The stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein.


Abstract

Pectate lyase C (pelC) was the first protein in which the parallel beta-helix structure was recognized. The unique features of parallel beta-helix-containing proteins-a relatively simple topology and unusual interactions among side chains-make pelC an interesting protein to study with respect to protein folding. In this paper, we report studies of the unfolding equilibrium of pelC. PelC is unfolded reversibly by gdn-HCl at pH 7 and 5, as monitored by far- and near-UV CD and fluorescence. The coincidence of these spectroscopically detected transitions is consistent with a two-state transition at pH 7, but the three probes are not coincident at pH 5. No evidence was found for a loosely folded intermediate in the transition region at pH 5. At pH 7, the for unfolding is 12.2 kcal/mol, with the midpoint of the transition at 0.99 M gdn-HCl and m = 12.3 kcal/(mol.M). Thus, pelC is unusually stable and has an m value that is much larger than for typical globular proteins. Thermal denaturation of pelC has been studied by differential scanning calorimetry (DSC) and by CD. Although thermal denaturation is not reversible, valid thermodynamic data can be obtained for the unfolding transition. DeltaH(van't Hoff)/DeltaH(cal) is less than 1 for pHs between 5 and 8, with a maximum value of 0.91 at pH 7 decreasing to 0.85 at pH 8 and to 0.68 at pH 5. At all pHs studied, the excess heat capacity can be deconvoluted into two components corresponding to two-state transitions that are nearly coincident at pH 7, but deviate more at higher and lower pH. Thus, pelC appears to consist of two domains that interact strongly and unfold in a cooperative fashion at pH 7, but the cooperativity decreases at higher and lower pH. The crystal structure of pelC shows no obvious domain structure, however. Study holds ProTherm entries: 10196, 10197, 10198, 10199, 10200, 10201 Extra Details: 218nm CD parallel beta-helix; folded intermediate; heat capacity; cooperative

Submission Details

ID: PK6RuxKP4

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:39 p.m.

Version: 1

Publication Details
Kamen DE;Griko Y;Woody RW,Biochemistry (2000) The stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein. PMID:11123920
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1O8L 2003-01-30 2.2 Pectate Lyase C from Erwinia Chrysanthemi at pH 4.5 with 5mM CA2+
1AIR 1997-06-16 2.2 PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI (EC16) TO A RESOLUTION OF 2.2 ANGSTROMS WITH 128 WATERS
1O8D 2003-01-30 2.2 Pectate Lyase C from Erwinia Chrysanthemi at pH 11.2 with 5mM CA2+
1O8H 2003-01-30 2.2 Pectate Lyase C from Erwinia Chrysanthemi at pH 9.5 with 0.3mM Ca2+ Added
2EWE 2005-11-15 2.2 Crystal structure of Pectate Lyase C R218K mutant in complex with pentagalacturonic acid
1O8E 2003-01-30 2.2 Pectate Lyase C from Erwinia Chrysanthemi at pH 11.2 with 1mM Ca2+
1PLU 1999-07-13 2.2 PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI WITH 1 LU+3 ION IN THE PUTATIVE CALCIUM BINDING SITE
1O8M 2003-01-30 2.2 Pectate Lyase C from Erwinia Chrysanthemi at pH 4.5 with no Ca2+ Added
1O8G 2003-01-30 2.2 Pectate Lyase C from Erwinia Chrysanthemi at pH 9.5 with 5mM Ca2+
1O8I 2003-01-30 2.2 Pectate Lyase C from Erwinia Chrysanthemi at pH 9.5 with no Ca2+ Added
2PEC 1995-02-14 2.2 THE REFINED THREE-DIMENSIONAL STRUCTURE OF PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT 2.2 ANGSTROMS RESOLUTION: IMPLICATIONS FOR AN ENZYMATIC MECHANISM
1O88 2003-01-30 2.2 Pectate Lyase C From Erwinia Chrysanthemi at pH 11.2 with 30mM Ca2+
1O8F 2003-01-30 2.2 Pectate Lyase C from Erwinia Chrysanthemi at pH 9.5 with 30mM Ca2+
1O8J 2003-01-30 2.2 Pectate Lyase C from Erwinia Chrysanthemi at pH 4.5 with 30mM CA2+
1O8K 2003-01-30 2.2 Pectate Lyase C from Erwinia Chrysanthemi at pH 4.5 with 20mM CA2+

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Pectate lyase C P11073 PLYC_DICCH