PDBsum entry 2jnh

Ligase

PDB id: 2jnh

Contents

Protein chain

44 a.a. *

* Residue conservation analysis

PDB id:

2jnh

Name:

Ligase

Title:

Solution structure of the uba domain from cbl-b

Structure:

E3 ubiquitin-protein ligase cbl-b. Chain: a. Fragment: uba domain. Synonym: signal transduction protein cbl-b, sh3-binding protein cbl- b, casitas b-lineage lymphoma proto-oncogene b, ring finger protein 56. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cblb, rnf56. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

15 models

Authors:

C.Zhou,Z.Zhou,D.Lin,H.Hu

Key ref:

Z.R.Zhou et al. (2008). Differential ubiquitin binding of the UBA domains from human c-Cbl and Cbl-b: NMR structural and biochemical insights. Protein Sci, 17, 1805-1814. PubMed id: 18596201 DOI: 10.1110/ps.036384.108

Date:

24-Jan-07 Release date: 05-Feb-08

Protein chain

Q13191  (CBLB_HUMAN) -  E3 ubiquitin-protein ligase CBL-B from Homo sapiens

Seq: 982 a.a.

Struc: 44 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

DOI no: 10.1110/ps.036384.108

Protein Sci 17:1805-1814 (2008)

PubMed id: 18596201

Differential ubiquitin binding of the UBA domains from human c-Cbl and Cbl-b: NMR structural and biochemical insights.

Z.R.Zhou, H.C.Gao, C.J.Zhou, Y.G.Chang, J.Hong, A.X.Song, D.H.Lin, H.Y.Hu.

ABSTRACT

The Cbl proteins, RING-type E3 ubiquitin ligases, are responsible for ubiquitinating the activated tyrosine kinases and targeting them for degradation. Both c-Cbl and Cbl-b have a UBA (ubiquitin-associated) domain at their C-terminal ends, and these two UBA domains share a high sequence similarity (75%). However, only the UBA from Cbl-b, but not from c-Cbl, can bind ubiquitin (Ub). To understand the mechanism by which the UBA domains specifically interact with Ub with different affinities, we determined the solution NMR structures of these two UBA domains, cUBA from human c-Cbl and UBAb from Cbl-b. Their structures show that these two UBA domains share the same fold, a compact three-helix bundle, highly resembling the typical UBA fold. Chemical shift perturbation experiments reveal that the helix-1 and loop-1 of UBAb form a predominately hydrophobic surface for Ub binding. By comparing the Ub-interacting surface on UBAb and its counterpart on cUBA, we find that the hydrophobic patch on cUBA is interrupted by a negatively charged residue Glu12. Fluorescence titration data show that the Ala12Glu mutant of UBAb completely loses the ability to bind Ub, whereas the mutation disrupting the dimerization has no significant effect on Ub binding. This study provides structural and biochemical insights into the Ub binding specificities of the Cbl UBA domains, in which the hydrophobic surface distribution on the first helix plays crucial roles in their differential affinities for Ub binding. That is, the amino acid residue diversity in the helix-1 region, but not the dimerization, determines the abilities of various UBA domains binding with Ub.

Selected figure(s)

Figure 3.
Both cUBA and UBAb domain structures are stabilized by a hydrophobic core. (A) Hydrophobic core of cUBA. The side chains of the residues in the hydrophobic core are displayed in neon style (orange); these residues include Leu7, Ile11, Leu14, Ile24, Leu28, Ile35, Ala38, and Leu42. (B) Hydrophobic core of UBAb. The core residues are Val7, Ile11, Leu14, Val24, Leu28, Val35, Ala38, and Leu42. (C) Overlay of the secondary structure elements of cUBA (cyan) and UBAb (red).

Figure 6.
Comparison of the electrostatic surfaces of cUBA (A) and UBAb (B). The orientation of both cUBA and UBAb is identical to that of panels C and D in Figure 4 Figure 4.-. The positive charges are shown in blue, and the negative charges are colored in red. The surface presentation shows that the Ub recognition surface on UBAb is predominately hydrophobic with positively charged edges while the corresponding surface on cUBA is something negatively charged in the center. The Ub recognition surface on UBAb and its counterpart on cUBA are highlighted by green parallelograms and labeled with amino acid residues. The dimeric interfaces (indicated by green circles) of cUBA (C) and UBAb (D) are rotated by [similar]180[deg] relative to those in A and B, respectively. Residues I30 and I41 that are involved in homodimerization are labeled. The PDB codes for the structures are 2JUJ for cUBA and 2JNH for UBAb. (E) Glutamic acid; (A) alanine; (I) isoleucine.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2008, 17, 1805-1814) copyright 2008.

Figures were selected by the author.