Vesicular trafficking pathways sort transmembrane proteins and lipids into small vesicles that invaginate into the endosome. Endosomes coordinate the transport of endocytic, biosynthetic and recycling cargoes. Multivesicular bodies (MVBs) are late endosomes which contain lumenal vesicles that are sorted for delivery either in the lysosome in metazoans, or into the vacuole in yeast or may be targeted for extracellular release. MVBs fuse with the vacuole/lysosome where the vesicles and their contents are degraded by hydrolases. The sorting of MVB cargo and budding of vesicles into the MVB lumen require the endosomal sorting complex required for transport (ESCRT) complexes I, II and III. The ESCRT-III complex of yeast assembles on endosomal membranes for the formation of a new vesicle within the MVB cargo.

The BRO1 domain is a ~390 residue domain, present in proteins such as yeast BRO1 and human PDCD6IP/Alix that are involved in protein targeting to the vacuole or lysosome. The BRO1 domain of fungal and mammalian proteins binds with multivesicular body components (ESCRT-III proteins) such as yeast Snf7 and mammalian CHMP4b, and can function to target BRO1 domain-containing proteins to endosomes [1,2,3].

The 3D structure of the BRO1 domain has a boomerang shape composed of 14 α helices and 3 β sheets (see <PDB:1ZB1>) and contains a TPR-like substructure (see <PDOC50005>) in the central part [1]. The C-terminus is less conserved.

Some proteins known to contain a BRO1 domain:

• Fungal vacuolar protein-sorting protein BRO1 involved in concentration and sorting of cargo proteins of the MVB for incorporation into intralumenal vesicles.
• Mammalian programmed cell death 6-interacting protein (PDCD6IP), a BRO1 homolog. Human PDCD6IP is also required for HIV budding.
• Mammalian tyrosine-protein phosphatase non-receptor type 23 (PTPN23).
• Vertebrate rhophilin, a GTP-Rho binding protein.
• Fungal pH-response regulator proteins RIM20/palA and palC, which are required for the proteolytic activation of the transcription factor RIM101 in response to alkaline ambient pH [3].
• Caenorhabditis elegans apoptosis-linked gene 2-interacting protein X 1 (alx-1), a BRO1 homolog, involved in post-internalization trafficking and degradation.

The profile we developed covers the entire BRO1 domain and has been manually adapted to detect the less conserved C-terminal parts.