6KAM | pdb_00006kam

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 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CDPClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view detailsBest fitted RB0Click on this verticalbar to view details

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]
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 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CDPClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view detailsBest fitted RB0Click on this verticalbar to view details

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