PDBsum entry 1pam

Glycosyltransferase

PDB id: 1pam

Contents

Protein chains

686 a.a. *

Metals

_CA ×4

Waters ×805

* Residue conservation analysis

PDB id:

1pam

Name:

Glycosyltransferase

Title:

Cyclodextrin glucanotransferase

Structure:

Cyclodextrin glucanotransferase. Chain: a, b. Engineered: yes

Source:

Bacillus sp.. Organism_taxid: 1410. Strain: 1011. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: alkalophilic bacillus sp. 1011

Resolution:

1.80Å R-factor: 0.161 R-free: 0.211

Authors:

K.Harata,K.Haga,A.Nakamura,M.Aoyagi,K.Yamane

Key ref:

K.Harata et al. (1996). X-ray structure of cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011. Comparison of two independent molecules at 1.8 A resolution. Acta Crystallogr D Biol Crystallogr, 52, 1136-1145. PubMed id: 15299574 DOI: 10.1107/S0907444996008438

Date:

08-Jul-96 Release date: 11-Jan-97

Protein chains

P05618  (CDGT_BACS0) -  Cyclomaltodextrin glucanotransferase from Bacillus sp. (strain 1011)

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.

DOI no: 10.1107/S0907444996008438

Acta Crystallogr D Biol Crystallogr 52:1136-1145 (1996)

PubMed id: 15299574

X-ray structure of cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011. Comparison of two independent molecules at 1.8 A resolution.

K.Harata, K.Haga, A.Nakamura, M.Aoyagi, K.Yamane.

ABSTRACT

Cyclodextrin glucanotransferase (CGTase) is an enzyme which produces cyclodextrins by the degradation of starch. The enzyme from alkalophilic Bacillus sp. 1011, consisting of 686 amino acid residues, was crystallized from the solution containing 20% PEG 3000 and 20% 2-propanol at pH 5.6 adjusted with citrate buffer. The space group was P1 and the unit cell contained two molecules (V(m) = 2.41 A(3) Da(-1)). The structure was solved by the molecular replacement method and refined to a conventional R value of 0.161 (R(free) = 0.211) for the reflections in the resolution range 1.8-10 A by energy minimization combined with simulated annealing. The molecule consists of five domains, designated A-E, and its backbone structure is similar to the structure of other bacterial CGTases. The molecule has two calcium binding sites where calcium ions are coordinated by seven ligands, forming a distorted pentagonal bipyramid. The two independent molecules are related by a pseudotwofold symmetry and are superimposed with an r.m.s. deviation value of 0.32 A for equivalent C(alpha) atoms. Comparison of these molecules indicated the relatively large mobility of domains C and E with respect to domain A. The active site is filled with water molecules forming a hydrogen-bond network with polar side-chain groups. Two water molecules commonly found in the active center of both molecules link to several catalytically important residues by hydrogen bonds and participate in maintaining a similar orientation of side chains in the two independent molecules.

Selected figure(s)

Figure 4.
Fig. 4. The backbone structure of CGTase drwn using the program (Kraulis, 1991). The five domains are shown with colrs, blu (domain A), yellow (domain B), green (domain C), red (domain D) and light blue (domain E). Calcim ions are denoted by pink­colored circles.

Figure 5.
Fig. 5. Suprposition of the backbone structure of CGTase from B. spp. 1011 (wite), B. stearothermophilus (red), B. circulans strain 8 (bue) and B. circulans strain 251 (green).

Figure 13.
Fig. 13. Schematic dra\ving of the geometry of active center. Inter­ atomic distances in molecule (2) are given in parenthe~,es.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 1136-1145) copyright 1996.

Figures were selected by an automated process.