5H6Z

Crystal structure of Set7, a novel histone methyltransferase in Schizossacharomyces pombe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Set7 Is a H3K37 Methyltransferase in Schizosaccharomyces pombe and Is Required for Proper Gametogenesis.

Shen, Y.Mevius, D.E.H.F.Caliandro, R.Carrozzini, B.Roh, Y.Kim, J.Kim, S.Ha, S.C.Morishita, M.di Luccio, E.

(2019) Structure 27: 631-638.e8

  • DOI: 10.1016/j.str.2019.01.011
  • Primary Citation of Related Structures:  
    5H6Z, 5WW0

  • PubMed Abstract: 
  • Histone methylation by histone methyltransferases (HMTases) has a key role in transcriptional regulation. Discrepancies between the known HMTases and the histone lysine methylome suggest that HMTases remain to be identified. Here we report the discovery, characterization, and crystal structure of Schizosaccharomyces pombe Set7, an HMTase methylating the uncharted histone H3 lysine 37 (H3K37) mark ...

    Histone methylation by histone methyltransferases (HMTases) has a key role in transcriptional regulation. Discrepancies between the known HMTases and the histone lysine methylome suggest that HMTases remain to be identified. Here we report the discovery, characterization, and crystal structure of Schizosaccharomyces pombe Set7, an HMTase methylating the uncharted histone H3 lysine 37 (H3K37) mark. Set7 forms a dimer with its substrate-binding site structurally specific to K37, not the neighboring well-studied K36 mark. We also discovered that H3K37 methylation levels dramatically increase during gametogenesis. Set7 deletion mutant cells show defects in gametogenesis and produce the abnormal number of spores with aberrant morphology. S. pombe gametogenesis shares similarities with mammalian spermatogenesis. These findings extend our understanding of epigenetic regulation during gametogenesis and support a link between Set7, the epigenetic H3K37 methyl mark, and proper gametogenesis.


    Organizational Affiliation

    Department of Genetic Engineering, School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea. Electronic address: eric.diluccio@gmail.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SET domain-containing protein 7A, B169Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: set7SPCC297.04c
EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt)
UniProt
Find proteins for Q9Y7Q6 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9Y7Q6 
Go to UniProtKB:  Q9Y7Q6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y7Q6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.181α = 90
b = 66.181β = 90
c = 257.699γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
Sir2014phasing
PHENIXmodel building

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
BK21 Plus KNU Creative BioResearch Group, Kyungpook National UniversityKorea, Republic Of--
National Research Foundation of Korea (NRF)Korea, Republic OfNRF-2013R1A1A2012486
NRFKorea, Republic OfCNR-NRF joint projects 2016-2017 #9
National Research Council (CNR)ItalyCNR-NRF joint projects 2016-2017 #9

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Database references, Structure summary
  • Version 1.2: 2019-05-15
    Changes: Data collection, Database references