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 

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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: https://doi.org/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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosaminoglycan xylosylkinase
A, B
393Hydra vulgarisMutation(s): 0 
Gene Names: FAM20B
UniProt
Find proteins for T2MHS6 (Hydra vulgaris)
Explore T2MHS6 
Go to UniProtKB:  T2MHS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2MHS6
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-xylopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G78098IA
GlyCosmos:  G78098IA
GlyGen:  G78098IA
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADN
Query on ADN

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MBN
Query on MBN

Download Ideal Coordinates CCD File 
F [auth A]TOLUENE
C7 H8
YXFVVABEGXRONW-UHFFFAOYSA-N
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

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Entry History & Funding Information

Deposition Data


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
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary