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Prot Cell    2011, Vol. 2 Issue (3) : 202-214    https://doi.org/10.1007/s13238-011-1018-1      PMID: 21468892
REVIEW
Structure and function of WD40 domain proteins
Chao Xu1, Jinrong Min1,2()
1. Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario, M5G 1L7, Canada; 2. Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Abstract

The WD40 domain exhibits a β-propeller architecture, often comprising seven blades. The WD40 domain is one of the most abundant domains and also among the top interacting domains in eukaryotic genomes. In this review, we will discuss the identification, definition and architecture of the WD40 domains. WD40 domain proteins are involved in a large variety of cellular processes, in which WD40 domains function as a protein-protein or protein-DNA interaction platform. WD40 domain mediates molecular recognition events mainly through the smaller top surface, but also through the bottom surface and sides. So far, no WD40 domain has been found to display enzymatic activity. We will also discuss the different binding modes exhibited by the large versatile family of WD40 domain proteins. In the last part of this review, we will discuss how post-translational modifications are recognized by WD40 domain proteins.
Keywords WD40      beta-propeller      protein-protein interaction      scaffold      post-translational modification     
Corresponding Author(s): Min Jinrong,Email:jr.min@utoronto.ca   
Issue Date: 01 March 2011
 Cite this article:   
Chao Xu,Jinrong Min. Structure and function of WD40 domain proteins[J]. Prot Cell, 2011, 2(3): 202-214.
 URL:  
https://academic.hep.com.cn/pac/EN/10.1007/s13238-011-1018-1
https://academic.hep.com.cn/pac/EN/Y2011/V2/I3/202
Fig.1  Definition of WD40 repeat and WD40 domains.
(A) HMM logo of WD40 repeat from the website http://pfam.sanger.ac.uk/family?id=WD40#tabview=tab3 (). The letter size represents the conservation level of each amino acid in the WD40 repeat.The residues marked by stars are conserved hydrophobic residues involved in WD40 β-propeller stabilization. (B) Structure of a canonical WD40 repeat protein. Each repeat consists of four β-strands. (C) WD40 domain is stabilized mainly through hydrophobic interactions between the blades. (D) Structure comparison of the repeats in the same WD40 protein or between different WD40 proteins. The PDB accession codes for WDR5, WDR39, WDR61, WDR92 and Gβ are 2H9M, 3FM0, 3OW8, 3I2N and 1GP2, respectively.
Fig.1  Definition of WD40 repeat and WD40 domains.
(A) HMM logo of WD40 repeat from the website http://pfam.sanger.ac.uk/family?id=WD40#tabview=tab3 (). The letter size represents the conservation level of each amino acid in the WD40 repeat.The residues marked by stars are conserved hydrophobic residues involved in WD40 β-propeller stabilization. (B) Structure of a canonical WD40 repeat protein. Each repeat consists of four β-strands. (C) WD40 domain is stabilized mainly through hydrophobic interactions between the blades. (D) Structure comparison of the repeats in the same WD40 protein or between different WD40 proteins. The PDB accession codes for WDR5, WDR39, WDR61, WDR92 and Gβ are 2H9M, 3FM0, 3OW8, 3I2N and 1GP2, respectively.
Fig.2  Architecture of WD40 domain proteins shown in cartoon representation.
(A) WDR5 (2H9M); (B) Sif2p (1R5M); (C) Sec13 in complex with Sec31 (2PM6). The SEC13 is colored in green and Sec31 is colored in gray with the insertion repeat colored in salmon; (D) Aip1 (1NR0). The two seven-bladed β-propellers are colored in blue and green, respectively; (E) DDB1 (3EI3). The three seven-bladed β-propellers are colored in red, blue and green, respectively; (F) Superposition of DDB1 from three DDB1 structures. The first two β-propellers of DDB1 can be well superimposedx(colored in gray), but the third β-propeller exhibited significant shift. The shifted β-propeller is colored in red (2HYE), green (3EI2) and blue (2B5L), respectively.
Fig.2  Architecture of WD40 domain proteins shown in cartoon representation.
(A) WDR5 (2H9M); (B) Sif2p (1R5M); (C) Sec13 in complex with Sec31 (2PM6). The SEC13 is colored in green and Sec31 is colored in gray with the insertion repeat colored in salmon; (D) Aip1 (1NR0). The two seven-bladed β-propellers are colored in blue and green, respectively; (E) DDB1 (3EI3). The three seven-bladed β-propellers are colored in red, blue and green, respectively; (F) Superposition of DDB1 from three DDB1 structures. The first two β-propellers of DDB1 can be well superimposedx(colored in gray), but the third β-propeller exhibited significant shift. The shifted β-propeller is colored in red (2HYE), green (3EI2) and blue (2B5L), respectively.
Fig.3  WD40 domain proteins exhibit different binding modes.
(A) The different F-box proteins in the SCF ubiquitin ligase recruit different substrates through the WD40 domain; (B) The different DCAF WD40 proteins recognize different substrates for Cul4-DDB1 ubiquitin ligase; (C) Clathrin (purple) in complex with two different peptides (blue β-arrestin 2/AP-3 1C9I and yellow 1C9L); (D) WDR5 (blue) in complex with MLL (red, 3EMH) and unmodified H3K4 (yellow, 2H9M); (E) TLE1 (green) in complex with eh1 (red, 2CE8) and WRPW (yellow, 2CE9); (F) G protein beta (red)-gamma (blue) heterodimer in complex with alpha (cyan, PDB code: 1GP2) and phosducin (yellow, PDB code: 1A0R).
Fig.3  WD40 domain proteins exhibit different binding modes.
(A) The different F-box proteins in the SCF ubiquitin ligase recruit different substrates through the WD40 domain; (B) The different DCAF WD40 proteins recognize different substrates for Cul4-DDB1 ubiquitin ligase; (C) Clathrin (purple) in complex with two different peptides (blue β-arrestin 2/AP-3 1C9I and yellow 1C9L); (D) WDR5 (blue) in complex with MLL (red, 3EMH) and unmodified H3K4 (yellow, 2H9M); (E) TLE1 (green) in complex with eh1 (red, 2CE8) and WRPW (yellow, 2CE9); (F) G protein beta (red)-gamma (blue) heterodimer in complex with alpha (cyan, PDB code: 1GP2) and phosducin (yellow, PDB code: 1A0R).
Fig.4  Utilization of insertions and extentions inside WD40 repeat domains in ligand binding.
The WD40 protein is colored in gray except the insertion or extension (A) Bub3 (green) in complex with Mad3 (salmon, 2I3T); (B) RBBP7 (blue) in complex with H4 (yellow, 3CFS) and RBBP4 (blue) in complex with Fog-1 (salmon, 2XU7).
Fig.4  Utilization of insertions and extentions inside WD40 repeat domains in ligand binding.
The WD40 protein is colored in gray except the insertion or extension (A) Bub3 (green) in complex with Mad3 (salmon, 2I3T); (B) RBBP7 (blue) in complex with H4 (yellow, 3CFS) and RBBP4 (blue) in complex with Fog-1 (salmon, 2XU7).
Fig.5  Utilization of the inter-blade binding grooves of WD40 domain in ligand binding.
(A) Crystal structure of yeast Sro7 protein. The C-terminal tail of Sro7 is colored in yellow, and the insertion motif from the second WD40 domain of Sro7 is colored in salmon. (B) The first WD40 domain of Sro7 is displayed in surface representation and the two α-helixes from the C-terminal tail of Sro7 reside in two hydrophobic pockets formed between the second and third blades, and the third and fourth blades, respectively. (C) Crystal structure of the C-terminal WD40 domain of PALB2 and the BRCA2 peptide (aa 21-39). The BRCA2 peptide is colored in yellow. The short α-helix from the BRCA2 peptide is bound in a pocket formed between the fourth and fifth blades of the PALB2 WD40 β-propeller.
Fig.5  Utilization of the inter-blade binding grooves of WD40 domain in ligand binding.
(A) Crystal structure of yeast Sro7 protein. The C-terminal tail of Sro7 is colored in yellow, and the insertion motif from the second WD40 domain of Sro7 is colored in salmon. (B) The first WD40 domain of Sro7 is displayed in surface representation and the two α-helixes from the C-terminal tail of Sro7 reside in two hydrophobic pockets formed between the second and third blades, and the third and fourth blades, respectively. (C) Crystal structure of the C-terminal WD40 domain of PALB2 and the BRCA2 peptide (aa 21-39). The BRCA2 peptide is colored in yellow. The short α-helix from the BRCA2 peptide is bound in a pocket formed between the fourth and fifth blades of the PALB2 WD40 β-propeller.
Fig.6  Recognition of post-translational modification marks by WD40 domains.
(A) FBW7 (gray) in complex with cyclin E degron (yellow). The residues involved in binding with phosphorylated peptide are shown in cyan sticks. (B) WDR5 (gray) in complex with dimethylated-H3K4 (red). Residues involved in interaction with H3R2 are shown in green sticks. (C) EED (gray) in complex with trimethylated-H3K27 (yellow). Residues involved in direct interaction with the peptide are shown in blue sticks.
Fig.6  Recognition of post-translational modification marks by WD40 domains.
(A) FBW7 (gray) in complex with cyclin E degron (yellow). The residues involved in binding with phosphorylated peptide are shown in cyan sticks. (B) WDR5 (gray) in complex with dimethylated-H3K4 (red). Residues involved in interaction with H3R2 are shown in green sticks. (C) EED (gray) in complex with trimethylated-H3K27 (yellow). Residues involved in direct interaction with the peptide are shown in blue sticks.
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