PDBsum entry: 1lf6

Hydrolase

PDB id: 1lf6

Contents

Protein chains

674 a.a. *

Ligands

SO4 ×2

Waters ×908

* Residue conservation analysis

PDB id:

1lf6

Name:

Hydrolase

Title:

Crystal structure of bacterial glucoamylase

Structure:

Glucoamylase. Chain: a, b. Synonym: glucan 1,4-alpha-glucosidase, 1,4-alpha-d-glucan glucohydrolase, amyloglucosidase, gamma-amylase, lysosomal alpha-glucosidase, exo-1,4-alpha-glucosidase. Ec: 3.2.1.3

Source:

Thermoanaerobacterium thermosaccharolyticum. Organism_taxid: 1517. Strain: dsm 571

Resolution:

2.10Å R-factor: 0.194 R-free: 0.232

Authors:

A.E.Aleshin,P.-H.Feng,R.B.Honzatko,P.J.Reilly

Key ref:

A.E.Aleshin et al. (2003). Crystal structure and evolution of a prokaryotic glucoamylase. J Mol Biol, 327, 61-73. PubMed id: 12614608 DOI: 10.1016/S0022-2836(03)00084-6

Date:

10-Apr-02 Release date: 25-Feb-03

Protein chains

O85672  (O85672_THETR) -  Glucoamylase (Fragment)

Seq: 695 a.a.

Struc: 674 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.2.1.3 - Glucan 1,4-alpha-glucosidase.
• Reaction: Hydrolysis of terminal 1,4-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose.

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (6 terms)

DOI no: 10.1016/S0022-2836(03)00084-6

J Mol Biol 327:61-73 (2003)

PubMed id: 12614608

Crystal structure and evolution of a prokaryotic glucoamylase.

A.E.Aleshin, P.H.Feng, R.B.Honzatko, P.J.Reilly.

ABSTRACT

The first crystal structures of a two-domain, prokaryotic glucoamylase were determined to high resolution from the clostridial species Thermoanaerobacterium thermosaccharolyticum with and without acarbose. The N-terminal domain has 18 antiparallel strands arranged in beta-sheets of a super-beta-sandwich. The C-terminal domain is an (alpha/alpha)(6) barrel, lacking the peripheral subdomain of eukaryotic glucoamylases. Interdomain contacts are common to all prokaryotic Family GH15 proteins. Domains similar to those of prokaryotic glucoamylases in maltose phosphorylases (Family GH65) and glycoaminoglycan lyases (Family PL8) suggest evolution from a common ancestor. Eukaryotic glucoamylases may have evolved from prokaryotic glucoamylases by the substitution of the N-terminal domain with the peripheral subdomain and by the addition of a starch-binding domain.

Selected figure(s)

Figure 2.
Figure 2. Structures of tGA and the aGA a-domain. (a) Stereo view of the tGA b-domain. (b) Structural correspondence between the b-domain and linker region of tGA (left) and the N-glycan of aGA (right). Tan and red loops are on the catalytic side of the a-domain. Loops aL1 and aL6 of tGA that interact with the b-domain and linker are red, as are loops that interact with a corresponding N-glycosylation site of aGA. Catalytic residues are blue. Acarbose in the tGA active site is gray. Conserved N-glycosylation of fungal GAs (aGA-specific O-glycosylation sites are not shown for clarity) is in black. The conserved subdomain of fungal GAs consisting of helix aH10' (previously labeled helix 11[5]) and a b-strand hairpin is in dark green.

Figure 4.
Figure 4. Structurally homologous carbohydrases consisting of a and b-domains. (a) tGA. (b) Maltose phosphorylase (PDB entry 1H54). (c) Hyalorunate lyase (PDB entry 1EGU). The a and b-domains and linker regions are tan, blue and green, respectively. Additional C-terminal domains of maltose phosphorylase and hyaluronate lyase are brown. Conserved interfacial b-strands and a-helices are dark blue and red, respectively. Glu438 and Glu636, the catalytic acid and base of tGA; Glu487 and His671, the putative catalytic acid and phosphoryl binding residue of maltose phosphorylase; and His399, a proton acceptor of hyalorunate lyase, are black.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 61-73) copyright 2003.

Figures were selected by the author.