PDBsum entry 1zw7

Structural protein

PDB id

1zw7

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Contents

			Protein chain

					82 a.a. *

* Residue conservation analysis

PDB id:

1zw7

Links

Name:

Structural protein

Title:

Elimination of thE C-cap in ubiquitin structure, dynamics and thermodynamic consequences

Structure:

Ubiquitin. Chain: a. Engineered: yes. Mutation: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ubi1, rpl40a. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

21 models

Authors:

D.N.Ermolenko,B.Dangi,A.M.Gronenborn,G.I.Makhatadze

Key ref:

D.N.Ermolenko et al. (2007). Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences. Biophys Chem, 126, 25-35. PubMed id: 16713063

Date:

03-Jun-05

Release date:

16-May-06

PROCHECK

	Headers

	References

Protein chain

P0CG63 (UBI4P_YEAST) - Polyubiquitin from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: Struc:					381 a.a. 82 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 6 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.?

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	Biophys Chem 126:25-35 (2007)
PubMed id: 16713063

Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences.
D.N.Ermolenko, B.Dangi, A.Gvritishvili, A.M.Gronenborn, G.I.Makhatadze.

ABSTRACT

Single amino acid substitutions rarely produce substantial changes in protein structure. Here we show that substitution of the C-cap residue in the alpha-helix of ubiquitin with proline (34P variant) leads to dramatic structural changes. The resulting conformational perturbation extends over the last two turns of the alpha-helix and leads to enhanced flexibility for residues 27-37. Thermodynamic analysis of this ubiquitin variant using differential scanning calorimetry reveals that the thermal unfolding transition remains highly cooperative, exhibiting two-state behavior. Similarities with the wild type in the thermodynamic parameters (heat capacity change upon unfolding and m-value) of unfolding monitored by DSC and chemical denaturation suggests that the 34P variant has comparable buried surface area. The hydrophobic core of 34P variant is not packed as well as that of the wild type protein as manifested by a lower enthalpy of unfolding. The increased mobility of the polypeptide chain of this ubiquitin variant allows the transient opening of the hydrophobic core as evidenced by ANS binding. Taken together, these results suggest exceptional robustness of cooperativity in protein structures.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19196981

A.V.Gribenko, M.M.Patel, J.Liu, S.A.McCallum, C.Wang, and G.I.Makhatadze (2009).
Rational stabilization of enzymes by computational redesign of surface charge-charge interactions.

Proc Natl Acad Sci U S A, 106, 2601-2606.

PDB codes:

2k7j 2k7k

19626709

H.Fu, G.R.Grimsley, A.Razvi, J.M.Scholtz, and C.N.Pace (2009).
Increasing protein stability by improving beta-turns.

Proteins, 77, 491-498.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.