2JV0

SET domain of RIZ1 tumor suppressor (PRDM2)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 16 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural studies of the SET domain from RIZ1 tumor suppressor

Briknarova, K.Zhou, X.Satterthwait, A.Hoyt, D.W.Ely, K.R.Huang, S.

(2008) Biochem.Biophys.Res.Commun. 366: 807-813

  • DOI: 10.1016/j.bbrc.2007.12.034

  • PubMed Abstract: 
  • RIZ1 is a transcriptional regulator and tumor suppressor that catalyzes methylation of lysine 9 of histone H3. It contains a distinct SET domain, sometimes referred to as PR (PRDI-BF1 and RIZ1 homology) domain, that is responsible for its catalytic a ...

    RIZ1 is a transcriptional regulator and tumor suppressor that catalyzes methylation of lysine 9 of histone H3. It contains a distinct SET domain, sometimes referred to as PR (PRDI-BF1 and RIZ1 homology) domain, that is responsible for its catalytic activity. We determined the solution structure of the PR domain from RIZ1 and characterized its interaction with S-adenosyl-l-homocysteine (SAH) and a peptide from histone H3. Despite low sequence identity with canonical SET domains, the PR domain displays a typical SET fold including a pseudo-knot at the C-terminus. The N-flanking sequence of RIZ1 PR domain adopts a novel conformation and interacts closely with the SET fold. The C-flanking sequence contains an alpha-helix that points away from the protein face that harbors active site in other SET domains. The SET fold of RIZ1 does not have detectable affinity for SAH but it interacts with a synthetic peptide comprising residues 1-20 of histone H3.


    Organizational Affiliation

    Department of Chemistry, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PR domain zinc finger protein 2
A
163Homo sapiensMutation(s): 2 
Gene Names: PRDM2 (KMT8, RIZ)
EC: 2.1.1.43
Find proteins for Q13029 (Homo sapiens)
Go to Gene View: PRDM2
Go to UniProtKB:  Q13029
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
IAS
Query on IAS
A
L-beta-peptide, C-gamma linkingC4 H7 N O4

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 16 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 2JV0 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-09-10 
  • Released Date: 2008-01-22 
  • Deposition Author(s): Briknarova, K.

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-27
    Type: Database references, Derived calculations, Non-polymer description