PDBsum entry 1umh

Ligase

PDB id: 1umh

Contents

Protein chain

184 a.a. *

Metals

_NI

Waters ×112

* Residue conservation analysis

PDB id:

1umh

Name:

Ligase

Title:

Structural basis of sugar-recognizing ubiquitin ligase

Structure:

F-box only protein 2. Chain: a. Fragment: sbd domain. Synonym: fbs1. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: mouse. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.00Å R-factor: 0.155 R-free: 0.192

Authors:

T.Mizushima,T.Hirao,Y.Yoshida,S.J.Lee,T.Chiba,K.Iwai,Y.Yamaguchi, K.Kato,T.Tsukihara,K.Tanaka,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

T.Mizushima et al. (2004). Structural basis of sugar-recognizing ubiquitin ligase. Nat Struct Mol Biol, 11, 365-370. PubMed id: 14990996 DOI: 10.1038/nsmb732

Date:

01-Oct-03 Release date: 06-Apr-04

Protein chain

Q80UW2  (FBX2_MOUSE) -  F-box only protein 2 from Mus musculus

Seq: 297 a.a.

Struc: 184 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.6.3.2.19 - Transferred entry: 2.3.2.23, 2.3.2.27 and 6.2.1.45.
• Reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine

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

reference

DOI no: 10.1038/nsmb732

Nat Struct Mol Biol 11:365-370 (2004)

PubMed id: 14990996

Structural basis of sugar-recognizing ubiquitin ligase.

T.Mizushima, T.Hirao, Y.Yoshida, S.J.Lee, T.Chiba, K.Iwai, Y.Yamaguchi, K.Kato, T.Tsukihara, K.Tanaka.

ABSTRACT

SCF(Fbs1) is a ubiquitin ligase that functions in the endoplasmic reticulum (ER)-associated degradation pathway. Fbs1/Fbx2, a member of the F-box proteins, recognizes high-mannose oligosaccharides. Efficient binding to an N-glycan requires di-N-acetylchitobiose (chitobiose). Here we report the crystal structures of the sugar-binding domain (SBD) of Fbs1 alone and in complex with chitobiose. The SBD is composed of a ten-stranded antiparallel beta-sandwich. The structure of the SBD-chitobiose complex includes hydrogen bonds between Fbs1 and chitobiose and insertion of the methyl group of chitobiose into a small hydrophobic pocket of Fbs1. Moreover, NMR spectroscopy has demonstrated that the amino acid residues adjoining the chitobiose-binding site interact with the outer branches of the carbohydrate moiety. Considering that the innermost chitobiose moieties in N-glycans are usually involved in intramolecular interactions with the polypeptide moieties, we propose that Fbs1 interacts with the chitobiose in unfolded N-glycoprotein, pointing the protein moiety toward E2 for ubiquitination.

Selected figure(s)

Figure 1.
Figure 1. Tertiary structure of SBD in Fbs1. (a) Overall structure of SBD of Fbs1 shown as a ribbon diagram. -strands belonging to S1 and S2 are blue and red, respectively. Loops and helices are black and yellow, respectively. (b) A topology diagram of SBD. The -helices are yellow cylinders labeled 1 and 2. The -strands are arrows labeled 1 - 10. The left and right forms of -strands correspond to S1 and S2, respectively, as in a. N and C, N and C termini, respectively. (c) Amino acid sequences of SBD in Fbs1 and corresponding region of Fbs2. Amino acid residues are numbered in the N-to-C direction, for example, from position 117 to position 297 (C-terminal end) of Fbs1, and from 69 to 295 (C-terminal end) of Fbs2. Identical residues are boxed. Secondary structure elements are colored as a. Substrate-binding residues are red characters.

Figure 2.
Figure 2. Structure of SBD in complex with chitobiose. (a) Stereo view of the difference-density map (F[o] - F[c] with phase from the Fbs1 model) of binding chitobiose, contoured at 2.1 , modeled into the electron density. -strands belonging to S1 and S2 are blue and red, respectively. Loops are black. The bound chitobiose is orange, and the residues involved in the substrate binding (FYWK, see Fig. 1c) are green. (b) Molecular surface representation of the chitobiose-binding region. The bound chitobiose is shown in ball-and-stick representation. Two GlcNAc residues are represented by A and B. Cyan spheres are two water molecules of wild type SBD that are fixed on the molecular surface through hydrogen bonds with the backbone N and O of Lys281, respectively. These water molecules are replaced by O3 and O6 of the chitobiose upon formation of the SBD -chitobiose complex. (c) Stick representation of the amino acids involved in binding. Hydrogen bonds are dashed lines. Oxygen and nitrogen are red and blue, respectively. Symbols of two water molecules are as in b.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 365-370) copyright 2004.

Figures were selected by an automated process.