PDBsum entry 2agd

Transferase

PDB id: 2agd

Contents

Protein chain

273 a.a. *

Ligands

BMA-MAN-NAG ×3

SO4 ×16

UDH ×3

GOL ×8

DIO

MES

Metals

_MN ×3

Waters ×532

* Residue conservation analysis

PDB id:

2agd

Name:

Transferase

Title:

Crystal structure of human m340h-beta-1,4-galactosyltransferase- i(m340h-b4gal-t1) in complex with glcnac-beta1,4-man-alpha1,3-man- beta-or

Structure:

Beta-1,4-galactosyltransferase 1. Chain: a, b, c. Fragment: catalytic domain, residues 126-398. Synonym: beta-1,4-galtase 1. Beta4gal-t1. B4gal-t1. Udp- galactose:beta-n-acetylglucosamine beta-1,4-galactosyltransferase 1. Engineered: yes. Mutation: yes. Other_details: n-acetyllactosamine synthase part

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: b4galt1, ggtb2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Other_details: n-terminal carries t7 tag of 11 amino acids followed by gly, ser & ala

Resolution:

1.90Å R-factor: 0.202 R-free: 0.228

Authors:

V.Ramasamy,B.Ramakrishnan,E.Boeggeman,D.M.Ratner,P.H.Seeberger, P.K.Qasba

Key ref:

V.Ramasamy et al. (2005). Oligosaccharide preferences of beta1,4-galactosyltransferase-I: crystal structures of Met340His mutant of human beta1,4-galactosyltransferase-I with a pentasaccharide and trisaccharides of the N-glycan moiety. J Mol Biol, 353, 53-67. PubMed id: 16157350 DOI: 10.1016/j.jmb.2005.07.050

Date:

26-Jul-05 Release date: 04-Oct-05

Protein chains

P15291  (B4GT1_HUMAN) -  Beta-1,4-galactosyltransferase 1 from Homo sapiens

Seq: 398 a.a.

Struc: 273 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.4.1.- - ?????
• Enzyme class 2: E.C.2.4.1.22 - lactose synthase.
• Reaction: D-glucose + UDP-alpha-D-galactose = lactose + UDP + H⁺

D-glucose (Bound ligand (Het Group name = BMA) corresponds exactly) + UDP-alpha-D-galactose = lactose + UDP + H(+) (Bound ligand (Het Group name = UDH) matches with 78.12% similarity)

• Enzyme class 3: E.C.2.4.1.275 - neolactotriaosylceramide beta-1,4-galactosyltransferase.
• Reaction: a beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-beta-D-Glc-(1<->1)- Cer(d18:1(4E)) + UDP-alpha-D-galactose = a neolactoside nLc4Cer(d18:1(4E)) + UDP + H⁺

beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-beta-D-Glc-(1<->1)- Cer(d18:1(4E)) + UDP-alpha-D-galactose = neolactoside nLc4Cer(d18:1(4E)) + UDP + H(+) (Bound ligand (Het Group name = UDH) matches with 78.12% similarity)

• Enzyme class 4: E.C.2.4.1.38 - beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase.
• Reaction: an N-acetyl-beta-D-glucosaminyl derivative + UDP-alpha-D-galactose = a beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + UDP + H⁺

N-acetyl-beta-D-glucosaminyl derivative + UDP-alpha-D-galactose = beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + UDP + H(+) (Bound ligand (Het Group name = UDH) matches with 78.12% similarity)

• Enzyme class 5: E.C.2.4.1.90 - N-acetyllactosamine synthase.
• Reaction: N-acetyl-D-glucosamine + UDP-alpha-D-galactose = beta-D-galactosyl- (1->4)-N-acetyl-D-glucosamine + UDP + H⁺

N-acetyl-D-glucosamine (Bound ligand (Het Group name = NAG) matches with 93.33% similarity) + UDP-alpha-D-galactose = beta-D-galactosyl- (1->4)-N-acetyl-D-glucosamine + UDP + H(+) (Bound ligand (Het Group name = UDH) matches with 78.12% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/j.jmb.2005.07.050

J Mol Biol 353:53-67 (2005)

PubMed id: 16157350

Oligosaccharide preferences of beta1,4-galactosyltransferase-I: crystal structures of Met340His mutant of human beta1,4-galactosyltransferase-I with a pentasaccharide and trisaccharides of the N-glycan moiety.

V.Ramasamy, B.Ramakrishnan, E.Boeggeman, D.M.Ratner, P.H.Seeberger, P.K.Qasba.

ABSTRACT

beta-1,4-Galactosyltransferase-I (beta4Gal-T1) transfers galactose from UDP-galactose to N-acetylglucosamine (GlcNAc) residues of the branched N-linked oligosaccharide chains of glycoproteins. In an N-linked biantennary oligosaccharide chain, one antenna is attached to the 3-hydroxyl-(1,3-arm), and the other to the 6-hydroxyl-(1,6-arm) group of mannose, which is beta-1,4-linked to an N-linked chitobiose, attached to the aspargine residue of a protein. For a better understanding of the branch specificity of beta4Gal-T1 towards the GlcNAc residues of N-glycans, we have carried out kinetic and crystallographic studies with the wild-type human beta4Gal-T1 (h-beta4Gal-T1) and the mutant Met340His-beta4Gal-T1 (h-M340H-beta4Gal-T1) in complex with a GlcNAc-containing pentasaccharide and several GlcNAc-containing trisaccharides present in N-glycans. The oligosaccharides used were: pentasaccharide GlcNAcbeta1,2-Manalpha1,6 (GlcNAcbeta1,2-Manalpha1,3)Man; the 1,6-arm trisaccharide, GlcNAcbeta1,2-Manalpha1,6-Manbeta-OR (1,2-1,6-arm); the 1,3-arm trisaccharides, GlcNAcbeta1,2-Manalpha1,3-Manbeta-OR (1,2-1,3-arm) and GlcNAcbeta1,4-Manalpha1,3-Manbeta-OR (1,4-1,3-arm); and the trisaccharide GlcNAcbeta1,4-GlcNAcbeta1,4-GlcNAc (chitotriose). With the wild-type h-beta4Gal-T1, the K(m) of 1,2-1,6-arm is approximately tenfold lower than for 1,2-1,3-arm and 1,4-1,3-arm, and 22-fold lower than for chitotriose. Crystal structures of h-M340H-beta4Gal-T1 in complex with the pentasaccharide and various trisaccharides at 1.9-2.0A resolution showed that beta4Gal-T1 is in a closed conformation with the oligosaccharide bound to the enzyme, and the 1,2-1,6-arm trisaccharide makes the maximum number of interactions with the enzyme, which is in concurrence with the lowest K(m) for the trisaccharide. Present studies suggest that beta4Gal-T1 interacts preferentially with the 1,2-1,6-arm trisaccharide rather than with the 1,2-1,3-arm or 1,4-1,3-arm of a bi- or tri-antennary oligosaccharide chain of N-glycan.

Selected figure(s)

Figure 1.
Figure 1. A depiction of complex penta-antennary N-glycan structure. The pentasaccharide and the trisaccharides of the N-glycan moiety, used for the kinetic and crystallographic studies, are highlighted by colored arrows. GlcNAcb1,2-Mana1,6(GlcNAcb1,2-Mana1,3)-Man pentasaccharide (blue and green arrows); GlcNAcb1,2-Mana1,6-Manb-OR (1,2-1,6-arm) (blue arrows); GlcNAcb1,2-Mana1,3-Manb-OR (1,2-1,3-arm) (green arrows); GlcNAcb1,4-Man a1,3-Manb-OR (1,4-1,3-arm) (purple arrows).

Figure 2.
Figure 2. Effects of varying the oligosaccharide acceptor substrate concentration on the initial rate of galactose transfer (n) by the h-b4Gal-T1. Chitobiose (GlcNAcb1,4-GlcNAc) and chitotriose GlcNAcb1,4-GlcNAcb1,4-GlcNAc (0M), GlcNAcb1,2-Man ( triangle, open ), GlcNAcb1,2-Mana1,6-Manb-OR (sB), GlcNAcb1,2-Mana1,3-Manb-OR ( open ), GlcNAcb1,4-Mana1,3-Manb-OR ( triangle, filled ), pentasaccharide GlcNAcb1,2-Mana1,6(GlcNAcb1,2-Mana1,3)Man( ).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 353, 53-67) copyright 2005.

Figures were selected by an automated process.