2FID

Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin

Summary for 2FID

• Entry DOI: 10.2210/pdb2fid/pdb
• Related: 2FIF
• Descriptor: Ubiquitin, Rab5 GDP/GTP exchange factor, ZINC ION, ... (4 entities in total)
• Functional Keywords: zinc finger, helix, protein turnover-endocytosis complex, protein turnover/endocytosis
• Biological source: Bos taurus (cattle); More
• Cellular location: Cytoplasm: O18973
• Total number of polymer chains: 2
• Total formula weight: 16766.22

Authors

Lee, S.,Hurley, J.H. (deposition date: 2005-12-29, release date: 2006-02-07, Last modification date: 2024-02-14)

Primary citation

Lee, S.,Tsai, Y.C.,Mattera, R.,Smith, W.J.,Kostelansky, M.S.,Weissman, A.M.,Bonifacino, J.S.,Hurley, J.H.
Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5
Nat.Struct.Mol.Biol., 13:264-271, 2006

PubMed Abstract: Rabex-5 is an exchange factor for Rab5, a master regulator of endosomal trafficking. Rabex-5 binds monoubiquitin, undergoes covalent ubiquitination and contains an intrinsic ubiquitin ligase activity, all of which require an N-terminal A20 zinc finger followed immediately by a helix. The structure of the N-terminal portion of Rabex-5 bound to ubiquitin at 2.5-A resolution shows that Rabex-5-ubiquitin interactions occur at two sites. The first site is a new type of ubiquitin-binding domain, an inverted ubiquitin-interacting motif, which binds with approximately 29-microM affinity to the canonical Ile44 hydrophobic patch on ubiquitin. The second is a diaromatic patch on the A20 zinc finger, which binds with approximately 22-microM affinity to a polar region centered on Asp58 of ubiquitin. The A20 zinc-finger diaromatic patch mediates ubiquitin-ligase activity by directly recruiting a ubiquitin-loaded ubiquitin-conjugating enzyme.

PubMed: 16462746
DOI: 10.1038/nsmb1064

Experimental method

X-RAY DIFFRACTION (2.8 Å)