PDBsum entry 1kp8

Chaperone

PDB id: 1kp8

Contents

Protein chains

(+ 8 more) 525 a.a. *

Ligands

SO4 ×22

AGS ×14

Metals

_MG ×14

__K ×16

Waters ×2541

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural basis for groel-Assisted protein folding from the crystal structure of (groel-Kmgatp)14 at 2.0a resolution.

Authors

J.Wang, D.C.Boisvert.

Ref.

J Mol Biol, 2003, 327, 843-855. [DOI no: 10.1016/S0022-2836(03)00184-0]

PubMed id

12654267

Abstract

Nucleotide regulates the affinity of the bacterial chaperonin GroEL for protein substrates. GroEL binds protein substrates with high affinity in the absence of ATP and with low affinity in its presence. We report the crystal structure of (GroEL-KMgATP)(14) refined to 2.0 A resolution in which the ATP triphosphate moiety is directly coordinated by both K(+) and Mg(2+). Upon the binding of KMgATP, we observe previously unnoticed domain rotations and a 102 degrees rotation of the apical domain surface helix I. Two major consequences are a large lateral displacement of, and a dramatic reduction of hydrophobicity in, the apical domain surface. These results provide a basis for the nucleotide-dependent regulation of protein substrate binding and suggest a mechanism for GroEL-assisted protein folding by forced unfolding.

Figure 1.
Figure 1. The KMgATP binding site and a model for ATP hydrolysis. (A) An electron density map is contoured at 4s (green) and 6s (magenta) in the s[A]-weighted residual F[o] -F[c] map using the final model with all coordinated water molecules removed. Coordination bonds to metal ions are shown in green, coordination polyhedron in silver, and hydrogen bonds in red dashes. Coordination bond lengths calculated from all 14 subunits for Mg to O2a, O1b, O3g, W555, W556, and D87 are 2.24(±0.07), 2.32(±0.10), 2.21(±0.08), 2.27(±0.14), 2.10(±0.11), and 2.33(±0.05) Å, respectively. The coordination bond lengths for K to O1a, W551, W552, W553, W554, T30, and K51 are 2.55(±0.05), 2.50(±0.06), 2.78(±0.06), 2.60(±0.10), 2.59(±0.09), 2.59(±0.05), and 2.53(±0.08) Å, respectively. (B) A hypothetical attacking hydroxyl ("W999") for ATP hydrolysis is placed on the line connecting D52 to the gP atom at a distance of 2.8 Å to D52.

Figure 6.
Figure 6. Structure-based GroEL-assisted protein folding pathways. The affinity of GroEL for protein substrate at the apical domain and ATP at the equatorial is labeled as H for high and L for low; the underlined labels are asymmetric within each ring and the lowercase indicates the process of switching. Dashed and dotted arrows are minor alternative pathways. The lower pathway is for large protein substrates that cannot be encapsulated inside the GroEL/GroES cavity. The upper pathway is for small protein substrates that can be encapsulated. A minor upper pathway includes the migration of bound ATP from the trans-ring to the cis-ring, before the formation of the asymmetric GroEL/GroES complex. The formation of the GroEL/GroES complex always requires the binding of ATP in the cis-ring. ATP hydrolysis leads to the dead-end GroEL/ES asymmetric complex, which can only be disassembled by the binding of ATP in the low affinity sites of the trans-ring. The symmetric (GroES)[7](GroEL)[14](GroES)[7] complex, which has been observed under the physiological conditions,[8., 9., 10. and 11.] is not included in the diagram, because it has no accessible binding sites for the protein substrates and may represent a storage form for the excess chaperonins.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 843-855) copyright 2003.

Secondary reference #1

Title

The 2.4 a crystal structure of the bacterial chaperonin groel complexed with ATP gamma s.

Authors

D.C.Boisvert, J.Wang, Z.Otwinowski, A.L.Horwich, P.B.Sigler.

Ref.

Nat Struct Biol, 1996, 3, 170-177.

PubMed id

8564544

Secondary reference #2

Title

The crystal structure of the bacterial chaperonin groel at 2.8 a.

Authors

K.Braig, Z.Otwinowski, R.Hegde, D.C.Boisvert, A.Joachimiak, A.L.Horwich, P.B.Sigler.

Ref.

Nature, 1994, 371, 578-586.

PubMed id

7935790

Secondary reference #3

Title

Conformational variability in the refined structure of the chaperonin groel at 2.8 a resolution.

Authors

K.Braig, P.D.Adams, A.T.Brünger.

Ref.

Nat Struct Biol, 1995, 2, 1083-1094.

PubMed id

8846220

Secondary reference #4

Title

The crystal structure of the asymmetric groel-Groes-(Adp)7 chaperonin complex.

Authors

Z.Xu, A.L.Horwich, P.B.Sigler.

Ref.

Nature, 1997, 388, 741-750. [DOI no: 10.1038/41944]

PubMed id

9285585

Figure 1.
Figure 1 Overall architecture and dimensions of the GroEL-GroES complex. a, Van der Waals space-filling model of the entire complex in a top view looking down from the GroES-binding (cis) side; b, as a, but in a side view. The complex is colour coded as follows: trans GroEL ring, red; cis GroEL ring, green; GroES, gold. c, C drawing of the 'inside' of the GroEL-GroES complex. The view was produced by cutting the assembly open with a plane containing the 7-fold axis. ADP molecules bound to cis GroEL ring are shown as space-filling models. a, b, Produced using MidasPlus (Computer Graphics Laboratory, University of California, San Francisco); c, produced using program O53.

Figure 6.
Figure 6 Nucleotide-binding site in the cis ring of the GroEL-GroES complex. a, Stereo pair of a SigmaA-weighted 2F[o] - F[c] electron-density map contoured at 2 showing the ADP-binding pocket in a subunit of the cis GroEL ring. ADP, white, protein, yellow. 'Mg' denotes a bound magnesium ion. b, Stereo view of direct Mg2+-ADP interactions with the protein. The protein is shown as a skeletal model and is coloured as in Fig. 2. The ADP is a white ball-and-stick model, the Mg2+ is a red sphere, hydrogen bonds are shown as white dotted lines and magnesium coordinations are red dotted lines. c, Schematic representation of direct Mg2+-ADP interactions with the protein (less than 3.2 å). Amino-acid residues from the equatorial domain are blue, and those from the intermediate domain are green, as in Fig. 2. Hydrogen bonds are shown as single-arrow dashed lines, and magnesium coordinations are shown as double-arrow dashed lines. Residues interacting with ADP through van der Waals contacts are shown along a curved line. OG, OG1, OD1, OD2 and NH stand for O , O 1, O 1, O 2 and peptide NH, respectively. a, Produced using O53; b, produced using InsightII (BioSym Technology).

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd