1Q5W

Ubiquitin Recognition by Npl4 Zinc-Fingers

Summary for 1Q5W

• Entry DOI: 10.2210/pdb1q5w/pdb
• Related: 1NJ3
• Descriptor: homolog of yeast nuclear protein localization 4, Ubiquitin, ZINC ION (3 entities in total)
• Functional Keywords: ubiquitin, protein-protein complex, zinc-finger, rubredoxin knuckle, nzf domain, protein binding
• Biological source: Rattus norvegicus (Norway rat); More
• Cellular location: Cytoplasm, cytosol: Q9ES54
• Total number of polymer chains: 2
• Total formula weight: 12019.10

Authors

Alam, S.L.,Sun, J.,Payne, M.,Welch, B.D.,Blake, B.K.,Davis, D.R.,Meyer, H.H.,Emr, S.D.,Sundquist, W.I. (deposition date: 2003-08-11, release date: 2004-03-30, Last modification date: 2024-05-22)

Primary citation

Alam, S.L.,Sun, J.,Payne, M.,Welch, B.D.,Blake, B.K.,Davis, D.R.,Meyer, H.H.,Emr, S.D.,Sundquist, W.I.
Ubiquitin interactions of NZF zinc fingers.
Embo J., 23:1411-1421, 2004

PubMed Abstract: Ubiquitin (Ub) functions in many different biological pathways, where it typically interacts with proteins that contain modular Ub recognition domains. One such recognition domain is the Npl4 zinc finger (NZF), a compact zinc-binding module found in many proteins that function in Ub-dependent processes. We now report the solution structure of the NZF domain from Npl4 in complex with Ub. The structure reveals that three key NZF residues (13TF14/M25) surrounding the zinc coordination site bind the hydrophobic 'Ile44' surface of Ub. Mutations in the 13TF14/M25 motif inhibit Ub binding, and naturally occurring NZF domains that lack the motif do not bind Ub. However, substitution of the 13TF14/M25 motif into the nonbinding NZF domain from RanBP2 creates Ub-binding activity, demonstrating the versatility of the NZF scaffold. Finally, NZF mutations that inhibit Ub binding by the NZF domain of Vps36/ESCRT-II also inhibit sorting of ubiquitylated proteins into the yeast vacuole. Thus, the NZF is a versatile protein recognition domain that is used to bind ubiquitylated proteins during vacuolar protein sorting, and probably many other biological processes.

PubMed: 15029239
DOI: 10.1038/sj.emboj.7600114

Experimental method

SOLUTION NMR