PDBsum entry 2nbd

Protein binding

PDB id: 2nbd

Contents

Protein chain

76 a.a.

PDB id:

2nbd

Name:

Protein binding

Title:

Solution structure of v26a mutant of ubiquitin at ph 6.0

Structure:

Entity. Chain: a. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

P.Surana,R.Das

Key ref:

P.Surana and R.Das (2016). Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR. Protein Sci, 25, 1438-1450. PubMed id: 27111887 DOI: 10.1002/pro.2940

Date:

04-Feb-16 Release date: 18-May-16

Protein chain

P62987  (RL40_HUMAN) -  Ubiquitin-ribosomal protein eL40 fusion protein from Homo sapiens

Seq: 128 a.a.

Struc: 76 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1002/pro.2940

Protein Sci 25:1438-1450 (2016)

PubMed id: 27111887

Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR.

P.Surana, R.Das.

ABSTRACT

The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states. Here, we observe the high resolution structure of a hydrophobic core mutant of Ubiquitin at an extreme acidic pH by nuclear magnetic resonance (NMR) spectroscopy. In the structure, the native secondary and tertiary structure is conserved for a major part of the protein. However, a long loop between the beta strands β3 and β5 is partially unfolded. The altered structure is supported by fluorescence data and the difference in free energies between the native state and the intermediate is reflected in the denaturant induced melting curves. The unfolded region includes amino acids that are critical for interaction with cofactors as well as for assembly of poly-Ubiquitin chains. The structure at acidic pH resembles a late folding intermediate of Ubiquitin and indicates that upon stabilization of the protein's core, the long loop converges on the core in the final step of the folding process.