (34.2) 5.6 (33.8) 9.8 (21.0)I∕σI 17.6 (2.0) 19.1 (2.2) 18.3 (2.5) 21.2 (2.6) 11.8 (6.8)Redundancy 2.0 (1.6) 3.1 (2.3) 3.5 (2.7) 3.0 (2.9) 4.6 (3.9)
RefinementResolution, Å 20–2.2 20–2.4 20–2.3 20–2.3No. reflections 117,902 76,178 91,058 89,108Rwork∕Rfree 22.3∕25.4 22.3∕25.3 22.0∕25.5 22.8∕26.6No. atoms
Protein 14,723 14,660 14,683 14,776Ligand/ion 325 633 633 631Water 341 180 272 253
B-factors, Å2
MBP 67.5 62.1 55.5 51.3MalF 70.0 65.4 61.1 54.5MalG 50.3 43.9 44.4 39.1MalK (chain A) 46.3 55.8 52.1 43.5MalK (chain B) 50.7 75.1 68.0 57.1Maltose 49.9 40.6 40.6 32.4Nucleotide/analog/Mg2þ 33.7 37.1 37.5 32.3Lipid/detergent 77.4 68.8 69.3 50.0Water 47.7 46.9 44.3 38.8
Rms deviationsBond lengths, Å 0.007 0.006 0.006 0.011Bond angles, ° 1.012 0.936 1.003 1.306
*SAD (single-wavelength anomalous dispersion) indicates diffraction data taken at 7 keV near the absorption wavelength for vanadium.†Highest resolution shell is shown in parentheses.
Table S2. Data completeness after anisotropic truncation
AMP-PNP ADP-VO4 ADP-AlF4 ADP-BeF3
Resolution, Å20.00–6.61 20.00–7.14 20.00–6.88 20.00–6.886.61–4.80 7.14–5.22 6.88–5.01 6.88–5.014.80–3.96 5.22–4.31 5.01–4.14 5.01–4.143.96–3.45 4.31–3.75 4.14–3.60 4.14–3.603.45–3.09 3.75–3.37 3.60–3.23 3.60–3.233.09–2.83 3.37–3.08 3.23–2.96 3.23–2.962.83–2.62 3.08–2.86 2.96–2.74 2.96–2.742.62–2.46 2.86–2.68 2.74–2.57 2.74–2.572.46–2.32 2.68–2.53 2.57–2.42 2.57–2.422.32–2.20 2.53–2.40 2.42–2.30 2.42–2.30
Completeness, %71.9 95.8 98.1 92.792.2 99.6 99.5 99.390.5 99.3 99.2 98.695.0 99.2 99.0 98.796.5 96.8 98.1 97.496.3 81.9 85.2 82.895.5 61.2 65.2 63.792.4 42.7 49.2 45.781.6 26.6 32.5 30.356.7 16.2 20.6 19.3
Oldham and Chen www.pnas.org/cgi/doi/10.1073/pnas.1108858108 4 of 4
