Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98.12 kDa 
• Atom Count: 6598 
• Residue Count: 709 
• Unique protein chains: 1

5VCM

Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound UDP and Manganese

• DOI: 10.2210/pdb5VCM/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-03-31 Released: 2018-04-11 
• Deposition Author(s): Sanders, J.H., Kadirvelraj, R., Wood, Z.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.220 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 

Literature

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

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

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

• PubMed: 29666272 
• DOI: 10.1073/pnas.1716988115
• Primary Citation of Related Structures:  
  5VCS, 5VCR, 5VCM


• PubMed 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 Mn ²⁺ -UDP donor analog complex and as a GlcNAcMan ₃ GlcNAc ₂ -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.

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Organizational Affiliation: 

Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-4712.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase	A, B	419	Homo sapiens	Mutation(s): 0  Gene Names: MGAT2 EC: 2.4.1.143
Find proteins for Q10469 (Homo sapiens) Explore Q10469  Go to UniProtKB:  Q10469
NIH Common Fund Data Resources
PHAROS:  Q10469 GTEx:  ENSG00000168282

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	A	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
NAG	B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
DMS	A, B	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	A, B	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.220 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.13	α = 90
b = 139.33	β = 111.08
c = 63.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-03-31 
• Released Date: 2018-04-11 
Deposition Author(s): Sanders, J.H., Kadirvelraj, R., Wood, Z.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1P01GM107012-02

Revision History 

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2018-05-02
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2018-05-16
  Changes: Data collection, Database references
• Version 1.4: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.5: 2020-01-01
  Changes: Author supporting evidence
• Version 1.6: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary