PDBsum entry: 1bt0

Signaling protein

PDB id: 1bt0

Contents

Protein chain

73 a.a. *

Ligands

EDO ×3

Metals

_ZN ×2

Waters ×75

* Residue conservation analysis

PDB id:

1bt0

Name:

Signaling protein

Title:

Structure of ubiquitin-like protein, rub1

Structure:

Protein (ubiquitin-like protein 7, rub1). Chain: a. Engineered: yes. Mutation: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.70Å R-factor: 0.180 R-free: 0.246

Authors:

W.P.Delacruz,A.J.Fisher

Key ref:

C.Rao-Naik et al. (1998). The rub family of ubiquitin-like proteins. Crystal structure of Arabidopsis rub1 and expression of multiple rubs in Arabidopsis. J Biol Chem, 273, 34976-34982. PubMed id: 9857029 DOI: 10.1074/jbc.273.52.34976

Date:

02-Sep-98 Release date: 30-Dec-98

Protein chain

Q9SHE7  (RUB1_ARATH) -  Ubiquitin-NEDD8-like protein RUB1

Seq: 156 a.a.

Struc: 73 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1074/jbc.273.52.34976

J Biol Chem 273:34976-34982 (1998)

PubMed id: 9857029

The rub family of ubiquitin-like proteins. Crystal structure of Arabidopsis rub1 and expression of multiple rubs in Arabidopsis.

C.Rao-Naik, W.delaCruz, J.M.Laplaza, S.Tan, J.Callis, A.J.Fisher.

ABSTRACT

Several proteins with significant identity to ubiquitin have been characterized recently. In contrast to ubiquitin's main role in targeting proteins for degradation, a described function of one family of ubiquitin-related proteins, the Rub family, is to serve as a stable post-translational modification of a complex involved in the G1-to-S cell cycle transition. Rub proteins have been found in animals, plants, and fungi and consist of 76 residues with 52-63% identity to ubiquitin. In this study three different RUB proteins within the plant Arabidopsis are identified; two differ by only 1 amino acid, while the third is only 77.6% identical to the other two. Genes encoding all three are expressed in multiple organs. In addition, we report the crystal structure of higher plant RUB1 at 1.7-A resolution to help elucidate the functional differences between Rub and ubiquitin. RUB1 contains a single globular domain with a flexible COOH-terminal extension. The overall RUB1 structure is very similar to ubiquitin. The majority of the amino acid differences between RUB1 and ubiquitin map to the surface. These changes alter the electrostatic surface potential in two regions and likely confer specificity between ubiquitin and RUB1 and their ubiquitin-activating enzyme (E1) or E1-like activating enzymes.

Selected figure(s)

Figure 3.
Fig. 3. Ribbon diagram of RUB1. Shown are all the secondary structure elements in RUB, which are conserved in ubiquitin (37). The last 3 residues at the carboxyl terminus (74-76) in RUB1 are not drawn because of poor electron density in this region and unsatisfactory refinement statistics when included.

Figure 5.
Fig. 5. Electrostatic potential surface map. Electrostatic surface comparison using the program GRASP (54) shows significant differences on one face of RUB1 (a) in comparison with the corresponding face of ubiquitin (b). The residues that contribute to the electronegative surface in RUB1 are Glu28 and Glu31, which are Ala and Gln, respectively, in ubiquitin. The opposite side of RUB1 (c) and ubiquitin (d) (view rotated 180° along the vertical from a and b), on the other hand, is highly conserved, with the exception of the presence of positively charged Lys4 and negatively charged Glu12 and Glu14 in RUB1. Blue denotes electropositive, while red denotes electronegative.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 34976-34982) copyright 1998.

Figures were selected by an automated process.