PDBsum entry 2gbm

Protein binding

PDB id: 2gbm

Contents

Protein chains

81 a.a. *

Ligands

ARS ×3

Waters ×361

* Residue conservation analysis

PDB id:

2gbm

Name:

Protein binding

Title:

Crystal structure of the 35-36 8 glycine insertion mutant of ubiquitin

Structure:

Ubiquitin. Chain: a, b, c, d. Engineered: yes

Source:

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

Resolution:

1.55Å R-factor: 0.213 R-free: 0.227

Authors:

D.M.Ferraro,D.J.Ferraro,S.Ramaswamy,A.D.Robertson

Key ref:

D.M.Ferraro et al. (2006). Structures of ubiquitin insertion mutants support site-specific reflex response to insertions hypothesis. J Mol Biol, 359, 390-402. PubMed id: 16647719 DOI: 10.1016/j.jmb.2006.03.047

Date:

10-Mar-06 Release date: 16-May-06

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 81 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2006.03.047

J Mol Biol 359:390-402 (2006)

PubMed id: 16647719

Structures of ubiquitin insertion mutants support site-specific reflex response to insertions hypothesis.

D.M.Ferraro, D.J.Ferraro, S.Ramaswamy, A.D.Robertson.

ABSTRACT

We previously concluded that, judging from NMR chemical shifts, the effects of insertions into ubiquitin on its conformation appear to depend primarily on the site of insertion rather than the sequence of the insertion. To obtain a more complete and atomic-resolution understanding of how these insertions modulate the conformation of ubiquitin, we have solved the crystal structures of four insertional mutants of ubiquitin. Insertions between residues 9 and 10 of ubiquitin are minimally perturbing to the remainder of the protein, while larger alterations occur when the insertion is between residues 35 and 36. Further, the alterations in response to insertions are very similar for each mutant at a given site. Two insertions, one at each site, were designed from structurally homologous proteins. Interestingly, the secondary structure within these five to seven amino acid residue insertions is conserved in the new protein. Overall, the crystal structures support the previous conclusion that the conformational effects of these insertions are determined largely by the site of insertion and only secondarily by the sequence of the insert.

Selected figure(s)

Figure 1.
Figure 1. Predicted effects of insertions at the 35-36 loop on ubiquitin structure.10 Residues 9 and 10 are shown in red and residues 35 and 36 are shown in green. The curved arrow indicates the predicted bend of the helix away from the 35-36 loop insertion site. The straight arrows indicate the predicted hydrogen bond lengthening of the sheet near the insertion site and shortening away from the insertion site.

Figure 3.
Figure 3. Global alignments of loop insertion mutant structures (green) to wild-type ubiquitin (blue). Alignments were calculated in the program Indonesia (Madsen et al., unpublished) and Figures were generated using PyMol (http://pymol.sourceforge.net/). Residues that lack electron density are shown with transparency. (a) 9-10 G8 chain A versus wild-type. (b) 9-10 MoaD chain A versus wild-type. (c) 35-36 G8 chain A versus wild-type. (d) 35-36 MoaD chain B versus wild-type.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 390-402) copyright 2006.

Figures were selected by an automated process.