PDBsum entry 1ud7

Ubiquitin

PDB id: 1ud7

Contents

Protein chain

76 a.a. *

* Residue conservation analysis

PDB id:

1ud7

Name:

Ubiquitin

Title:

Solution structure of the designed hydrophobic core mutant of ubiquitin, 1d7

Structure:

Protein (ubiquitin core mutant 1d7). Chain: a. Engineered: yes. Mutation: yes

Source:

Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: plyss.

NMR struc:

20 models

Authors:

E.C.Johnson,G.A.Lazar,J.R.Desjarlais,T.M.Handel

Key ref:

E.C.Johnson et al. (1999). Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin. Structure Fold Des, 7, 967-976. PubMed id: 10467150 DOI: 10.1016/S0969-2126(99)80123-3

Date:

07-Apr-99 Release date: 06-May-99

Protein chain

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/S0969-2126(99)80123-3

Structure Fold Des 7:967-976 (1999)

PubMed id: 10467150

Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin.

E.C.Johnson, G.A.Lazar, J.R.Desjarlais, T.M.Handel.

ABSTRACT

BACKGROUND: The recent merger of computation and protein design has resulted in a burst of success in the generation of novel proteins with native-like properties. A critical component of this coupling between theory and experiment is a detailed analysis of the structures and stabilities of designed proteins to assess and improve the accuracy of design algorithms. RESULTS: Here we report the solution structure of a hydrophobic core variant of ubiquitin, referred to as 1D7, which was designed with the core-repacking algorithm ROC. As a measure of conformational specificity, we also present amide exchange protection factors and backbone and sidechain dynamics. The results indicate that 1D7 is similar to wild-type (WT) ubiquitin in backbone structure and degree of conformational specificity. We also observe a good correlation between experimentally determined sidechain structures and those predicted by ROC. However, evaluation of the core sidechain conformations indicates that, in general, 1D7 has more sidechains in less statistically favorable conformations than WT. CONCLUSIONS: Our results provide an explanation for the lower stability of 1D7 compared to WT, and suggest modifications to design algorithms that may improve the accuracy with which structure and stability are predicted. The results also demonstrate that core packing can affect conformational flexibility in subtle ways that are likely to be important for the design of function and protein-ligand interactions.

Selected figure(s)

Figure 1.
Figure 1. Structures of 1D7 versus WT. (a) Stereoview of an ensemble of the 20 lowest energy structures of 1D7. Sidechains of core residues are displayed in green and the N and C termini are labeled. (b) Superposition of the structure of 1D7 closest to the mean (blue) with the crystal structure (red; accession code 1UBI [15]) the coordinates of which were used for the design. (c) Residual dipolar NH couplings of partially oriented 1D7 (y axis) versus WT ubiquitin (x axis) in DMPC:DHPC bicelles [16]. WT dipolar couplings were taken from Cornilescu et al. [25]. The difference in the range of dipolar couplings between the two samples is due to differences in bicelle content.

The above figure is reprinted by permission from Cell Press: Structure Fold Des (1999, 7, 967-976) copyright 1999.

Figure was selected by an automated process.