PDBsum entry: 1cxk

Transferase

PDB id: 1cxk

Contents

Protein chain

686 a.a. *

Ligands

GLC-GLC

GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC

GLC-GLC-GLC-GLC ×2

Metals

_CA ×2

Waters ×633

* Residue conservation analysis

PDB id:

1cxk

Name:

Transferase

Title:

Complex between a maltononaose substrate and bacillus circulans strain 251 cgtase e257q/d229n

Structure:

Protein (cyclodextrin-glycosyltransferase). Chain: a. Synonym: cgtase. Engineered: yes. Mutation: yes

Source:

Bacillus circulans. Organism_taxid: 1397. Strain: 251. Expressed in: bacillus subtilis. Expression_system_taxid: 1423. Other_details: mutants were constructed in ecoli strain mc1061

Resolution:

2.09Å R-factor: 0.158 R-free: 0.210

Authors:

J.C.M.Uitdehaag,K.H.Kalk,B.W.Dijkstra

Key ref:

J.C.Uitdehaag et al. (1999). X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-amylase family. Nat Struct Biol, 6, 432-436. PubMed id: 10331869 DOI: 10.1038/8235

Date:

24-Feb-99 Release date: 03-May-99

Protein chain

P43379  (CDGT2_BACCI) -  Cyclomaltodextrin glucanotransferase

Seq: 713 a.a.

Struc: 686 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.4.1.19 - Cyclomaltodextrin glucanotransferase.
• Reaction: Degrades starch to cyclodextrins by formation of a 1,4-alpha-D- glucosidic bond.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biological process: carbohydrate metabolic process (1 term)
• Biochemical function: catalytic activity (9 terms)

DOI no: 10.1038/8235

Nat Struct Biol 6:432-436 (1999)

PubMed id: 10331869

X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-amylase family.

J.C.Uitdehaag, R.Mosi, K.H.Kalk, B.A.van der Veen, L.Dijkhuizen, S.G.Withers, B.W.Dijkstra.

ABSTRACT

Cyclodextrin glycosyltransferase (CGTase) is an enzyme of the alpha-amylase family, which uses a double displacement mechanism to process alpha-linked glucose polymers. We have determined two X-ray structures of CGTase complexes, one with an intact substrate at 2.1 A resolution, and the other with a covalently bound reaction intermediate at 1.8 A resolution. These structures give evidence for substrate distortion and the covalent character of the intermediate and for the first time show, in atomic detail, how catalysis in the alpha-amylase family proceeds by the concerted action of all active site residues.

Selected figure(s)

Figure 1.
Figure 1. Scheme of the CGTase reaction mechanism. The first step, leading to intermediate formation, is explained in the text. In the second step, Glu 257 activates an acceptor that subsequently reacts with the intermediate, leading to product formation. This proceeds with a mechanism that is essentially the reverse of the first step. The glucoside ring atom nomenclature is incorporated in the left-most picture. The shaded orbital represents the electrons that are in a proper orientation to participate in the cleavage of the substrate -glycosidic bond according to the stereo-electronic theory^22. However, when the intermediate -glycosyl-enzyme bond is cleaved, such a correctly oriented orbital is not present, as pointed out in the text.

Figure 2.
Figure 2. Stereoview of the substrate bound to CGTase. The maltononaose binds from subsites -7 to +2, but for clarity only subsites -2, -1 and +1 are shown. The arrow indicates the scissile bond. a, Showing how the substrate fits into the 2F[o] - F[c] electron density (1 contoured), which was calculated with F[c] and phases from unliganded CGTase to avoid bias^16. b, The substrate distortion at the catalytic subsite -1 (central sugar ring) is revealed by superposition with the minimum energy conformation of maltose (orange)^15. The superposition is based on the glucose C3, C4 and C5 atoms in subsite -1. Comparing the substrate ring puckering parameters with a potential map from molecular mechanics calculations indicates that the glucose ring at the catalytic subsite is strained by ~17 kJ mol^−1 and has a ^4C[1] chair conformation distorted towards a ^2H[3] half chair^15. c, Undistorted (free) maltose clearly does not fit the 2F[o] - F[c] electron density at subsite -1. The glycosidic bond torsion angles of maltose were adjusted to fit the density at subsite +1.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 432-436) copyright 1999.

Figures were selected by an automated process.