2XK5

Crystal structure of K6-linked diubiquitin

Summary for 2XK5

• Entry DOI: 10.2210/pdb2xk5/pdb
• Related: 1C3T 1D3Z 1F9J 1FXT 1G6J 1GJZ 1NBF 1OGW 1Q5W 1S1Q 1SIF 1TBE 1UBI 1UBQ 1XD3 1XQQ 1YX5 1YX6 1ZGU 2AYO 2BGF 2G45 2GBJ 2GBK 2GBM 2GBN 2J7Q 2JF5 2W9N 2WDT 2XEW
• Descriptor: UBIQUITIN, ZINC ION (3 entities in total)
• Functional Keywords: signal transduction, brca1, protein binding
• Biological source: HOMO SAPIENS (HUMAN); More
• Total number of polymer chains: 2
• Total formula weight: 17624.57

Authors

Virdee, S.,Chin, J.W.,Komander, D. (deposition date: 2010-07-07, release date: 2010-08-25, Last modification date: 2023-12-20)

Primary citation

Virdee, S.,Ye, Y.,Nguyen, D.P.,Komander, D.,Chin, J.W.
Engineered Diubiquitin Synthesis Reveals K29-Isopeptide Specificity of an Otu Deubiquitinase
Nat.Chem.Biol., 6:750-, 2010

PubMed Abstract: Ubiquitination is a reversible post-translational modification that regulates a myriad of eukaryotic functions. Our ability to study the effects of ubiquitination is often limited by the inaccessibility of homogeneously ubiquitinated proteins. In particular, elucidating the roles of the so-called 'atypical' ubiquitin chains (chains other than Lys48- or Lys63-linked ubiquitin), which account for a large fraction of ubiquitin polymers, is challenging because the enzymes for their biosynthesis are unknown. Here we combine genetic code expansion, intein chemistry and chemoselective ligations to synthesize 'atypical' ubiquitin chains. We solve the crystal structure of Lys6-linked diubiquitin, which is distinct from that of structurally characterized ubiquitin chains, providing a molecular basis for the different biological functions this linkage may regulate. Moreover, we profile a panel containing 10% of the known human deubiquitinases on Lys6- and Lys29-linked ubiquitin and discover that TRABID cleaves the Lys29 linkage 40-fold more efficiently than the Lys63 linkage.

PubMed: 20802491
DOI: 10.1038/NCHEMBIO.426

Experimental method

X-RAY DIFFRACTION (3 Å)