PDBsum entry 1d3c

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Transferase PDB id
Protein chain
686 a.a. *
_CA ×3
Waters ×639
* Residue conservation analysis

References listed in PDB file
Key reference
Title The cyclization mechanism of cyclodextrin glycosyltransferase (cgtase) as revealed by a gamma-Cyclodextrin-Cgtase complex at 1.8-A resolution.
Authors J.C.Uitdehaag, K.H.Kalk, B.A.Van der veen, L.Dijkhuizen, B.W.Dijkstra.
Ref. J Biol Chem, 1999, 274, 34868-34876. [DOI no: 10.1074/jbc.274.49.34868]
PubMed id 10574960
The enzyme cyclodextrin glycosyltransferase is closely related to alpha-amylases but has the unique ability to produce cyclodextrins (circular alpha(1-->4)-linked glucoses) from starch. To characterize this specificity we determined a 1.8-A structure of an E257Q/D229N mutant cyclodextrin glycosyltransferase in complex with its product gamma-cyclodextrin, which reveals for the first time how cyclodextrin is competently bound. Across subsites -2, -1, and +1, the cyclodextrin ring binds in a twisted mode similar to linear sugars, giving rise to deformation of its circular symmetry. At subsites -3 and +2, the cyclodextrin binds in a manner different from linear sugars. Sequence comparisons and site-directed mutagenesis experiments support the conclusion that subsites -3 and +2 confer the cyclization activity in addition to subsite -6 and Tyr-195. On this basis, a role of the individual residues during the cyclization reaction cycle is proposed.
Figure 3.
Fig. 3. Stereo picture indicating the maltononaose (7) (gray) and -cyclodextrin (black) conformation in the CGTase active site. The white C backbone has the conformation observed in the -cyclodextrin complex. The backbone conformations of the loops 87-93 144-151, 175-182, and 190-199 in the maltononaose complex are indicated in gray.
Figure 5.
Fig. 5. Overview of the interactions between CGTase and maltononaose (7) (A) or -cyclodextrin (B). The distances associated with the interactions are in Table III. For clarity, not all interactions at subsites 2, 1, and +1 are shown. Symm rel. contacts, contacts made to a symmetry-related CGTase molecule in the crystal.
The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 34868-34876) copyright 1999.
Secondary reference #1
Title X-Ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-Amylase family.
Authors J.C.Uitdehaag, R.Mosi, K.H.Kalk, B.A.Van der veen, L.Dijkhuizen, S.G.Withers, B.W.Dijkstra.
Ref. Nat Struct Biol, 1999, 6, 432-436. [DOI no: 10.1038/8235]
PubMed id 10331869
Full text Abstract
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 reproduced from the cited reference with permission from Macmillan Publishers Ltd
Secondary reference #2
Title Crystallographic studies of the interaction of cyclodextrin glycosyltransferase from bacillus circulans strain 251 with natural substrates and products.
Authors R.M.Knegtel, B.Strokopytov, D.Penninga, O.G.Faber, H.J.Rozeboom, K.H.Kalk, L.Dijkhuizen, B.W.Dijkstra.
Ref. J Biol Chem, 1995, 270, 29256-29264.
PubMed id 7493956
Secondary reference #3
Title Structure of cyclodextrin glycosyltransferase complexed with a maltononaose inhibitor at 2.6 angstrom resolution. Implications for product specificity.
Authors B.Strokopytov, R.M.Knegtel, D.Penninga, H.J.Rozeboom, K.H.Kalk, L.Dijkhuizen, B.W.Dijkstra.
Ref. Biochemistry, 1996, 35, 4241-4249. [DOI no: 10.1021/bi952339h]
PubMed id 8672460
Full text Abstract
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