PDBsum entry 3qml

Chaperone/protein transport

PDB id: 3qml

Contents

Protein chains

377 a.a.

262 a.a.

273 a.a.

Ligands

PO4 ×8

Metals

_MG ×3

Waters ×206

PDB id:

3qml

Name:

Chaperone/protein transport

Title:

The structural analysis of sil1-bip complex reveals the mechanism for sil1 to function as a novel nucleotide exchange factor

Structure:

78 kda glucose-regulated protein homolog. Chain: a, b. Fragment: unp residues 43-426. Synonym: grp-78, immunoglobulin heavy chain-binding protein homolog, bip. Engineered: yes. Nucleotide exchange factor sil1. Chain: c, d. Fragment: unp residues 113-421.

Source:

Saccharomyces cerevisiae. Brewer's yeast,lager beer yeast,yeast. Organism_taxid: 4932. Gene: kar2, grp78, ssd1, yjl034w, j1248. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: sil1, per100, sls1, yol031c. Expression_system_taxid: 562

Resolution:

2.31Å R-factor: 0.213 R-free: 0.271

Authors:

M.Yan,J.Z.Li,B.D.Sha

Key ref:

M.Yan et al. (2011). Structural analysis of the Sil1-Bip complex reveals the mechanism for Sil1 to function as a nucleotide-exchange factor. Biochem J, 438, 447-455. PubMed id: 21675960

Date:

04-Feb-11 Release date: 29-Jun-11

Protein chains

P16474  (BIP_YEAST) -  Endoplasmic reticulum chaperone BiP from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 682 a.a.

Struc: 377 a.a.

Protein chain

Q08199  (SIL1_YEAST) -  Nucleotide exchange factor SIL1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 421 a.a.

Struc: 262 a.a.

Protein chain

Q08199  (SIL1_YEAST) -  Nucleotide exchange factor SIL1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 421 a.a.

Struc: 273 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.3.6.4.10 - non-chaperonin molecular chaperone ATPase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

• Enzyme class 2: Chains C, D: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

Biochem J 438:447-455 (2011)

PubMed id: 21675960

Structural analysis of the Sil1-Bip complex reveals the mechanism for Sil1 to function as a nucleotide-exchange factor.

M.Yan, J.Li, B.Sha.

ABSTRACT

Sil1 functions as a NEF (nucleotide-exchange factor) for the ER (endoplasmic reticulum) Hsp70 (heat-shock protein of 70 kDa) Bip in eukaryotic cells. Sil1 may catalyse the ADP release from Bip by interacting directly with the ATPase domain of Bip. In the present study we show the complex crystal structure of the yeast Bip and the NEF Sil1 at the resolution of 2.3 Å (1 Å=0.1 nm). In the Sil1-Bip complex structure, the Sil1 molecule acts as a 'clamp' which binds lobe IIb of the Bip ATPase domain. The binding of Sil1 causes the rotation of lobe IIb ~ 13.5° away from the ADP-binding pocket. The complex formation also induces lobe Ib to swing in the opposite direction by ~ 3.7°. These conformational changes open up the nucleotide-binding pocket in the Bip ATPase domain and disrupt the hydrogen bonds between Bip and bound ADP, which may catalyse ADP release. Mutation of the Sil1 residues involved in binding the Bip ATPase domain compromise the binding affinity of Sil1 to Bip, and these Sil1 mutants also abolish the ability to stimulate the ATPase activity of Bip.