5XOO

The structure of hydra Fam20 with sugar

  • Classification: TRANSFERASE
  • Organism(s): Hydra vulgaris
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2017-05-29 Released: 2018-04-11 
  • Deposition Author(s): Zhang, H., Xiao, J.
  • Funding Organization(s): National Science Foundation of China, National Key Research & Development Plan

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structure and evolution of the Fam20 kinases

Zhang, H.Zhu, Q.Cui, J.Wang, Y.Chen, M.J.Guo, X.Tagliabracci, V.S.Dixon, J.E.Xiao, J.

(2018) Nat Commun 9: 1218-1218

  • DOI: 10.1038/s41467-018-03615-z
  • Primary Citation of Related Structures:  
    5XOM, 5XOO, 5YH0, 5YH2, 5YH3

  • PubMed Abstract: 
  • The Fam20 proteins are novel kinases that phosphorylate secreted proteins and proteoglycans. Fam20C phosphorylates hundreds of secreted proteins and is activated by the pseudokinase Fam20A. Fam20B phosphorylates a xylose residue to regulate proteoglycan synthesis ...

    The Fam20 proteins are novel kinases that phosphorylate secreted proteins and proteoglycans. Fam20C phosphorylates hundreds of secreted proteins and is activated by the pseudokinase Fam20A. Fam20B phosphorylates a xylose residue to regulate proteoglycan synthesis. Despite these wide-ranging and important functions, the molecular and structural basis for the regulation and substrate specificity of these kinases are unknown. Here we report molecular characterizations of all three Fam20 kinases, and show that Fam20C is activated by the formation of an evolutionarily conserved homodimer or heterodimer with Fam20A. Fam20B has a unique active site for recognizing Galβ1-4Xylβ1, the initiator disaccharide within the tetrasaccharide linker region of proteoglycans. We further show that in animals the monomeric Fam20B preceded the appearance of the dimeric Fam20C, and the dimerization trait of Fam20C emerged concomitantly with a change in substrate specificity. Our results provide comprehensive structural, biochemical, and evolutionary insights into the function of the Fam20 kinases.


    Organizational Affiliation

    The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China. junyuxiao@pku.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosaminoglycan xylosylkinaseA, B393Hydra vulgarisMutation(s): 0 
Gene Names: FAM20B
UniProt
Find proteins for T2MHS6 (Hydra vulgaris)
Explore T2MHS6 
Go to UniProtKB:  T2MHS6
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-xylopyranoseC2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G78098IA
GlyCosmos:  G78098IA
GlyGen:  G78098IA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.601α = 90
b = 123.58β = 90
c = 143.936γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-29 
  • Released Date: 2018-04-11 
  • Deposition Author(s): Zhang, H., Xiao, J.

Funding OrganizationLocationGrant Number
National Science Foundation of ChinaChina31570735
National Key Research & Development PlanChina2016YFC0906000

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary