PDBsum entry 2wc7

Hydrolase

PDB id: 2wc7

Contents

Protein chain

470 a.a. *

Waters ×140

* Residue conservation analysis

PDB id:

2wc7

Name:

Hydrolase

Title:

Crystal structure of nostoc punctiforme debranching enzyme(npde) (acarbose soaked)

Structure:

Alpha amylase, catalytic region. Chain: a. Synonym: nostoc punctiforme debranching enzyme. Engineered: yes

Source:

Nostoc punctiforme. Organism_taxid: 272131. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.37Å R-factor: 0.215 R-free: 0.269

Authors:

A.-B.Dumbrepatil,H.-N.Song,J.-H.Choi,K.-H.Park,E.-J.Woo

Key ref:

A.B.Dumbrepatil et al. (2010). Structural features of the Nostoc punctiforme debranching enzyme reveal the basis of its mechanism and substrate specificity. Proteins, 78, 348-356. PubMed id: 19768689 DOI: 10.1002/prot.22548

Date:

10-Mar-09 Release date: 29-Sep-09

Protein chain

B2IUW9  (B2IUW9_NOSP7) -  Alpha amylase, catalytic region from Nostoc punctiforme (strain ATCC 29133 / PCC 73102)

Seq: 488 a.a.

Struc: 470 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.54 - cyclomaltodextrinase.
• Reaction: cyclomaltodextrin + H2O = linear maltodextrin

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

Added reference

DOI no: 10.1002/prot.22548

Proteins 78:348-356 (2010)

PubMed id: 19768689

Structural features of the Nostoc punctiforme debranching enzyme reveal the basis of its mechanism and substrate specificity.

A.B.Dumbrepatil, J.H.Choi, J.T.Park, M.J.Kim, T.J.Kim, E.J.Woo, K.H.Park.

ABSTRACT

The debranching enzyme Nostoc punctiforme debranching enzyme (NPDE) from the cyanobacterium Nostoc punctiforme (PCC73102) hydrolyzes the alpha-1,6 glycosidic linkages of malto-oligosaccharides. Despite its high homology to cyclodextrin/pullulan (CD/PUL)-hydrolyzing enzymes from glycosyl hydrolase 13 family (GH-13), NPDE exhibits a unique catalytic preference for longer malto-oligosaccharides (>G8), performing hydrolysis without the transgylcosylation or CD-hydrolyzing activities of other GH-13 enzymes. To investigate the molecular basis for the property of NPDE, we determined the structure of NPDE at 2.37-A resolution. NPDE lacks the typical N-terminal domain of other CD/PUL-hydrolyzing enzymes and forms an elongated dimer in a head-to-head configuration. The unique orientation of residues 25-55 in NPDE yields an extended substrate binding groove from the catalytic center to the dimeric interface. The substrate binding groove with a lengthy cavity beyond the -1 subsite exhibits a suitable architecture for binding longer malto-oligosaccharides (>G8). These structural results may provide a molecular basis for the substrate specificity and catalytic function of this cyanobacterial enzyme, distinguishing it from the classical neopullulanases and CD/PUL-hydrolyzing enzymes.

Selected figure(s)

Figure 3.
Figure 3. Dimeric arrangement of NPDE monomers. a: The dimer interface comprised of a monomer subunit is shown. Helix 6 is shown in violet with their residues rendered as sticks. The residues involved in the dimer interaction hydrogen bonding are Gly100, Ala104, Arg86, Thr46, Ala82, Asp84, Phe132, His90, Arg31, and Glu140. b: An NPDE dimer view from the side at the active site is shown. The Helix 6 (131-150) and the loop region of 23-56 are shown in green and magenta, respectively. The violet residues are from Mol A, and those in orange color are from Mol B of the NPDE dimer. c: Estimation of the molecular weight of NPDE by gel permeation chromatography.

Figure 4.
Figure 4. Active site architecture of NPDE. a: The active site of NPDE is shown as a cartoon. The catalytic residues and the subsite site residues are shown as sticks. The residue R283 is shown to interact by hydrogen bonding with D284 and D323. The W242 residue creating the steep geometry is shown. The F213 residue is shown and the loop region 211-218 is highlighted in red color. b: The active site steep geometry is highlighted, which helps in the binding of kinked substrates, thus causing the enzyme's preference for , 1-6 bond over , 1-4 and the subsite -1 interacting residues in sticks along with the active site residues. c: Molecular model of the NPDE in complex with maltotriose (left). The catalytic residues (green), Trp242 residue (red), and the Tyr 87 residue (dark pink) are shown as sticks in the models. The reducing glucose unit of maltotriose with -1, 4-glucosidic linkage is held in position by Trp242, Trp172, and Arg283 at +1 subsite. The second sugar ring is slightly offset at -1 subsite above the Tyr 87 residue in the model. d: Molecular model of the NPDE in complex with isopanose. The substrate with -1, 6-glucosidic linkage shows proper stacking interaction and orientation at both +1 and -1 subsites with positioning of glucosidic oxygen at the catalytic center in the model.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2010, 78, 348-356) copyright 2010.

Figures were selected by an automated process.