6F4Q

Human JMJD5 (Q275C) in complex with Mn(II), NOG and RPS6-A138C (129-144) (complex-2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

JMJD5 is a human arginyl C-3 hydroxylase.

Wilkins, S.E.Islam, S.Gannon, J.M.Markolovic, S.Hopkinson, R.J.Ge, W.Schofield, C.J.Chowdhury, R.

(2018) Nat Commun 9: 1180-1180

  • DOI: 10.1038/s41467-018-03410-w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Oxygenase-catalysed post-translational modifications of basic protein residues, including lysyl hydroxylations and N <sup>ε </sup>-methyl lysyl demethylations, have important cellular roles. Jumonji-C (JmjC) domain-containing protein 5 (JMJD5), which ...

    Oxygenase-catalysed post-translational modifications of basic protein residues, including lysyl hydroxylations and N ε -methyl lysyl demethylations, have important cellular roles. Jumonji-C (JmjC) domain-containing protein 5 (JMJD5), which genetic studies reveal is essential in animal development, is reported as a histone N ε -methyl lysine demethylase (KDM). Here we report how extensive screening with peptides based on JMJD5 interacting proteins led to the finding that JMJD5 catalyses stereoselective C-3 hydroxylation of arginine residues in sequences from human regulator of chromosome condensation domain-containing protein 1 (RCCD1) and ribosomal protein S6 (RPS6). High-resolution crystallographic analyses reveal overall fold, active site and substrate binding/product release features supporting the assignment of JMJD5 as an arginine hydroxylase rather than a KDM. The results will be useful in the development of selective oxygenase inhibitors for the treatment of cancer and genetic diseases.


    Organizational Affiliation

    Leicester Institute of Structural and Chemical Biology and Department of Chemistry, University of Leicester, Lancaster Road, Leicester, LE1 7RH, UK.,Stanford University School of Medicine, Department of Molecular and Cellular Physiology, Clark Center, Stanford, CA, 94305-5345, USA. rashed.chowdhury@stanford.edu.,The Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK. christopher.schofield@chem.ox.ac.uk.,The Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,The Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK. rashed.chowdhury@stanford.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
JmjC domain-containing protein 5
A
255Homo sapiensMutation(s): 5 
Gene Names: KDM8 (JMJD5)
EC: 1.14.11.-, 3.4.-.-
Find proteins for Q8N371 (Homo sapiens)
Go to Gene View: KDM8
Go to UniProtKB:  Q8N371
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
B
16Homo sapiensMutation(s): 1 
Gene Names: RPS6
Find proteins for P62753 (Homo sapiens)
Go to Gene View: RPS6
Go to UniProtKB:  P62753
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

Download SDF File 
Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.139 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.406α = 90.00
b = 65.073β = 90.00
c = 77.769γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release