PDBsum entry 1mnf

Chaperone

PDB id: 1mnf

Contents

Protein chains

(+ 8 more) 525 a.a. *

(+ 8 more) 12 a.a. *

Waters ×213

* Residue conservation analysis

PDB id:

1mnf

Name:

Chaperone

Title:

Domain motions in groel upon binding of an oligopeptide

Structure:

Groel protein. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n. Synonym: protein cpn60, groel protein, ams. Engineered: yes. 12-residue peptide substrate. Chain: o, p, q, r, s, t, u, v, w, x, y, z, 1, 2. Synonym: sbp, strong binding peptide. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized.

Biol. unit:

28mer (from PQS)

Resolution:

3.00Å R-factor: 0.236 R-free: 0.259

Authors:

J.Wang,L.Chen

Key ref:

J.Wang and L.Chen (2003). Domain motions in GroEL upon binding of an oligopeptide. J Mol Biol, 334, 489-499. PubMed id: 14623189 DOI: 10.1016/j.jmb.2003.09.074

Date:

02-Dec-03 Release date: 07-Oct-03

Protein chains

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

Seq: 548 a.a.

Struc: 525 a.a.

Protein chains

No UniProt id for this chain

Struc: 12 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N: 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/j.jmb.2003.09.074

J Mol Biol 334:489-499 (2003)

PubMed id: 14623189

Domain motions in GroEL upon binding of an oligopeptide.

J.Wang, L.Chen.

ABSTRACT

GroEL assists protein folding by preventing the interaction of partially folded molecules with other non-native proteins. It binds them, sequesters them, and then releases them so that they can fold in an ATP-driven cycle. Previous studies have also shown that protein substrates, GroES, and oligopeptides bind to partially overlapped sites on the apical domain surfaces of GroEL. In this study, we have determined the crystal structure at 3.0A resolution of a symmetric (GroEL-peptide)(14) complex. The binding of each of these small 12 amino acid residue peptides to GroEL involves interactions between three adjacent apical domains of GroEL. Each peptide interacts primarily with a single GroEL subunit. Residues R231 and R268 from adjacent subunits isolate each substrate-binding pocket, and prevent bound substrates from sliding into adjacent binding pockets. As a consequence of peptide binding, domains rotate and inter-domain interactions are greatly enhanced. The direction of rotation of the apical domain of each GroEL subunit is opposite to that of its intermediate domain. Viewed from outside, the apical domains rotate clockwise within one GroEL ring, while the ATP-induced apical domain rotation is counter-clockwise.

Selected figure(s)

Figure 3.
Figure 3. Peptide-induced domain rotations. A, Subunit comparison in a view approximately perpendicular to the 7-fold axis. B, View along the 7-fold axis. All subunits are superimposed using equatorial domains (cyan). Subunits in the apo structure[33.] are in cyan. Domains of subunits in this structure are green and red for the intermediate and apical domains, respectively. Red and green arrows indicate the rotations of the apical and intermediate domains in this structure.

Figure 4.
Figure 4. Peptide-induced domain rotations are distinct from ATP-induced ones. A, View nearly perpendicular to the 7-fold axis. B, View along the 7-fold axis. Averaged coordinates are used for the apo structure[33.] (cyan), the KMgATP bound structure [30.] (silver), and this complex structure (apical domain, red; intermediate domain, green; and equatorial domain, cyan) with the bound peptide in yellow. Arrows indicate the rotations of both intermediate and apical domains upon binding of ATP.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 334, 489-499) copyright 2003.

Figures were selected by an automated process.