PDBsum entry 5vcs

Transferase

PDB id: 5vcs

Contents

Protein chains

354 a.a.

323 a.a.

Ligands

NAG-BMA-MAN-NAG-MAN ×2

NAG ×2

DMS ×3

PEG

Waters ×112

PDB id:

5vcs

Name:

Transferase

Title:

Alpha-1,6-mannosyl-glycoprotein 2-beta-n-acetylglucosaminyltransferase with bound acceptor

Structure:

Alpha-1,6-mannosyl-glycoprotein 2-beta-n- acetylglucosaminyltransferase. Chain: a, b. Fragment: unp residues 29-447. Synonym: beta-1,2-n-acetylglucosaminyltransferase ii, glcnac-t ii, gnt-ii, mannoside acetylglucosaminyltransferase 2, n-glycosyl- oligosaccharide-glycoprotein n-acetylglucosaminyltransferase ii. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: mgat2. Expressed in: homo sapiens. Expression_system_taxid: 9606

Resolution:

2.80Å R-factor: 0.249 R-free: 0.275

Authors:

J.H.Sanders,R.Kadirvelraj,Z.A.Wood

Key ref:

R.Kadirvelraj et al. (2018). Human N-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite. Proc Natl Acad Sci U S A, 115, 4637-4642. PubMed id: 29666272 DOI: 10.1073/pnas.1716988115

Date:

31-Mar-17 Release date: 11-Apr-18

Protein chain

Q10469  (MGAT2_HUMAN) -  Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase from Homo sapiens

Seq: 447 a.a.

Struc: 354 a.a.

Protein chain

Q10469  (MGAT2_HUMAN) -  Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase from Homo sapiens

Seq: 447 a.a.

Struc: 323 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: E.C.2.4.1.143 - alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase.
• Pathway: Mannosyl-glycoprotein N-acetylglucosaminyltransferases
• Reaction: an N₄-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]- beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl- [protein] + UDP-N-acetyl-alpha-D-glucosamine = N₄-{beta-D-GlcNAc- (1->2)-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta- D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP + H⁺

N(4)-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]- beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl- [protein] + UDP-N-acetyl-alpha-D-glucosamine = N(4)-{beta-D-GlcNAc- (1->2)-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta- D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP (Bound ligand (Het Group name = NAG) matches with 42.86% similarity) + H(+)

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

Key reference

DOI no: 10.1073/pnas.1716988115

Proc Natl Acad Sci U S A 115:4637-4642 (2018)

PubMed id: 29666272

Human N-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite.

R.Kadirvelraj, J.Y.Yang, J.H.Sanders, L.Liu, A.Ramiah, P.K.Prabhakar, G.J.Boons, Z.A.Wood, K.W.Moremen.

ABSTRACT

Asn-linked oligosaccharides are extensively modified during transit through the secretory pathway, first by trimming of the nascent glycan chains and subsequently by initiating and extending multiple oligosaccharide branches from the trimannosyl glycan core. Trimming and branching pathway steps are highly ordered and hierarchal based on the precise substrate specificities of the individual biosynthetic enzymes. A key committed step in the synthesis of complex-type glycans is catalyzed by N-acetylglucosaminyltransferase II (MGAT2), an enzyme that generates the second GlcNAcβ1,2- branch from the trimannosyl glycan core using UDP-GlcNAc as the sugar donor. We determined the structure of human MGAT2 as a Mn²⁺-UDP donor analog complex and as a GlcNAcMan₃GlcNAc₂-Asn acceptor complex to reveal the structural basis for substrate recognition and catalysis. The enzyme exhibits a GT-A Rossmann-like fold that employs conserved divalent cation-dependent substrate interactions with the UDP-GlcNAc donor. MGAT2 interactions with the extended glycan acceptor are distinct from other related glycosyltransferases. These interactions are composed of a catalytic subsite that binds the Man-α1,6- monosaccharide acceptor and a distal exosite pocket that binds the GlcNAc-β1,2Man-α1,3Manβ- substrate "recognition arm." Recognition arm interactions are similar to the enzyme-substrate interactions for Golgi α-mannosidase II, a glycoside hydrolase that acts just before MGAT2 in the Asn-linked glycan biosynthetic pathway. These data suggest that substrate binding by MGAT2 employs both conserved and convergent catalytic subsite modules to provide substrate selectivity and catalysis. More broadly, the MGAT2 active-site architecture demonstrates how glycosyltransferases create complementary modular templates for regiospecific extension of glycan structures in mammalian cells.