PDBsum entry: 1ll0

Transferase

PDB id: 1ll0

Contents

Protein chains

(+ 3 more) 264 a.a. *

251 a.a. *

* Residue conservation analysis

PDB id:

1ll0

Name:

Transferase

Title:

Crystal structure of rabbit muscle glycogenin

Structure:

Glycogenin-1. Chain: a, b, c, d, e, f, g, h, i, j. Engineered: yes

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Tissue: skeletal muscle. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

3.43Å R-factor: 0.252 R-free: 0.287

Authors:

B.J.Gibbons,P.J.Roach,T.D.Hurley

Key ref:

B.J.Gibbons et al. (2002). Crystal structure of the autocatalytic initiator of glycogen biosynthesis, glycogenin. J Mol Biol, 319, 463-477. PubMed id: 12051921 DOI: 10.1016/S0022-2836(02)00305-4

Date:

26-Apr-02 Release date: 15-May-02

Protein chains

P13280  (GLYG_RABIT) -  Glycogenin-1

Seq: 333 a.a.

Struc: 264 a.a.

Protein chain

P13280  (GLYG_RABIT) -  Glycogenin-1

Seq: 333 a.a.

Struc: 251 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J: E.C.2.4.1.186 - Glycogenin glucosyltransferase.
• Reaction: UDP-alpha-D-glucose + glycogenin = UDP + alpha-D-glucosylglycogenin
• Cofactor: Manganese

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

 Gene Ontology (GO) functional annotation 

• Biological process: glycogen biosynthetic process (1 term)
• Biochemical function: transferase activity (4 terms)

reference

DOI no: 10.1016/S0022-2836(02)00305-4

J Mol Biol 319:463-477 (2002)

PubMed id: 12051921

Crystal structure of the autocatalytic initiator of glycogen biosynthesis, glycogenin.

B.J.Gibbons, P.J.Roach, T.D.Hurley.

ABSTRACT

Glycogen is an important storage reserve of glucose present in many organisms, from bacteria to humans. Its biosynthesis is initiated by a specialized protein, glycogenin, which has the unusual property of transferring glucose from UDP-glucose to form an oligosaccharide covalently attached to itself at Tyr194. Glycogen synthase and the branching enzyme complete the synthesis of the polysaccharide. The structure of glycogenin was solved in two different crystal forms. Tetragonal crystals contained a pentamer of dimers in the asymmetric unit arranged in an improper non-crystallographic 10-fold relationship, and orthorhombic crystals contained a monomer in the asymmetric unit that is arranged about a 2-fold crystallographic axis to form a dimer. The structure was first solved to 3.4 A using the tetragonal crystal form and a three-wavelength Se-Met multi-wavelength anomalous diffraction (MAD) experiment. Subsequently, an apo-enzyme structure and a complex between glycogenin and UDP-glucose/Mn2+ were solved by molecular replacement to 1.9 A using the orthorhombic crystal form. Glycogenin contains a conserved DxD motif and an N-terminal beta-alpha-beta Rossmann-like fold that are common to the nucleotide-binding domains of most glycosyltransferases. Although sequence identity amongst glycosyltransferases is minimal, the overall folds are similar. In all of these enzymes, the DxD motif is essential for coordination of the catalytic divalent cation, most commonly Mn2+. We propose a mechanism in which the Mn2+ that associates with the UDP-glucose molecule functions as a Lewis acid to stabilize the leaving group UDP and to facilitate the transfer of the glucose moiety to an intermediate nucleophilic acceptor in the enzyme active site, most likely Asp162. Following transient transfer to Asp162, the glucose moiety is then delivered to the final acceptor, either directly to Tyr194 or to glucose residues already attached to Tyr194. The positioning of the bound UDP-glucose far from Tyr194 in the glycogenin structure raises questions as to the mechanism for the attachment of the first glucose residues. Possibly the initial glucosylation is via inter-dimeric catalysis with an intra-molecular mechanism employed later in oligosaccharide synthesis.

Selected figure(s)

Figure 7.
Figure 7. Glycogenin dimer ribbons diagram with a-helices colored blue and green, b-sheets colored red and yellow, and coils colored gray. UDP-glucose molecules and Tyr194 side-chains are shown as ball-and-stick models and Mn2+ is colored magenta. The distances between the C1'' atom of the glucose in UDP-glucose and the Tyr194 hydroxyls are indicated with arrows. This Figure was generated using SwissPdb Viewer[54] and rendered using POV-Ray for Windows (downloaded from: www.povray.org).

Figure 8.
Figure 8. (a) A stereoview of the cis peptide bond between Glu118 and Leu119 is shown in a refined 2F[o] -F[c] simulated annealing omit map contoured at 1.0s in which the contents of the Figure were omitted from the structure factor calculations. (b). A stereo view showing an F[o] -F[c] difference density map contoured at 3.0s for the peptide bond between Glu118 and Leu119 refined in the trans conformation. The aligned cis conformation is shown in gold for reference. (c) The cis peptide bond and surrounding residues are shown, in stereo, as ball-and-stick models. The amino acid residues interacting with Glu118 and Leu119 are labeled. The helix between Phe170 and Asp162 is shown as a green ribbon. These Figures were generated using SwissPdb Viewer[54] and rendered using POV-Ray for Windows (downloaded from: www.povray.org).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 319, 463-477) copyright 2002.

Figures were selected by the author.