6KAL

Crystal structure of FKRP in complex with Mg ion and CMP

  • 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: 2.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: 1Go to GlyGen: Q9H9S5-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C5P (Subject of Investigation/LOI)
Query on C5P

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
S [auth C],
Y [auth D]
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]
K [auth B]
L [auth B]
Q [auth C]
R [auth C]
F [auth A],
K [auth B],
L [auth B],
Q [auth C],
R [auth C],
W [auth D],
X [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
P [auth C],
V [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D]
H [auth A]
I [auth A]
N [auth B]
O [auth B]
AA [auth D],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
T [auth C],
U [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.583α = 90
b = 118.674β = 90
c = 252.695γ = 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 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary