PDBsum entry 1gjz

Ubiquitin

PDB id: 1gjz

Contents

Protein chains

53 a.a. *

* Residue conservation analysis

PDB id:

1gjz

Name:

Ubiquitin

Title:

Solution structure of a dimeric n-terminal fragment of human ubiquitin

Structure:

Ubiquitin. Chain: a, b. Fragment: residues 1-51. Engineered: yes. Other_details: fragment contains first 51 residues of human ubiquitin preceded at the n-terminus by glycine and serine

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 511693.

NMR struc:

16 models

Authors:

D.Bolton,P.A.Evans,K.Stott,R.W.Broadhurst

Key ref:

D.Bolton et al. (2001). Structure and properties of a dimeric N-terminal fragment of human ubiquitin. J Mol Biol, 314, 773-787. PubMed id: 11733996 DOI: 10.1006/jmbi.2001.5181

Date:

06-Aug-01 Release date: 13-Dec-01

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 53 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1006/jmbi.2001.5181

J Mol Biol 314:773-787 (2001)

PubMed id: 11733996

Structure and properties of a dimeric N-terminal fragment of human ubiquitin.

D.Bolton, P.A.Evans, K.Stott, R.W.Broadhurst.

ABSTRACT

Previous peptide dissection and kinetic experiments have indicated that in vitro folding of ubiquitin may proceed via transient species in which native-like structure has been acquired in the first 45 residues. A peptide fragment, UQ(1-51), encompassing residues 1 to 51 of ubiquitin was produced in order to test whether this portion has propensity for independent self-assembly. Surprisingly, the construct formed a folded symmetrical dimer that was stabilised by 0.8 M sodium sulphate at 298 K (the S state). The solution structure of the UQ(1-51) dimer was determined by multinuclear NMR spectroscopy. Each subunit of UQ(1-51) consists of an N-terminal beta-hairpin followed by an alpha-helix and a final beta-strand, with orientations similar to intact ubiquitin. The dimer is formed by the third beta-strand of one subunit interleaving between the hairpin and third strand of the other to give a six-stranded beta-sheet, with the two alpha-helices sitting on top. The helix-helix and strand portions of the dimer interface also mimic related features in the structure of ubiquitin. The structural specificity of the UQ(1-51) peptide is tuneable: as the concentration of sodium sulphate is decreased, near-native alternative conformations are populated in slow chemical exchange. Magnetization transfer experiments were performed to characterize the various species present in 0.35 M sodium sulphate, namely the S state and two minor forms. Chemical shift differences suggest that one minor form is very similar to the S state, while the other experiences a significant conformational change in the third strand. A segmental rearrangement of the third strand in one subunit of the S state would render the dimer asymmetric, accounting for most of our results. Similar small-scale transitions in proteins are often invoked to explain solvent exchange at backbone amide proton sites that have an intermediate level of protection.

Selected figure(s)

Figure 3.
Figure 3. (a) Stereo view of a superposition of backbone traces from the final ensemble of 16 solution structures of the S state dimer of UQ(1-51), with one subunit in red and the other in blue. (b) A representation of the fold of the S state dimer, with b-strands labelled. (c) A representation of the fold of wild-type ubiquitin with b-strands labelled.

Figure 5.
Figure 5. Comparison of details of the structures of wild-type ubiquitin (left) and the S state of UQ(1-51) (right). (a) Interaction between strand U[2] from the N-terminal hairpin and the a-helix. (b) Interface between the a-helix and the 3[10]-helix in ubiquitin and between the two a-helices of UQ(1-51). (c) Arrangement of strands U[1], U[5] and U[3] of ubiquitin and strands U[3], U'[3] and U[1]of UQ(1-51).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 773-787) copyright 2001.

Figures were selected by the author.