3FK3

Structure of the Yeats Domain, Yaf9

Summary for 3FK3

• Entry DOI: 10.2210/pdb3fk3/pdb
• Descriptor: Protein AF-9 homolog (2 entities in total)
• Functional Keywords: beta-sandwich, activator, chromatin regulator, dna damage, dna repair, nucleus, transcription, transcription regulation
• Biological source: Saccharomyces cerevisiae (yeast)
• Cellular location: Cytoplasm: P53930
• Total number of polymer chains: 3
• Total formula weight: 57053.94

Authors

Wang, A.Y.,Schulze, J.M.,Skordalakes, E.,Berger, J.M.,Rine, J.,Kobor, M.S. (deposition date: 2008-12-15, release date: 2009-10-27, Last modification date: 2021-03-31)

Primary citation

Wang, A.Y.,Schulze, J.M.,Skordalakes, E.,Gin, J.W.,Berger, J.M.,Rine, J.,Kobor, M.S.
Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation
Proc.Natl.Acad.Sci.USA, 106:21573-21578, 2009

PubMed Abstract: Chromatin can be modified by posttranslational modifications of histones, ATP-dependent remodeling, and incorporation of histone variants. The Saccharomyces cerevisiae protein Yaf9 is a subunit of both the essential histone acetyltransferase complex NuA4 and the ATP-dependent chromatin remodeling complex SWR1-C, which deposits histone variant H2A.Z into euchromatin. Yaf9 contains a YEATS domain, found in proteins associated with multiple chromatin-modifying enzymes and transcription complexes across eukaryotes. Here, we established the conservation of YEATS domain function from yeast to human, and determined the structure of this region from Yaf9 by x-ray crystallography to 2.3 A resolution. The Yaf9 YEATS domain consisted of a beta-sandwich characteristic of the Ig fold and contained three distinct conserved structural features. The structure of the Yaf9 YEATS domain was highly similar to that of the histone chaperone Asf1, a similarity that extended to an ability of Yaf9 to bind histones H3 and H4 in vitro. Using structure-function analysis, we found that the YEATS domain was required for Yaf9 function, histone variant H2A.Z chromatin deposition at specific promoters, and H2A.Z acetylation.

PubMed: 19966225
DOI: 10.1073/pnas.0906539106

Experimental method

X-RAY DIFFRACTION (2.3 Å)