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

PDB id:

1kp8

Name:

Chaperone

Title:

Structural basis for groel-assisted protein folding from the crystal structure of (groel-kmgatp)14 at 2.0 a resolution

Structure:

Groel protein. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n. Synonym: 60 kda chaperonin, protein cpn60, groel protein, ams. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.243 R-free: 0.258

Authors:

J.Wang

Key ref:

J.Wang and D.C.Boisvert (2003). Structural basis for GroEL-assisted protein folding from the crystal structure of (GroEL-KMgATP)14 at 2.0A resolution. J Mol Biol, 327, 843-855. PubMed id: 12654267 DOI: 10.1016/S0022-2836(03)00184-0

Date:

30-Dec-01 Release date: 25-Mar-03

Supersedes:

1der

Protein chains

P0A6F5  (CH60_ECOLI) -  Chaperonin GroEL from Escherichia coli (strain K12)

Seq: 548 a.a.

Struc: 525 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.5.6.1.7 - chaperonin ATPase.
• Reaction: ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide

ATP (Bound ligand (Het Group name = AGS) matches with 93.75% similarity) + H2O + folded polypeptide = ADP + phosphate + unfolded polypeptide

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S0022-2836(03)00184-0

J Mol Biol 327:843-855 (2003)

PubMed id: 12654267

Structural basis for GroEL-assisted protein folding from the crystal structure of (GroEL-KMgATP)14 at 2.0A resolution.

J.Wang, D.C.Boisvert.

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.

Selected figure(s)

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.

Figures were selected by an automated process.