PDBsum entry: 2rnz

Transferase

PDB id: 2rnz

Contents

Protein chain

94 a.a. *

* Residue conservation analysis

PDB id:

2rnz

Name:

Transferase

Title:

Solution structure of the presumed chromodomain of the yeast histone acetyltransferase, esa1

Structure:

Histone acetyltransferase esa1. Chain: a. Fragment: residues 17-89. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 469008.

NMR struc:

20 models

Authors:

H.Shimojo,N.Sano,Y.Moriwaki,M.Okuda,M.Horikoshi,Y.Nishimura

Key ref:

H.Shimojo et al. (2008). Novel structural and functional mode of a knot essential for RNA binding activity of the Esa1 presumed chromodomain. J Mol Biol, 378, 987. PubMed id: 18407291 DOI: 10.1016/j.jmb.2008.03.021

Date:

01-Mar-08 Release date: 29-Apr-08

Protein chain

Q08649  (ESA1_YEAST) -  Histone acetyltransferase ESA1

Seq: 445 a.a.

Struc: 94 a.a.*

* PDB and UniProt seqs differ at 15 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.3.1.48 - Histone acetyltransferase.
• Reaction: Acetyl-CoA + [histone] = CoA + acetyl-[histone]

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

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (2 terms)
• Biological process: chromatin assembly or disassembly (1 term)
• Biochemical function: chromatin binding (1 term)

Added reference

DOI no: 10.1016/j.jmb.2008.03.021

J Mol Biol 378:987 (2008)

PubMed id: 18407291

Novel structural and functional mode of a knot essential for RNA binding activity of the Esa1 presumed chromodomain.

H.Shimojo, N.Sano, Y.Moriwaki, M.Okuda, M.Horikoshi, Y.Nishimura.

ABSTRACT

Chromodomains are methylated histone binding modules that have been widely studied. Interestingly, some chromodomains are reported to bind to RNA and/or DNA, although the molecular basis of their RNA/DNA interactions has not been solved. Here we propose a novel binding mode for chromodomain-RNA interactions. Essential Sas-related acetyltransferase 1 (Esa1) contains a presumed chromodomain in addition to a histone acetyltransferase domain. We initially determined the solution structure of the Esa1 presumed chromodomain and showed it to consist of a well-folded structure containing a five-stranded beta-barrel similar to the tudor domain rather than the canonical chromodomain. Furthermore, the domain showed no RNA/DNA binding ability. Because the N-terminus of the protein forms a helical turn, we prepared an N-terminally extended construct, which we surprisingly found to bind to poly(U) and to be critical for in vivo function. This extended protein contains an additional beta-sheet that acts as a knot for the tudor domain and binds to oligo(U) and oligo(C) with greater affinity compared with other oligo-RNAs and DNAs examined thus far. The knot does not cause a global change in the core structure but induces a well-defined loop in the tudor domain itself, which is responsible for RNA binding. We made 47 point mutants in an esa1 mutant gene in yeast in which amino acids of the Esa1 knotted tudor domain were substituted to alanine residues and their functional abilities were examined. Interestingly, the knotted tudor domain mutations that were lethal to the yeast lost poly(U) binding ability. Amino acids that are related to RNA interaction sites, as revealed by both NMR and affinity binding experiments, are found to be important in vivo. These findings are the first demonstration of how the novel structure of the knotted tudor domain impacts on RNA binding and how this influences in vivo function.

Selected figure(s)

Figure 2.
Fig. 2. Overall structure of the Esa1 short tudor domain. (a) Stereo view of the superposition of the 20 representative structures of the Esa1 presumed chromodomain structure with the lowest energy. The region unassigned by NMR is shown in blue. The His-tag region is not shown. (b) Ribbon diagram of the Esa1 short tudor domain structure. The structure closest to the mean structure of the 20 lowest energy structures is shown with the secondary structural elements labeled.

Figure 3.
Fig. 3. Overall structure of the Esa1 knotted tudor domain. (a) Stereo view of the superimposition of 20 representative structures of the Esa1 knotted tudor domain with the lowest energy. (b) Ribbon diagram of the Esa1 knotted tudor domain structure. The structure closest to the mean structure of the 20 lowest energy structures is shown with the secondary structural elements labeled.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 378, 987-0) copyright 2008.

Figures were selected by an automated process.