Abstract
The C-terminal domain of α-COP, an essential subunit of the COPI coatomer complex, is composed of an all α-helical region and a small β-sheet domain. We show that this β-sheet domain is a Really Interesting New Gene (RING)-like treble clef zinc finger. The zinc-binding residues are substituted by other aminoacids in many homologs including the structurally-characterized proteins from Saccharomyces cerevisiae and Bos taurus. This RING-like domain is possibly related to those of other vesicle membrane-associated complexes, such as CORVET, HOPS and SEA, and likely mediates interactions with Dsl1p and assist in coat oligomerization.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-015-0099-9) contains supplementary material, which is available to authorized users.
Highlights
The C-terminal domain of α-Cytoplasmic coat protein (COP), an essential subunit of the coat protein I (COPI) coatomer complex, is composed of an all α-helical region and a small β-sheet domain
Finding The cytoplasmic coat protein I (COPI) complex, which coats the vesicles involved in retrograde transport of proteins from the Golgi apparatus to the endoplasmic reticulum (ER), and in intra-Golgi protein trafficking, comprises of a coatomer and ADP-ribosylation factor 1 (ARF) GTPase [1,2,3]
The coatomer is a heptameric protein complex with two distinct subcomplexes: an inner cargo-binding heterotetrameric F-subcomplex consisting of β, γ, δ- and ζ-COP, and an outer cage-forming heterotrimeric B-subcomplex consisting of α, β’- and ε-COP. αCOP subunit is a ~1200-residue protein with a N-terminal β-propeller domain (~600-residues; PDBid 4J8G_A), an αhelical region (~200-residues; partial structure in PDBid 3MKQ_B), an unstructured region (~100-residues) and a C-terminal domain (CTD; ~300-residues; PDBid 3MKR_B from Bos taurus; PDBid 3MV3_A from Saccharomyces cerevisiae) (Fig. 1a) [4,5,6,7]
Summary
The C-terminal domain of α-COP, an essential subunit of the COPI coatomer complex, is composed of an all α-helical region and a small β-sheet domain. We show that the β-sheet region of α-COP CTD (PDBid 3MKR_B, residues 1164–1212; PDBid 3MV3_A, residues 1145–1193) is a Really Interesting New Gene (RING)-like binuclear treble clef zinc finger domain. A multiple sequence alignment of the β-sheet domain of representative α-COP sequences, obtained after PSIBLAST [13] and JackHMMER [14] sequence-similarity searches (Additional file 1), reveals putative zinc-chelating residues in homologous sequences at expected structural positions of a RING-like domain (Fig. 1b).
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