PDBsum entry 1kk8

Contractile protein

PDB id: 1kk8

Contents

Protein chains

793 a.a. *

139 a.a. *

154 a.a. *

Ligands

BEF-ADP

GOL

Metals

_MG ×2

_CA

Waters ×185

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystallographic findings on the internally uncoupled and near-Rigor states of myosin: further insights into the mechanics of the motor.

Authors

D.M.Himmel, S.Gourinath, L.Reshetnikova, Y.Shen, A.G.Szent-Györgyi, C.Cohen.

Ref.

Proc Natl Acad Sci U S A, 2002, 99, 12645-12650. [DOI no: 10.1073/pnas.202476799]

PubMed id

12297624

Abstract

Here we report a 2.3-A crystal structure of scallop myosin S1 complexed with ADP.BeF(x), as well as three additional structures (at 2.8-3.8 A resolution) for this S1 complexed with ATP analogs, some of which are cross-linked by para-phenyl dimaleimide, a short intramolecular cross-linker. In all cases, the complexes are characterized by an unwound SH1 helix first seen in an unusual 2.5-A scallop myosin-MgADP structure and described as corresponding to a previously unrecognized actin-detached internally uncoupled state. The unwinding of the SH1 helix effectively uncouples the converter/lever arm module from the motor and allows cross-linking by para-phenyl dimaleimide, which has been shown to occur only in weak actin-binding states of the molecule. Mutations near the metastable SH1 helix that disable the motor can be accounted for by viewing this structural element as a clutch controlling the transmission of torque to the lever arm. We have also determined a 3.2-A nucleotide-free structure of scallop myosin S1, which suggests that in the near-rigor state there are two conformations in the switch I loop, depending on whether nucleotide is present. Analysis of the subdomain motions in the weak actin-binding states revealed by x-ray crystallography, together with recent electron microscopic results, clarify the mechanical roles of the parts of the motor in the course of the contractile cycle and suggest how strong binding to actin triggers both the power stroke and product release.

Figure 1.
Fig. 1. Overview of the internally uncoupled scallop S1 conformation. (A) (Center) The internally uncoupled S1-ADP·BeF[x] structure (50-kDa upper subdomain is shown in red, 50-kDa lower subdomain is shown in pink, N-terminal subdomain is shown in blue, converter is shown in green, lever arm heavy chain is shown in purple, essential light chain is shown in cyan, regulatory light chain is shown in magenta). Notable features of the structure include the unusual position of the lever arm and the unwound SH1 helix. Three other scallop structures (S1-AMPPNP, S1-ATP[ -S]-p-PDM, and S1-ADP-p-PDM), as well as the previously reported scallop S1-MgADP (1), show the same conformation, although the orientations of the respective lever arms vary slightly. (Right Inset) Expanded view of the nucleotide binding size. (Left) Schematic diagram of the internally uncoupled conformation, showing the subdomains and the approximate location of the disordered SH1 helix (light chains not shown). (B) For comparison, a two-dimensional projection of the three weak actin-binding S1 conformations observed in scallop crystal structures (light chains not shown) (1, 2). The 50-kDa upper and N-terminal subdomains of the three structures are superimposed to show the large changes in the relative positions of the converter and lever arm (see also ref. 2). In each conformation, the 50-kDa lower subdomain adopts a slightly different position with respect to the 50-kDa upper and N-terminal subdomains, leading to a markedly different orientation of the converter. The converter, in turn, controls the position of the lever arm (1). Movement of the 50-kDa lower subdomain is not represented in this schematic diagram. This subdomain rotates to maintain contact with the converter as S1 adopts each of the three conformations. See Fig. 5 for a more detailed three-dimensional description of the subdomain motions.

Figure 4.
Fig. 4. Electron density for the cross-linker. Shown is the simulated annealing F[o] F[c] omit map for the electron density of p-PDM together with the cross-linker modeled into the structure of S1-ADP-p-PDM. To generate this map, contoured at the 3.0 level, residues C693 and K705 were omitted along with the p-PDM model. The SH1 helix is disordered, including the SH1 sulfhydryl (C703). Biochemical studies with rabbit muscle myosin have indicated that this thiol can be cross-linked to the SH2 sulfhydryl (C693) by p-PDM (15, 24, 25). However, this map reveals that, in scallop S1, p-PDM cross-links the SH2 sulfhydryl to the side chain of K705, instead of SH1. The scallop S1-ATP[ -S]-p-PDM structure gives the same result.

Secondary reference #1

Title

Atomic structure of scallop myosin subfragment s1 complexed with mgadp: a novel conformation of the myosin head.

Authors

A.Houdusse, V.N.Kalabokis, D.Himmel, A.G.Szent-Györgyi, C.Cohen.

Ref.

Cell, 1999, 97, 459-470. [DOI no: 10.1016/S0092-8674(00)80756-4]

PubMed id

10338210

Figure 3.
Figure 3. The ELC/Converter Interactions Modulate the Position of the Lever ArmDifferent positions of the converter in the three states result in major movements of the lever arm (see Figure 1 and Figure 2). This diagram illustrates how the converter and the ELC interact differently in chicken S1 (A), scallop S1 complexed with MgADP (B), and smooth MDE–AlF[4]^− (C). In this view, the converter (green) and the HP helix (yellow) appear to be in similar positions. Note that differences in the interactions between the C-terminal lobe of the ELC (pink) and the motor domain in these structures result in different bending of the heavy chain helix (cyan) after the first three turns (green) that are part of the converter.

Figure 5.
Figure 5. The Relay Controls the Position of the Converter to which It Is Linked by Strong Conserved InteractionsRibbon diagram of the interface between the relay (yellow) and the converter (β sheet and last helix in green) in chicken S1 (A), scallop S1 complexed with MgADP (B), and smooth MDE–AlF[4]^− (C) oriented so that the converters superimpose. Note that the orientation of the last three turns of the HP helix (yellow) is similar in all these structures, since three glutamate residues of this helix (brown) interact with residues of the converter (cyan) in all three states. In contrast, the conformation of the loop of the relay (yellow) is very different and is most rigid in (C) where it interacts with the SH1 helix (red). Conformational changes at both ends of the relay allow the orientation of the lower 50 kDa subdomain (white, HP and HQ helices) to differ with respect to that of the converter in these three states. Note also how the environment around the tryptophane residue (blue) of the relay varies in the three states.

The above figures are reproduced from the cited reference with permission from Cell Press