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Results: 7

1.
Figure 7

Figure 7. From: STRUCTURAL AND KINETIC STUDIES OF INDUCED FIT IN XYLULOSE KINASE FROM E. COLI.

The proposed catalytic mechanism for XK.

Eric DI LUCCIO, et al. J Mol Biol. ;365(3):783-798.
2.
Figure 3

Figure 3. From: STRUCTURAL AND KINETIC STUDIES OF INDUCED FIT IN XYLULOSE KINASE FROM E. COLI.

Sugar substrates used in substrate specificity studies

Eric DI LUCCIO, et al. J Mol Biol. ;365(3):783-798.
3.
Figure 6

Figure 6. From: STRUCTURAL AND KINETIC STUDIES OF INDUCED FIT IN XYLULOSE KINASE FROM E. COLI.

Pairwise sequence alignment of XK and ecGK. Green designates residues involved in tetramer formation in ecGK; yellow, the XK hinge segment; red, the dimeric interface of both XK end ecGK. Residues composing each XK domain and subdomain are as follows: domain I, 1-293; subdomain IA, (1-76, 151-161, 224-242); subdomain IB (77-105, 162-223, 243-245); domain II, 246-484; subdomain IIA (246-264, 282-307, 358-418); subdomain IIB (265-281, 308-357, 419-484).

Eric DI LUCCIO, et al. J Mol Biol. ;365(3):783-798.
4.

Figure 1. From: STRUCTURAL AND KINETIC STUDIES OF INDUCED FIT IN XYLULOSE KINASE FROM E. COLI.

The main chain trace of XK. A) A stereo view of XK looking into the substrate binding cleft. The molecule is colored from red (domain IA), pink (domain IB) to blue (domain IIA) and light blue (domain IIB). The hinge segment is colored yellow. B) A stereo view of the side of the enzyme emphasizing the deep substrate binding groove. Figures 1 and 5 were done using PyMOL (DeLano Scientific).

Eric DI LUCCIO, et al. J Mol Biol. ;365(3):783-798.
5.

Figure 4. From: STRUCTURAL AND KINETIC STUDIES OF INDUCED FIT IN XYLULOSE KINASE FROM E. COLI.

Kinetic results and proposed kinetic mechanism. A) Double-reciprocal plot of initial rate data for XK with D-xylulose varied at MgATP concentrations of 0.05 mM, squares; 0.13 mM, circles; 0.49 mM, triangles up; 1.46 mM, diamonds; 2.44 mM, hexagons; 4.88 mM, triangles down. Lines are calculated from a non linear fit of the data to eq. 2 B) Uncompetitive inhibition of 0.99 mM AMPPNP (circles) versus D -xylulose at 0.17 mM ATP. C) Substrate inhibition by ATP at 0.28 mM xylulose; squares uninhibited, circles 0.184 mM 5-F-xylulose. D) The kinetic mechanism for XK appears to involve ordered substrate binding with the sugar (A) binding first and MgATP (B) second. The formation of a dead-end EIB complex results in substrate inhibition by B.

Eric DI LUCCIO, et al. J Mol Biol. ;365(3):783-798.
6.

Figure 5. From: STRUCTURAL AND KINETIC STUDIES OF INDUCED FIT IN XYLULOSE KINASE FROM E. COLI.

Substrate-induced conformational changes in XK and modeling of the ternary structure using ecGK. A) A stereo view of domains I overlaps from apo XK (blue), xylulose bound XK (green) and the ecGK ternary complex (red) shows a ~37° opening of the former relative to the latter. The domain motion is indicated. B) Model of the XK ternary complex in open conformation (left) and closed ternary structure of ecGK (right) both in the same relative orientation. C) 2Fo-Fc electron density maps of the xylulose binding site contoured at 1.2σ (blue) and Fo-Fc electron density at 2σ for xylulose (red). Hydrogen bonds are shown with a dashed yellow line. D) Interactions details of both xylulose and MgATP in the XK active site model in closed-conformation. Hydrogen bonds are shown with a dashed yellow line. Xylulose carbons are shown in yellow. E) XK ternary complex model in closed conformation. A zoomed view of the active site is shown to illustrate interactions from various secondary structural elements.

Eric DI LUCCIO, et al. J Mol Biol. ;365(3):783-798.
7.

Figure 2. From: STRUCTURAL AND KINETIC STUDIES OF INDUCED FIT IN XYLULOSE KINASE FROM E. COLI.

Oligomeric structure of XK. A) The dimer observed within the asymmetric unit of XK resembles the O/Y dimer found in the allosterically-inhibited ecGK tetramer. A zoomed view of XK dimeric interface is shown and illustrates the interactions between β-interactions responsible for mediating the interface. B) A cryo-EM image of xylulose kinase particles in vitrified buffer. Arrows indicate dimeric XK particles. C) Some class averages. Number of particles in these classes with the panel size of 19.2 x 19.2 nm2: panel 1: 11; panel 2: 10; panel 3: 31; panel 4: 20; panel 5: 13; panel 6: 33; panel 7: 34; panel 8: 36; panel 9: 6; panel 10: 9. D) and E) Two views of the surface-rendered density map from cryo-EM limited to 36 Å resolution with and without the dimeric crystal structure superimposed. The surface threshold for the display of the 3D density map were chosen so that the included volume corresponds to 105.2 kDa, assuming a protein density of 0.82 Da/Å3 (1.35g/ml) and displayed using UCSF Chimera 55.

Eric DI LUCCIO, et al. J Mol Biol. ;365(3):783-798.

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