PDBsum entry 4lw3

Transferase

PDB id: 4lw3

Contents

Protein chain

242 a.a.

Ligands

GDU

Metals

_MN

Waters ×304

PDB id:

4lw3

Name:

Transferase

Title:

Crystal structure of the drosophila beta1,4galactosyltransferase7 catalytic domain d211n single mutant enzyme complex with manganese and udp-galactose

Structure:

Beta-4-galactosyltransferase 7. Chain: a. Fragment: catalytic domain, unp residues 71-311. Synonym: fi08434p. Engineered: yes. Mutation: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: 4-galactosyltransferase-7, beta-4galt7, beta1, beta4galt7, beta4galt7-ra, cg11780, dmel_cg11780. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.00Å R-factor: 0.176 R-free: 0.207

Authors:

B.Ramakrishnan,P.K.Qasba

Key ref:

Y.Tsutsui et al. (2013). Crystal structures of β-1,4-galactosyltransferase 7 enzyme reveal conformational changes and substrate binding. J Biol Chem, 288, 31963-31970. PubMed id: 24052259 DOI: 10.1074/jbc.M113.509984

Date:

26-Jul-13 Release date: 25-Sep-13

Protein chain

Q9VBZ9  (Q9VBZ9_DROME) -  Beta-1,4-galactosyltransferase 7 from Drosophila melanogaster

Seq: 322 a.a.

Struc: 242 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.4.1.133 - xylosylprotein 4-beta-galactosyltransferase.
• Pathway: Heparan and Chondroitin Biosynthesis; (early stages)
• Reaction: 3-O-(beta-D-xylosyl)-L-seryl-[protein] + UDP-alpha-D-galactose = 3-O- (beta-D-galactosyl-(1->4)-beta-D-xylosyl)-L-seryl-[protein] + UDP + H⁺

3-O-(beta-D-xylosyl)-L-seryl-[protein] + UDP-alpha-D-galactose = 3-O- (beta-D-galactosyl-(1->4)-beta-D-xylosyl)-L-seryl-[protein] (Bound ligand (Het Group name = GDU) matches with 69.44% similarity) + UDP + H(+)

• Cofactor: Mn(2+)

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

Key reference

DOI no: 10.1074/jbc.M113.509984

J Biol Chem 288:31963-31970 (2013)

PubMed id: 24052259

Crystal structures of β-1,4-galactosyltransferase 7 enzyme reveal conformational changes and substrate binding.

Y.Tsutsui, B.Ramakrishnan, P.K.Qasba.

ABSTRACT

The β-1,4-galactosyltransferase 7 (β4GalT7) enzyme is involved in proteoglycan synthesis. In the presence of a manganese ion, it transfers galactose from UDP-galactose to xylose on a proteoglycan acceptor substrate. We present here the crystal structures of human β4GalT7 in open and closed conformations. A comparison of these crystal structures shows that, upon manganese and UDP or UDP-Gal binding, the enzyme undergoes conformational changes involving a small and a long loop. We also present the crystal structures of Drosophila wild-type β4GalT7 and D211N β4GalT7 mutant enzymes in the closed conformation in the presence of the acceptor substrate xylobiose and the donor substrate UDP-Gal, respectively. To understand the catalytic mechanism, we have crystallized the ternary complex of D211N β4GalT7 mutant enzyme in the presence of manganese with the donor and the acceptor substrates together in the same crystal structure. The galactose moiety of the bound UDP-Gal molecule forms seven hydrogen bonds with the protein molecule. The nonreducing end of the xylose moiety of xylobiose binds to the hydrophobic acceptor sugar binding pocket created by the conformational changes, whereas its extended xylose moiety forms hydrophobic interactions with a Tyr residue. In the ternary complex crystal structure, the nucleophile O4 oxygen atom of the xylose molecule is found in close proximity to the C1 and O5 atoms of the galactose moiety. This is the first time that a Michaelis complex of a glycosyltransferase has been described, and it clearly suggests an SN2 type catalytic mechanism for the β4GalT7 enzyme.