PDBsum entry 5tdr

Transcription

PDB id: 5tdr

Contents

Protein chains

70 a.a.

11 a.a.

Metals

_NA ×2

_ZN ×2

Waters ×201

PDB id:

5tdr

Name:

Transcription

Title:

Set3 phd finger in complex with histone h3k4me2

Structure:

Set domain-containing protein 3. Chain: a. Fragment: unp residues 116-184. Engineered: yes. Histone h3. Chain: b. Engineered: yes

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: set3, ykr029c. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes.

Resolution:

1.42Å R-factor: 0.155 R-free: 0.200

Authors:

F.H.Andrews,M.Ali,T.G.Kutateladze

Key ref:

J.Gatchalian et al. (2017). Structural Insight into Recognition of Methylated Histone H3K4 by Set3. J Mol Biol, 429, 2066-2074. PubMed id: 27697561

Date:

19-Sep-16 Release date: 02-Nov-16

Protein chain

P36124  (SET3_YEAST) -  SET domain-containing protein 3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 751 a.a.

Struc: 70 a.a.*

Protein chain

P68431  (H31_HUMAN) -  Histone H3.1 from Homo sapiens

Seq: 136 a.a.

Struc: 11 a.a.*

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

J Mol Biol 429:2066-2074 (2017)

PubMed id: 27697561

Structural Insight into Recognition of Methylated Histone H3K4 by Set3.

J.Gatchalian, M.Ali, F.H.Andrews, Y.Zhang, A.S.Barrett, T.G.Kutateladze.

ABSTRACT

The plant homeodomain (PHD) finger of Set3 binds methylated lysine 4 of histone H3 in vitro and in vivo; however, precise selectivity of this domain has not been fully characterized. Here, we explore the determinants of methyllysine recognition by the PHD fingers of Set3 and its orthologs. We use X-ray crystallographic and spectroscopic approaches to show that the Set3 PHD finger binds di- and trimethylated states of H3K4 with comparable affinities and employs similar molecular mechanisms to form complexes with either mark. Composition of the methyllysine-binding pocket plays an essential role in determining the selectivity of the PHD fingers. The finding that the histone-binding activity is not conserved in the PHD finger of Set4 suggests different functions for the Set3 and Set4 paralogs.