4S1Z

Crystal structure of TRABID NZF1 in complex with K29 linked di-Ubiquitin

Summary for 4S1Z

• Entry DOI: 10.2210/pdb4s1z/pdb
• Related: 4S22
• Descriptor: Ubiquitin, Ubiquitin thioesterase ZRANB1, ZINC ION (3 entities in total)
• Functional Keywords: zinc finger, hydrolase, protease, ubiquitin binding
• Biological source: Homo sapiens (human); More
• Cellular location: Ubiquitin: Cytoplasm . 60S ribosomal protein L40: Cytoplasm : P62987; Cytoplasm : A6QP16
• Total number of polymer chains: 10
• Total formula weight: 63704.75

Authors

Kristariyanto, Y.A.,Abdul Rehman, S.A.,Campbell, D.G.,Morrice, N.A.,Johnson, C.,Toth, R.,Kulathu, Y. (deposition date: 2015-01-16, release date: 2015-04-08, Last modification date: 2023-09-20)

Primary citation

Kristariyanto, Y.A.,Abdul Rehman, S.A.,Campbell, D.G.,Morrice, N.A.,Johnson, C.,Toth, R.,Kulathu, Y.
K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of k29 polyubiquitin.
Mol.Cell, 58:83-94, 2015

PubMed Abstract: Polyubiquitin chains regulate diverse cellular processes through the ability of ubiquitin to form chains of eight different linkage types. Although detected in yeast and mammals, little is known about K29-linked polyubiquitin. Here we report the generation of K29 chains in vitro using a ubiquitin chain-editing complex consisting of the HECT E3 ligase UBE3C and the deubiquitinase vOTU. We determined the crystal structure of K29-linked diubiquitin, which adopts an extended conformation with the hydrophobic patches on both ubiquitin moieties exposed and available for binding. Indeed, the crystal structure of the NZF1 domain of TRABID in complex with K29 chains reveals a binding mode that involves the hydrophobic patch on only one of the ubiquitin moieties and exploits the flexibility of K29 chains to achieve linkage selective binding. Further, we establish methods to study K29-linked polyubiquitin and find that K29 linkages exist in cells within mixed or branched chains containing other linkages.

PubMed: 25752573
DOI: 10.1016/j.molcel.2015.01.041

Experimental method

X-RAY DIFFRACTION (3.03 Å)