6KAM

Crystal structure of FKRP in complex with Ba ion, CDP-ribtol, and sugar acceptor

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

  • Deposited: 2019-06-23 Released: 2020-01-15 
  • Deposition Author(s): Kuwabara, N.
  • Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Crystal structures of fukutin-related protein (FKRP), a ribitol-phosphate transferase related to muscular dystrophy.

Kuwabara, N.Imae, R.Manya, H.Tanaka, T.Mizuno, M.Tsumoto, H.Kanagawa, M.Kobayashi, K.Toda, T.Senda, T.Endo, T.Kato, R.

(2020) Nat Commun 11: 303-303

  • DOI: https://doi.org/10.1038/s41467-019-14220-z
  • Primary Citation of Related Structures:  
    6KAJ, 6KAK, 6KAL, 6KAM, 6KAN, 6L7S, 6L7T, 6L7U

  • PubMed Abstract: 

    α-Dystroglycan (α-DG) is a highly-glycosylated surface membrane protein. Defects in the O-mannosyl glycan of α-DG cause dystroglycanopathy, a group of congenital muscular dystrophies. The core M3 O-mannosyl glycan contains tandem ribitol-phosphate (RboP), a characteristic feature first found in mammals. Fukutin and fukutin-related protein (FKRP), whose mutated genes underlie dystroglycanopathy, sequentially transfer RboP from cytidine diphosphate-ribitol (CDP-Rbo) to form a tandem RboP unit in the core M3 glycan. Here, we report a series of crystal structures of FKRP with and without donor (CDP-Rbo) and/or acceptor [RboP-(phospho-)core M3 peptide] substrates. FKRP has N-terminal stem and C-terminal catalytic domains, and forms a tetramer both in crystal and in solution. In the acceptor complex, the phosphate group of RboP is recognized by the catalytic domain of one subunit, and a phosphate group on O-mannose is recognized by the stem domain of another subunit. Structure-based functional studies confirmed that the dimeric structure is essential for FKRP enzymatic activity.


  • Organizational Affiliation

    Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, 305-0801, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fukutin-related protein
A, B, C, D
455Homo sapiensMutation(s): 0 
Gene Names: FKRP
EC: 2.7.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9S5 (Homo sapiens)
Explore Q9H9S5 
Go to UniProtKB:  Q9H9S5
PHAROS:  Q9H9S5
GTEx:  ENSG00000181027 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H9S5
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q9H9S5-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose
E
3N/A
Glycosylation Resources
GlyTouCan:  G82715NG
GlyCosmos:  G82715NG
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDP (Subject of Investigation/LOI)
Query on CDP

Download Ideal Coordinates CCD File 
AA [auth D],
I [auth A],
N [auth B],
T [auth C]
CYTIDINE-5'-DIPHOSPHATE
C9 H15 N3 O11 P2
ZWIADYZPOWUWEW-XVFCMESISA-N
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
M [auth B]
R [auth C]
S [auth C]
G [auth A],
H [auth A],
M [auth B],
R [auth C],
S [auth C],
Y [auth D],
Z [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
RB0 (Subject of Investigation/LOI)
Query on RB0

Download Ideal Coordinates CCD File 
BA [auth D],
J [auth A],
O [auth B],
U [auth C]
D-ribitol
C5 H12 O5
HEBKCHPVOIAQTA-ZXFHETKHSA-N
BA (Subject of Investigation/LOI)
Query on BA

Download Ideal Coordinates CCD File 
CA [auth D],
K [auth A],
P [auth B],
V [auth C]
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
DA [auth D],
W [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
Q [auth C],
X [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.571α = 90
b = 119.24β = 90
c = 254.646γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2020-01-15 
  • Deposition Author(s): Kuwabara, N.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16K07284
Japan Society for the Promotion of ScienceJapan26840029

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary