Volume 3, Issue 3, Pages 299-307 (March 1995) Activity of the MAP kinase ERK2 is controlled by a flexible surface loop Jiandong Zhang, Faming Zhang, Douglas Ebert, Melanie H Cobb, Elizabeth J Goldsmith Structure Volume 3, Issue 3, Pages 299-307 (March 1995) DOI: 10.1016/S0969-2126(01)00160-5
Figure 1 Ribbon diagram of ERK2 drawn by Molscript [34]. (a) Standard kinase view; (b) view 45° rotation about the vertical axis. The disordered regions in the mutant Y185E or the double mutant T183E/Y185E are shown in black; the lip and loop199–205 are defined by residues 173–197 and 202–203, respectively. The ‘C loop’ is the catalytic loop, subdomain VI. The ‘P loop’ is the phosphate-binding site for ATP. The nomenclature used is based on the secondary-structure elements assigned in [18]. Intervening sequences, or linkers, are labeled L based on the terminology in [17], starting at L0, at the N-terminal extension from the core kinase domain. A few short helices that are not assigned in [18], are labelled here as linkers. α2L12 refers to the second helix in L12, etc. Structure 1995 3, 299-307DOI: (10.1016/S0969-2126(01)00160-5)
Figure 1 Ribbon diagram of ERK2 drawn by Molscript [34]. (a) Standard kinase view; (b) view 45° rotation about the vertical axis. The disordered regions in the mutant Y185E or the double mutant T183E/Y185E are shown in black; the lip and loop199–205 are defined by residues 173–197 and 202–203, respectively. The ‘C loop’ is the catalytic loop, subdomain VI. The ‘P loop’ is the phosphate-binding site for ATP. The nomenclature used is based on the secondary-structure elements assigned in [18]. Intervening sequences, or linkers, are labeled L based on the terminology in [17], starting at L0, at the N-terminal extension from the core kinase domain. A few short helices that are not assigned in [18], are labelled here as linkers. α2L12 refers to the second helix in L12, etc. Structure 1995 3, 299-307DOI: (10.1016/S0969-2126(01)00160-5)
Figure 2 The phosphorylation lip region drawn in INSIGHT. Regions that are disordered in the mutants are colored as follows: the phosphorylation lip is yellow, residues S200–Y203 in loop199–205 are purple, and E251–1254 in L14 are brown. β-strands are shown in green and α-helices are shown in dark blue with other regions in lighter blue. The carbon atoms of hydrophobic residues are colored green and those of polar or charged residues are colored purple. A sulfate ion is shown as red and yellow spheres. Hydrogen bonds are shown as dashed lines. Structure 1995 3, 299-307DOI: (10.1016/S0969-2126(01)00160-5)
Figure 3 Stereodiagram emphasizing the interaction between the lip and loop199–205 region. Structure 1995 3, 299-307DOI: (10.1016/S0969-2126(01)00160-5)
Figure 4 Electron-density maps drawn in O [29]. (a) The 2Fo–Fc map of the wild-type ERK2 around the lip calculated with data from 6–2.3 å contoured at 1.25σ. (b) T183E difference map computed with (|Fomutant|-|Fowild-type|) coefficients from 20–2.3 å and native model-derived phases (a) contoured at 2.5σ. Positive density is shown in blue. Negative density is shown in brown. (c) The (|Fo(mutant)|–|Fo(wild-type)| T183E/Y185E contoured at -2.5σ. (d) The 2Fo–Fc map of T183E/Y185E computed with refined phases and contoured at 1.25σ. Structure 1995 3, 299-307DOI: (10.1016/S0969-2126(01)00160-5)
Figure 4 Electron-density maps drawn in O [29]. (a) The 2Fo–Fc map of the wild-type ERK2 around the lip calculated with data from 6–2.3 å contoured at 1.25σ. (b) T183E difference map computed with (|Fomutant|-|Fowild-type|) coefficients from 20–2.3 å and native model-derived phases (a) contoured at 2.5σ. Positive density is shown in blue. Negative density is shown in brown. (c) The (|Fo(mutant)|–|Fo(wild-type)| T183E/Y185E contoured at -2.5σ. (d) The 2Fo–Fc map of T183E/Y185E computed with refined phases and contoured at 1.25σ. Structure 1995 3, 299-307DOI: (10.1016/S0969-2126(01)00160-5)
Figure 4 Electron-density maps drawn in O [29]. (a) The 2Fo–Fc map of the wild-type ERK2 around the lip calculated with data from 6–2.3 å contoured at 1.25σ. (b) T183E difference map computed with (|Fomutant|-|Fowild-type|) coefficients from 20–2.3 å and native model-derived phases (a) contoured at 2.5σ. Positive density is shown in blue. Negative density is shown in brown. (c) The (|Fo(mutant)|–|Fo(wild-type)| T183E/Y185E contoured at -2.5σ. (d) The 2Fo–Fc map of T183E/Y185E computed with refined phases and contoured at 1.25σ. Structure 1995 3, 299-307DOI: (10.1016/S0969-2126(01)00160-5)
Figure 4 Electron-density maps drawn in O [29]. (a) The 2Fo–Fc map of the wild-type ERK2 around the lip calculated with data from 6–2.3 å contoured at 1.25σ. (b) T183E difference map computed with (|Fomutant|-|Fowild-type|) coefficients from 20–2.3 å and native model-derived phases (a) contoured at 2.5σ. Positive density is shown in blue. Negative density is shown in brown. (c) The (|Fo(mutant)|–|Fo(wild-type)| T183E/Y185E contoured at -2.5σ. (d) The 2Fo–Fc map of T183E/Y185E computed with refined phases and contoured at 1.25σ. Structure 1995 3, 299-307DOI: (10.1016/S0969-2126(01)00160-5)
Figure 5 (a) Plot of B-factors (temperature factors in å) of the main-chain atoms as a function of sequence of the wild-type ERK2. The average B-factor of ordered main-chain atoms is 29.8 å2. The average B-factor of the main-chain atoms from residues 63–327 is 24.5 å2, from residues 17–62 and from residues 328–358 is 52.9 å2. (b) Plot of shifts in B-factor of main-chain atoms in ERK2 mutants relative to wild-type. In T183E/Y185E, the B-factor shifts for the indicated residues were as follows: residues 58–63 over 35 å2, 173–187 over 45 å2, 197–203 over 30 å2, and 248–254 over 25 å2. In T183E, the lip region has B-factor shifts over 30 å2, and residues 198–203 over 20 å2. Structure 1995 3, 299-307DOI: (10.1016/S0969-2126(01)00160-5)
Figure 5 (a) Plot of B-factors (temperature factors in å) of the main-chain atoms as a function of sequence of the wild-type ERK2. The average B-factor of ordered main-chain atoms is 29.8 å2. The average B-factor of the main-chain atoms from residues 63–327 is 24.5 å2, from residues 17–62 and from residues 328–358 is 52.9 å2. (b) Plot of shifts in B-factor of main-chain atoms in ERK2 mutants relative to wild-type. In T183E/Y185E, the B-factor shifts for the indicated residues were as follows: residues 58–63 over 35 å2, 173–187 over 45 å2, 197–203 over 30 å2, and 248–254 over 25 å2. In T183E, the lip region has B-factor shifts over 30 å2, and residues 198–203 over 20 å2. Structure 1995 3, 299-307DOI: (10.1016/S0969-2126(01)00160-5)