9F5H | pdb_00009f5h

Crystal structure of MGAT5 bump-and-hole mutant in complex with UDP and M592


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.242 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9F5H

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

A Bioorthogonal Precision Tool for Human N -Acetylglucosaminyltransferase V.

Liu, Y.Bineva-Todd, G.Meek, R.W.Mazo, L.Piniello, B.Moroz, O.Burnap, S.A.Begum, N.Ohara, A.Roustan, C.Tomita, S.Kjaer, S.Polizzi, K.Struwe, W.B.Rovira, C.Davies, G.J.Schumann, B.

(2024) J Am Chem Soc 146: 26707-26718

  • DOI: https://doi.org/10.1021/jacs.4c05955
  • Primary Citation Related Structures: 
    9F5H

  • PubMed Abstract: 

    Correct elaboration of N-linked glycans in the secretory pathway of human cells is essential in physiology. Early N-glycan biosynthesis follows an assembly line principle before undergoing crucial elaboration points that feature the sequential incorporation of the sugar N -acetylglucosamine (GlcNAc). The activity of GlcNAc transferase V (MGAT5) primes the biosynthesis of an N-glycan antenna that is heavily upregulated in cancer. Still, the functional relevance and substrate choice of MGAT5 are ill-defined. Here, we employ protein engineering to develop a bioorthogonal substrate analog for the activity of MGAT5. Chemoenzymatic synthesis is used to produce a collection of nucleotide-sugar analogs with bulky, bioorthogonal acylamide side chains. We find that WT-MGAT5 displays considerable activity toward such substrate analogues. Protein engineering yields an MGAT5 variant that loses activity against the native nucleotide sugar and increases activity toward a 4-azidobutyramide-containing substrate analogue. By such restriction of substrate specificity, we show that the orthogonal enzyme-substrate pair is suitable to bioorthogonally tag glycoproteins. Through X-ray crystallography and molecular dynamics simulations, we establish the structural basis of MGAT5 engineering, informing the design rules for bioorthogonal precision chemical tools.


  • Organizational Affiliation
    • Department of Chemistry, Imperial College London, London W12 0BZ, U.K.

Macromolecule Content 

  • Total Structure Weight: 119.42 kDa 
  • Atom Count: 8,396 
  • Modeled Residue Count: 1,008 
  • Deposited Residue Count: 1,030 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Secreted alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
A, B
515Homo sapiensMutation(s): 3 
Gene Names: MGAT5GGNT5
EC: 2.4.1.155
UniProt & NIH Common Fund Data Resources
Find proteins for Q09328 (Homo sapiens)
Explore Q09328 
Go to UniProtKB:  Q09328
PHAROS:  Q09328
GTEx:  ENSG00000152127 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09328
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP
(Subject of Investigation/LOI)

Query on UDP



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN

Query on MAN



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.242 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.200 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.507α = 108.208
b = 69.069β = 92.088
c = 90.993γ = 106.747
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union951231

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary