Transcription

PDB id

2jv0

Contents

			Protein chain

					163 a.a. *

* Residue conservation analysis

PDB id:

2jv0

Links

Name:

Transcription

Title:

Set domain of riz1 tumor suppressor (prdm2)

Structure:

Pr domain zinc finger protein 2. Chain: a. Fragment: set domain residues 1-161. Synonym: pr domain-containing protein 2, retinoblastoma pro interacting zinc finger protein, zinc finger protein riz, m protein, mtb-zf, gata-3-binding protein g3b. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: prdm2, riz. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

16 models

Authors:

K.Briknarova

Key ref:

K.Briknarová et al. (2008). Structural studies of the SET domain from RIZ1 tumor suppressor. Biochem Biophys Res Commun, 366, 807-813. PubMed id: 18082620 DOI: 10.1016/j.bbrc.2007.12.034

Date:

10-Sep-07

Release date:

22-Jan-08

PROCHECK

	Headers

	References

Protein chain

Q13029 (PRDM2_HUMAN) - PR domain zinc finger protein 2

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					1718 a.a. 163 a.a.*

Key:

PfamA domain

PfamB domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.2.1.1.43 - Histone-lysine N-methyltransferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N₆-methyl-L-lysine-[histone]

S-adenosyl-L-methionine	+	L-lysine-[histone]	=	S-adenosyl-L-homocysteine	+	N(6)-methyl-L-lysine-[histone]

Molecule diagrams generated from .mol files obtained from the KEGG ftp site



		Gene Ontology (GO) functional annotation

Biochemical function

protein binding

1 term

Added reference

DOI no: 10.1016/j.bbrc.2007.12.034	Biochem Biophys Res Commun 366:807-813 (2008)
PubMed id: 18082620

Structural studies of the SET domain from RIZ1 tumor suppressor.
K.Briknarová, X.Zhou, A.Satterthwait, D.W.Hoyt, K.R.Ely, S.Huang.

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 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.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19017266

C.F.Sautel, P.Ortet, N.Saksouk, S.Kieffer, J.Garin, O.Bastien, and M.A.Hakimi (2009).
The histone methylase KMTox interacts with the redox-sensor peroxiredoxin-1 and targets genes involved in Toxoplasma gondii antioxidant defences.

Mol Microbiol, 71, 212-226.

19325838

W.Sun, C.R.Geyer, and J.Yang (2008).
Cloning, Expression, Purification and Crystallization of the PR Domain of Human Retinoblastoma Protein-Binding Zinc Finger Protein 1 (RIZ1).

Int J Mol Sci, 9, 943-950.

18852888

W.Zhou, S.Alonso, D.Takai, S.C.Lu, F.Yamamoto, M.Perucho, and S.Huang (2008).
Requirement of RIZ1 for cancer prevention by methyl-balanced diet.

PLoS ONE, 3, e3390.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.