PDBsum entry: 1kcc

Hydrolase

PDB-id: 1kcc

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

333 a.a. *

Ligands

GTR

NAG ×2

Metal ions

_NA

_CL

Waters ×585

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1kcc

Name:

Hydrolase

Title:

Endopolygalacturonase i from stereum purpureum complexed with a galacturonate at 1.00 a resolution.

Structure:

Endopolygalacturonase. Chain: a. Fragment: residues 1-335. Ec: 3.2.1.15

Source:

Chondrostereum purpureum. Organism_taxid: 58369. Strain: asp-4b

UniProt:

P79074 (P79074_9AGAR)

Seq:

Struc:

Seq:

403 a.a.

Struc:

333 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.3.2.1.15   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Random hydrolysis of 1,4-alpha-D-galactosiduronic linkages in pectate and other galacturonans.

Resolution:

1.00Å

R-factor:

0.109

R-free:

0.140

Authors:

T.Shimizu,T.Nakatsu,K.Miyairi,T.Okuno,H.Kato

Key ref:

T.Shimizu et al. (2002). Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.. Biochemistry, 41, 6651-6659. [PubMed id: 12022868] [DOI: 10.1021/bi025541a]

Date:

08-Nov-01

Release date:

05-Jun-02

Related entries:

1k5c
1k5c contains an unliganded structure of the same enzyme.
1kcd
1kcd contains the same enzyme complexed with two
galacturonate.

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1021/bi025541a

Biochemistry 41:6651-6659 (2002)

PubMed id: 12022868

Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.

T.Shimizu, T.Nakatsu, K.Miyairi, T.Okuno, H.Kato.

ABSTRACT

Crystal structures of endopolygalacturonase from Stereum purpureum were solved in native and two galacturonic acid complex states at atomic resolution. Endopolygalacturonase catalyzes the hydrolysis of alpha-1,4-glycosidic linkage of polygalacturonate in pectin. The native structure was determined by the multiple wavelength anomalous dispersion method and was refined anisotropically with SHELXL-97, with an R factor of 11.4% and an R(free) factor of 14.0% at 0.96 A resolution. The enzyme folds into a right-handed parallel beta-helix with 10 complete turns. The crystal structures of its binary complex with one D-galacturonate and its ternary complex with two D-galacturonates were also determined to identify the substrate binding site at 1.0 and 1.15 A resolutions, respectively. In the binary complex, one beta-D-galactopyranuronate was found in the +1 subsite, thus proving the strong affinity of the +1 subsite expected from the bond cleavage frequency on oligogalacturonates. In the ternary complex, an additional beta-D-galactofuranuronate was found in the -1 subsite. In both subsites, the recognition of the galacturonate carboxy group is important in galacturonate binding. In the +1 subsite, the carboxy group interacts with three basic residues, His195, Arg226, and Lys228, which were conserved in all endopolygalacturonases. In the -1 subsite, the unique nonprolyl cis-peptide bond is believed to be involved in binding the carboxy group of the substrate. The active site architecture of the complexes provides insight into the mechanism of inverting glycosyl hydrolases and also sheds light on the basis of the differences between the family 28 and the other inverting glycosyl hydrolases.