PDBsum entry 1dkd

Chaperone

PDB id: 1dkd

Contents

Protein chains

146 a.a. *

11 a.a. *

12 a.a. *

Waters ×96

* Residue conservation analysis

PDB id:

1dkd

Name:

Chaperone

Title:

Crystal structure of a groel (apical domain) and a dodecameric peptide complex

Structure:

Groel. Chain: a, b, c, d. Fragment: apical domain. Synonym: chaperone hsp60. Engineered: yes. 12-mer peptide. Chain: e, f, g, h. Engineered: yes. Other_details: selected from phage display peptide library

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized and was selected from phage display peptide library.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.10Å R-factor: 0.215 R-free: 0.264

Authors:

L.Chen,P.B.Sigler

Key ref:

L.Chen and P.B.Sigler (1999). The crystal structure of a GroEL/peptide complex: plasticity as a basis for substrate diversity. Cell, 99, 757-768. PubMed id: 10619429 DOI: 10.1016/S0092-8674(00)81673-6

Date:

07-Dec-99 Release date: 12-Jan-00

Protein chains

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

Seq: 548 a.a.

Struc: 146 a.a.

Protein chains

No UniProt id for this chain

Struc: 11 a.a.

Protein chain

No UniProt id for this chain

Struc: 12 a.a.

Enzyme reactions

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

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

reference

DOI no: 10.1016/S0092-8674(00)81673-6

Cell 99:757-768 (1999)

PubMed id: 10619429

The crystal structure of a GroEL/peptide complex: plasticity as a basis for substrate diversity.

L.Chen, P.B.Sigler.

ABSTRACT

The chaperonin GroEL is a double toriodal assembly that with its cochaperonin GroES facilitates protein folding with an ATP-dependent mechanism. Nonnative conformations of diverse protein substrates bind to the apical domains surrounding the opening of the double toroid's central cavity. Using phage display, we have selected peptides with high affinity for the isolated apical domain. We have determined the crystal structures of the complexes formed by the most strongly bound peptide with the isolated apical domain, and with GroEL. The peptide interacts with the groove between paired alpha helices in a manner similar to that of the GroES mobile loop. Our structural analysis, combined with other results, suggests that various modes of molecular plasticity are responsible for tight promiscuous binding of nonnative substrates and their release into the shielded cis assembly.

Selected figure(s)

Figure 4.
Figure 4. Structural Comparisons of Three Peptides Interacting with Helices H and I of the Apical DomainSBP is yellow, the GroES mobile loop ([46]) is cyan, the N-terminal extension of the apical domain ( [6]) is magenta, and helices H and I are red.(A) Superposition of Cα coordinates of the apical domain of three structures, showing the backbone of three different peptides bound over the peptide-binding groove formed by helix H and helix I. Structure of the helices displayed here is taken from the structure of the SBP/apical domain complex.(B–D) Molecular surfaces color coded by curvature (green for convex, and gray for concave) of the binding groove in SBP/apical domain, GroEL/GroES/(ADP)[7], and N-terminal extension/apical domain, respectively. The orientation in these three figures is the same as in (A). For clarity, only side chains of residues located at the C-terminal arms of the β turn of the SBP (starting from W7) and the GroES mobile loop (starting from I25) are shown, as these segments form most of the contacts with the binding site. The N-terminal arms of the β turn of these two peptides are shown as a Cα trace. Residues in the peptides that form extensive side chain interactions with the binding site are labeled.(A) was produced using MOLSCRIPT and RASTER 3D ([22 and 31]), and (B)–(D) were generated with GRASP ( [32]).

Figure 6.
Figure 6. Molecular Surface Representation of the Substrate-Binding Sites in GroELThe molecular surface of the binding sites formed by helices H and I is highlighted in red. The binding sites form “elastic rings” located on the opening of the GroEL central cavities.(A) Top view of GroEL.(B) Stereo view of the central cavities of binding-competent GroEL.The three subunits from each of the rings nearest the reader were removed to show the inside of the central cavities. Figures were generated in GRASP ([32]).

The above figures are reprinted by permission from Cell Press: Cell (1999, 99, 757-768) copyright 1999.

Figures were selected by an automated process.