PDBsum entry: 1o8i

Hydrolase

PDB-id: 1o8i

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

353 a.a. *

Waters ×170

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1o8i

Name:

Hydrolase

Title:

Pectate lyasE C from erwinia chrysanthemi at ph 9.5 with no ca2+ added

Structure:

Pectate lyasE C. Chain: a. Engineered: yes

Source:

Erwinia chrysanthemi. Organism_taxid: 556. Expressed in: escherichia coli. Expression_system_taxid: 562

UniProt:

P11073 (PELC_ERWCH)

Seq:

Struc:

Seq:

375 a.a.

Struc:

353 a.a.

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

Enzyme class:

E.C.4.2.2.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Eliminative cleavage of pectate to give oligosaccharides with 4-deoxy- alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.

Pathway:

Pectin and Pectate Lyases

Resolution:

2.2Å

R-factor:

0.182

R-free:

0.219

Authors:

S.R.Herron,F.A.Jurnak

Key ref:

S.R.Herron et al. (2003). Characterization and implications of Ca2+ binding to pectate lyase C.. J Biol Chem, 278, 12271-12277. [PubMed id: 12540845] [DOI: 10.1074/jbc.M209306200]

Date:

27-Nov-02

Release date:

30-Jan-03

Related entries:

1air pectate lyasE C from erwinia chrysanthemi ( ec16) to a resolution of 2.2 angstroms with 128 waters
1o88 pectate lyasE C from erwinia chrysanthemi at ph 11.2 with 30mm ca2+
1o8d pectate lyasE C from erwinia chrysanthemi at ph 11.2 with 5mm ca2+
1o8e pectate lyasE C from erwinia chrysanthemi at ph 11.2 with 1mm ca2+
1o8f pectate lyasE C from erwinia chrysanthemi at ph 9.5 with 30mm ca2+
1o8g pectate lyasE C from erwinia chrysanthemi at ph 9.5 with 5mm ca2+
1o8h pectate lyasE C from erwinia chrysanthemi at ph 9.5 with 0.3mm ca2+ added
1o8j pectate lyasE C from erwinia chrysanthemi at ph 4.5 with 30mm ca2+
1o8k pectate lyasE C from erwinia chrysanthemi at ph 4.5 with 20mm ca2+
1o8l pectate lyasE C from erwinia chrysanthemi at ph 4.5 with 5mm ca2+
... plus others (see Header records)

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Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M209306200

J Biol Chem 278:12271-12277 (2003)

PubMed id: 12540845

Characterization and implications of Ca2+ binding to pectate lyase C.

S.R.Herron, R.D.Scavetta, M.Garrett, M.Legner, F.Jurnak.

ABSTRACT

Ca(2+) is essential for in vitro activity of Erwinia chrysanthemi pectate lyase C (PelC). Crystallographic analyses of 11 PelC-Ca(2+) complexes, formed at pH 4.5, 9.5, and 11.2 under varying Ca(2+) concentrations, have been solved and refined at a resolution of 2.2 A. The Ca(2+) site represents a new motif for Ca(2+), consisting primarily of beta-turns and beta-strands. The principal differences between PelC and the PelC-Ca(2+) structures at all pH values are the side-chain conformations of Asp-129 and Glu-166 as well as the occupancies of four water molecules. According to calculations of pK(a) values, the presence of Ca(2+) and associated structural changes lower the pK(a) of Arg-218, the amino acid responsible for proton abstraction during catalysis. The Ca(2+) affinity for PelC is weak, as the K(d) was estimated to be 0.132 (+/-0.004) mm at pH 9.5, 1.09 (+/-0.29) mm at pH 11.2, and 5.84 (+/-0.41) mm at pH 4.5 from x-ray diffraction studies and 0.133 (+/-0.045) mm at pH 9.5 from intrinsic tryptophan fluorescence measurements. Given the pH dependence of Ca(2+) affinity, PelC activity at pH 4.5 has been reexamined. At saturating Ca(2+) concentrations, PelC activity increases 10-fold at pH 4.5 but is less than 1% of maximal activity at pH 9.5. Taken together, the studies suggest that the primary Ca(2+) ion in PelC has multiple functions.

Selected figure(s)

Figure 1.
Fig. 1. Plot of the slow exchange of the solution bathing PelC crystals. The concentrations of ammonium sulfate ( ) and polyethylene glycol 8000 ( ) in the 1-ml drop containing a PelC crystal are plotted as a function of time.

Figure 6.
Fig. 6. Stereoviews of three types of Ca^2+ binding motifs. A, the Ca^2+ region of -lactalbumin exemplifies the continuous helix-loop-helix Ca^2+ binding motif, which is associated with tight binding. B, the Ca^2+ region of phospholipase A2 typifies the discontinuous helix-loop-helix Ca^2+ binding motif. C, the -turn/ -strand Ca^2+ binding motif of PelC exhibits weak binding affinity. In all figures, the polypeptide backbone of the protein is represented as a green ribbon, the Ca^2+ ions as yellow spheres, the oxygen atoms as red rods, and a disulfide bridge as a yellow bar.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 12271-12277) copyright 2003.

Figures were selected by an automated process.