PDBsum entry 1nhc

Hydrolase

PDB id: 1nhc

Contents

Protein chains

(+ 0 more) 336 a.a. *

Ligands

NAG-NAG

NAG-NAG-BMA-MAN-MAN-MAN

NAG-NAG-MAN

MAN ×11

SO4 ×16

GOL ×5

NAG ×3

Waters ×1353

* Residue conservation analysis

PDB id:

1nhc

Name:

Hydrolase

Title:

Structural insights into the processivity of endopolygalacturonase i from aspergillus niger

Structure:

Polygalacturonase i. Chain: a, b, c, d, e, f. Synonym: pg-i, pectinase, endopolygalacturonase i. Engineered: yes

Source:

Aspergillus niger. Organism_taxid: 5061. Expressed in: aspergillus niger. Expression_system_taxid: 5061

Resolution:

1.70Å R-factor: 0.176 R-free: 0.209

Authors:

G.Van Pouderoyen,H.J.Snijder,J.A.Benen,B.W.Dijkstra

Key ref:

G.van Pouderoyen et al. (2003). Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger. FEBS Lett, 554, 462-466. PubMed id: 14623112 DOI: 10.1016/S0014-5793(03)01221-3

Date:

19-Dec-02 Release date: 25-Nov-03

Protein chains

P26213  (PGLR1_ASPNG) -  Endopolygalacturonase I from Aspergillus niger

Seq: 368 a.a.

Struc: 336 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.15 - endo-polygalacturonase.
• Reaction: (1,4-alpha-D-galacturonosyl)n+m + H2O = (1,4-alpha-D-galacturonosyl)n + (1,4-alpha-D-galacturonosyl)m

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1016/S0014-5793(03)01221-3

FEBS Lett 554:462-466 (2003)

PubMed id: 14623112

Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger.

G.van Pouderoyen, H.J.Snijder, J.A.Benen, B.W.Dijkstra.

ABSTRACT

Endopolygalacturonase I is a processive enzyme, while the 60% sequence identical endopolygalacturonase II is not. The 1.70 A resolution crystal structure of endopolygalacturonase I reveals a narrowed substrate binding cleft. In addition, Arg96, a residue in this cleft previously shown to be critical for processivity, interacts with the substrate mimics glycerol and sulfate in several well-defined conformations in the six molecules in the asymmetric unit. From this we conclude that both Arg96 and the narrowed substrate binding cleft contribute to retaining the substrate while it moves through the active site after a cleavage event has occurred.

Selected figure(s)

Figure 1.
Fig. 1. The three-dimensional structure of (A) endopolygalacturonase I and (B) endopolygalacturonase II with the N- and C-termini indicated, viewed onto β-sheet PB2a (yellow). PB2b (blue) is the bottom β-sheet. PB1 is shown in green and PB3 is shown in red. The active site (Asp186, Asp207 and Asp208) is visible at the top, between the T1 loop regions (on the right side) and the T3 loop regions (on the left side). The glycosylation of endopolygalacturonase I and the loops bordering the active site cleft are shown in ball-and-stick representation (endopolygalacturonase I residues 124–128 (left) and 299–301 (right), endopolygalacturonase II residues 121–123 (left) and 293–295 (right)). The smallest distance at the entry of the active site cleft is indicated with a dashed line and the value is shown [34]. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Figure 2.
Fig. 2. N-Glycosylation at Asn246.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2003, 554, 462-466) copyright 2003.

Figures were selected by the author.