PDBsum entry 4yym

Protein binding

PDB id: 4yym

Contents

Protein chains

132 a.a.

Ligands

BTK-GLY-GLY-BTK-GLY-LEU-GLY

Metals

_CA

Waters ×199

PDB id:

4yym

Name:

Protein binding

Title:

Crystal structure of taf1 bd2 bromodomain bound to a butyryllysine peptide

Structure:

Transcription initiation factor tfiid subunit 1. Chain: a, b. Fragment: bromodomain (unp residues 1497-1638). Synonym: cell cycle gene 1 protein, tbp-associated factor 250 kda, p250, transcription initiation factor tfiid 250 kda subunit, tafii250. Engineered: yes. Histone h4. Chain: z.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: taf1, ba2r, ccg1, ccgs, taf2a. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 9606

Resolution:

1.50Å R-factor: 0.220 R-free: 0.261

Authors:

Y.Tang,S.Bellon,A.G.Cochran,F.Poy

Key ref:

E.M.Flynn et al. (2015). A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications. Structure, 23, 1801-1814. PubMed id: 26365797 DOI: 10.1016/j.str.2015.08.004

Date:

24-Mar-15 Release date: 16-Sep-15

Protein chains

P21675  (TAF1_HUMAN) -  Transcription initiation factor TFIID subunit 1 from Homo sapiens

Seq: 1872 a.a.

Struc: 132 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.3.1.48 - histone acetyltransferase.
• Reaction: L-lysyl-[protein] + acetyl-CoA = N₆-acetyl-L-lysyl-[protein] + CoA + H⁺
• Enzyme class 2: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/j.str.2015.08.004

Structure 23:1801-1814 (2015)

PubMed id: 26365797

A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications.

E.M.Flynn, O.W.Huang, F.Poy, M.Oppikofer, S.F.Bellon, Y.Tang, A.G.Cochran.

ABSTRACT

Bromodomains are epigenetic readers that are recruited to acetyllysine residues in histone tails. Recent studies have identified non-acetyl acyllysine modifications, raising the possibility that these might be read by bromodomains. Profiling the nearly complete human bromodomain family revealed that while most human bromodomains bind only the shorter acetyl and propionyl marks, the bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 also recognize the longer butyryl mark. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks. None of the human bromodomains tested binds succinyl marks. We characterized structurally and biochemically the binding to different acyl groups, identifying bromodomain residues and structural attributes that contribute to specificity. These studies demonstrate a surprising degree of plasticity in some human bromodomains but no single factor controlling specificity across the family. The identification of candidate butyryl- and crotonyllysine readers supports the idea that these marks could have specific physiological functions.