PDBsum entry: 1omz

Transferase

PDB id: 1omz

Contents

Protein chains

253 a.a. *

Ligands

UD2 ×2

EDO ×2

Metals

_MN ×2

Waters ×249

* Residue conservation analysis

PDB id:

1omz

Name:

Transferase

Title:

Crystal structure of mouse alpha-1,4-n- acetylhexosaminyltransferase (extl2) in complex with udpgalnac

Structure:

Alpha-1,4-n-acetylhexosaminyltransferase extl2. Chain: a, b. Fragment: catalytic domain. Synonym: alpha-galnact extl2, ext-related protein 2, exostosin-like 2. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: extl2 or extr2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Octamer (from PQS)

Resolution:

2.10Å R-factor: 0.201 R-free: 0.233

Authors:

L.C.Pedersen,J.Dong,F.Taniguchi,H.Kitagawa,J.M.Krahn, L.G.Pedersen,K.Sugahara,M.Negishi

Key ref:

L.C.Pedersen et al. (2003). Crystal structure of an alpha 1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis. J Biol Chem, 278, 14420-14428. PubMed id: 12562774 DOI: 10.1074/jbc.M210532200

Date:

26-Feb-03 Release date: 22-Apr-03

Protein chains

Q9ES89  (EXTL2_MOUSE) -  Exostosin-like 2

Seq: 330 a.a.

Struc: 253 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.1.223 - Glucuronyl-galactosyl-proteoglycan 4-alpha-N-
• Pathway: Heparan Biosynthesis; (later stages)
• Reaction: UDP-N-acetyl-D-glucosamine + beta-D-glucuronosyl-(1->3)-beta-D- galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl-proteoglycan = UDP + alpha-N-acetyl-D-glucosaminyl-(1->4)-beta-D-glucuronosyl-(1->3)- beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl- proteoglycan

UDP-N-acetyl-D-glucosamine (Bound ligand (Het Group name = UD2) corresponds exactly) + beta-D-glucuronosyl-(1->3)-beta-D- galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl-proteoglycan = UDP + alpha-N-acetyl-D-glucosaminyl-(1->4)-beta-D-glucuronosyl-(1->3)- beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl- proteoglycan

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

 Gene Ontology (GO) functional annotation 

• Cellular component: intrinsic to endoplasmic reticulum membrane (1 term)
• Biochemical function: transferase activity, transferring hexosyl groups (1 term)

Added reference

DOI no: 10.1074/jbc.M210532200

J Biol Chem 278:14420-14428 (2003)

PubMed id: 12562774

Crystal structure of an alpha 1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis.

L.C.Pedersen, J.Dong, F.Taniguchi, H.Kitagawa, J.M.Krahn, L.G.Pedersen, K.Sugahara, M.Negishi.

ABSTRACT

EXTL2, an alpha1,4-N-acetylhexosaminyltransferase, catalyzes the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta1-3[galactose]beta1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans. We have solved the x-ray crystal structure of the catalytic domain of mouse EXTL2 in the apo-form and with donor substrates UDP-N-acetylglucosamine and UDP-N-acetylgalactosamine. In addition, a structure of the ternary complex with UDP and the acceptor substrate analog [glucuronic acid]beta1-3[galactose]beta1-O-naphthalenemethanol has been determined. These structures reveal three highly conserved residues, Asn-243, Asp-246, and Arg-293, located at the active site. Mutation of these residues greatly decreases the activity. In the ternary complex, an interaction exists between the beta-phosphate of the UDP leaving group and the acceptor hydroxyl of the substrate that may play a functional role in catalysis. These structures represent the first structures from the exostosin gene family and provide important insight into the mechanisms of alpha1,4-N-acetylhexosaminyl transfer in heparan biosynthesis.

Selected figure(s)

Figure 1.
Fig. 1. A, ribbon diagram of the catalytic domain (Ala-63-Lys-327) of mEXTL2 with bound UDP (orange) and GlcUA 1-3Gal 1-O-naphthalenemethanol acceptor substrate analog (blue). The UDP-donor binding subdomain is colored lavender, and the acceptor binding subdomain is colored green. The catalytic Mn2+ ion (green) is pictured with water molecules (red), Asp-153 (of the DXD motif), and phosphate oxygens from UDP that define the inner coordination sphere. B, the same figure as Fig. 2A but rotated ~90° about a horizontal axis. These figures were created using Molscript and Raster3D (24, 25).

Figure 5.
Fig. 5. Stereo diagram of the superposition of the active sites of mEXTL2 with UDP-GalNAc (orange) modeled onto the UDP in the UDP/ GlcUA 1-3Gal 1-O-naphthalenemethanol (blue)/mEXTL2 structure (khaki) to the crystal structure of the retaining glycosyltransferase LgtC (green) with bound donor and acceptor analogs UDP-2-deoxy-2-fluoro-galactose and 4'-deoxylactose, respectively. The position of the 4'-hydroxyl of the acceptor lactose has been modeled for this figure. Residues with similar interactions with the donor sugar are displayed. This figure was created using Molscript and Raster3D (24, 25).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 14420-14428) copyright 2003.

Figures were selected by an automated process.