PDBsum entry 2wnb

Transferase

PDB id: 2wnb

Contents

Protein chain

273 a.a. *

Ligands

A2G-GAL

C5P

CG3

Waters ×365

* Residue conservation analysis

PDB id:

2wnb

Name:

Transferase

Title:

Crystal structure of a mammalian sialyltransferase in complex with disaccharide and cmp

Structure:

Cmp-n-acetylneuraminate-beta-galactosamide-alpha-2,3- sialyltransferase 1. Chain: a. Fragment: residues 46-343 compnd 12. Engineered: yes

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Gene: st3gal1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.55Å R-factor: 0.177 R-free: 0.213

Authors:

F.V.Rao,J.R.Rich,B.Raikic,W.W.Wakarchuk,S.G.Withers,N.C.J.Strynadka

Key ref:

F.V.Rao et al. (2009). Structural insight into mammalian sialyltransferases. Nat Struct Biol, 16, 1186-1188. PubMed id: 19820709 DOI: 10.1038/nsmb.1685

Date:

08-Jul-09 Release date: 13-Oct-09

Protein chain

Q02745  (SIA4A_PIG) -  CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1 from Sus scrofa

Seq: 343 a.a.

Struc: 273 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.4.3.2 - beta-D-galactosyl-(1->3)-N-acetyl-beta-D-galactosaminide alpha-2,3-
• Reaction: a beta-D-galactosyl-(1->3)-N-acetyl-beta-D-galactosaminyl derivative + CMP-N-acetyl-beta-neuraminate = an N-acetyl-alpha-neuraminyl-(2->3)-beta- D-galactosyl-(1->3)-N-acetyl-beta-D-galactosaminyl derivative + CMP + H⁺

beta-D-galactosyl-(1->3)-N-acetyl-beta-D-galactosaminyl derivative + CMP-N-acetyl-beta-neuraminate = N-acetyl-alpha-neuraminyl-(2->3)-beta- D-galactosyl-(1->3)-N-acetyl-beta-D-galactosaminyl derivative + CMP (Bound ligand (Het Group name = C5P) corresponds exactly) + H(+)

• Enzyme class 2: E.C.2.4.3.4 - beta-galactoside alpha-2,3-sialyltransferase.
• Reaction: a beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl derivative + CMP-N-acetyl-beta-neuraminate = an N-acetyl-alpha-neuraminyl-(2->3)-beta- D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl derivative + CMP + H⁺

beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl derivative + CMP-N-acetyl-beta-neuraminate = N-acetyl-alpha-neuraminyl-(2->3)-beta- D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl derivative + CMP (Bound ligand (Het Group name = C5P) corresponds exactly) + H(+)

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

Added reference

DOI no: 10.1038/nsmb.1685

Nat Struct Biol 16:1186-1188 (2009)

PubMed id: 19820709

Structural insight into mammalian sialyltransferases.

F.V.Rao, J.R.Rich, B.Rakić, S.Buddai, M.F.Schwartz, K.Johnson, C.Bowe, W.W.Wakarchuk, S.Defrees, S.G.Withers, N.C.Strynadka.

ABSTRACT

Mammalian cell surfaces are modified by complex arrays of glycoproteins, glycolipids and polysaccharides, many of which terminate in sialic acid and have central roles in essential processes including cell recognition, adhesion and immunogenicity. Sialylation of glycoconjugates is performed by a set of sequence-related enzymes known as sialyltransferases (STs). Here we present the crystal structure of a mammalian ST, porcine ST3Gal-I, providing a structural basis for understanding the mechanism and specificity of these enzymes and for the design of selective inhibitors.

Selected figure(s)

Figure 1.
Cartoon of pST3Gal-I in complex with product CMP and a disaccharide sugar acceptor (yellow stick model). A model of the missing lid (residues 305–316) is shown as dashed line (magenta) based on an equivalent loop in CstII. The catalytic base (His319) is highlighted in cyan. (a) The GT29 catalytic domain is linked to the transmembrane helix by a protease-sensitive stem region. Residues predicted to be glycosylated are shown as black sticks. (b) The four conserved sialyl motifs of GT29 STs.

Figure 2.
(a) Active site of pST3Gal-I, with CMP occupying the donor site and Gal 1,3GalNAc -PhNO[2] disaccharide defining the acceptor site (yellow carbon atoms). Amino acids of interest are shown as sticks, with the catalytic base represented in cyan. Black dotted lines indicate potential hydrogen bonds. For Gal 1,3GalNAc -PhNO[2], the unbiased 1.25-Å |F[o]| - |F[c]|, [calc] electron density map is shown, contoured at 2 . For CMP, the unbiased 1.55-Å |F[o]| - |F[c]|, [calc] electron density map is shown, contoured at 2 . (b) Observed disaccharide acceptor binding in pST3Gal-I (yellow) with a model of CMP3F-NeuAc (green) based on the CstII–CMP3F-NeuAc complex (PDB 1RO7)^18.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 1186-1188) copyright 2009.