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 8KB7 | pdb_00008kb7

Crystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2)

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

  • Deposited: 2023-08-04 Released: 2024-08-07 
  • Deposition Author(s): Satoh, T., Umezawa, F., Yagi, H., Kato, K.
  • Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.228 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.191 (Depositor) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8KB7

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Dynamic Organizational Strategies of Multidomain Glycosyltransferases Revealed by High-Speed AFM and Solution Biophysics.

Yagi, H., Lin, Y.R., Kanaoka, Y., Umezawa, F., Kim, A., Tomuro, K., Morishima, K., Kodama, A., Ishii, K., Uchiyama, S., Satoh, T., Sugiyama, M., Uchihashi, T., Kato, K.

(2026) Int J Mol Sci 27

  • DOI: https://doi.org/10.3390/ijms27146423
  • Primary Citation Related Structures: 
    8KB7

  • PubMed Abstract: 

    Glycosyltransferases often contain multiple structural modules that contribute to substrate recognition, catalytic coordination, and higher-order molecular organization. However, how multidomain glycosyltransferases dynamically organize their catalytic domains in solution remains poorly understood. Here, we investigated the assembly states and conformational dynamics of POMGNT2, LARGE1, K4CP, and L137 using high-speed atomic force microscopy (HS-AFM) integrated with complementary solution biophysical analyses. This multi-technique approach extends previous static structural studies by enabling a parallel comparison of solution-state dynamics among multiple glycosyltransferases. POMGNT2 formed a stable dimeric architecture with limited large-scale conformational fluctuation, consistent with its role in site-selective substrate recognition. In contrast, LARGE1 and K4CP exhibited concentration-dependent and heterogeneous assembly behavior. K4CP displayed pronounced open-closed interdomain motion and a tendency toward more compact conformations in the presence of substrate, suggesting dynamic catalytic-domain reorganization during glycan elongation. By comparison, the mimivirus glycosyltransferase candidate L137 predominantly behaved as a monomeric species under the tested conditions. These findings demonstrate that multidomain glycosyltransferases employ diverse dynamic organizational strategies ranging from rigid recognition architectures to highly flexible and reversible catalytic assemblies. Our results further suggest that glycosyltransferase function is governed not only by catalytic-domain structure, but also by dynamic conformational coordination adapted to distinct catalytic demands.


  • Organizational Affiliation: 
    • Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-Dori, Mizuho-Ku, Nagoya 467-8603, Japan.

Macromolecule Content 

  • Total Structure Weight: 260.83 kDa 
  • Atom Count: 16,869 
  • Modeled Residue Count: 2,041 
  • Deposited Residue Count: 2,232 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
A, B, C, D
558Homo sapiensMutation(s): 0 
Gene Names: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2
EC: 2.4.1.312
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NAT1 (Homo sapiens)
Explore Q8NAT1 
Go to UniProtKB:  Q8NAT1
PHAROS:  Q8NAT1
GTEx:  ENSG00000144647 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NAT1
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q8NAT1-1
Sequence Annotations
Expand
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
E [auth A],
J [auth B],
N [auth C],
S [auth D]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
K [auth B]
O [auth C]
P [auth C]
F [auth A],
G [auth A],
K [auth B],
O [auth C],
P [auth C],
T [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
(Subject of Investigation/LOI)

Query on MAN



Download:Ideal Coordinates CCD File
H [auth A],
L [auth B],
Q [auth C],
U [auth D]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A],
M [auth B],
R [auth C],
V [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.228 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.191 (Depositor) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.019α = 90
b = 150.002β = 90
c = 191.481γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan23gm6410010h0004
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanJP19H03361

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Structure summary
  • Version 1.2: 2026-09-23
    Changes: Database references