2JF5

crystal structure of Lys63-linked di-ubiquitin

Summary for 2JF5

• Entry DOI: 10.2210/pdb2jf5/pdb
• Related: 1C3T 1D3Z 1F9J 1FXT 1G6J 1GJZ 1NBF 1OGW 1Q5W 1S1Q 1SIF 1TBE 1UBI 1UBQ 1XD3 1XQQ 1YX5 1YX6 1ZGU 2AYO 2BGF 2FCM 2FCN 2FCQ 2FCS 2FUH 2G45 2GBK 2GBM 2GBN 2J7Q
• Descriptor: UBIQUITIN, CADMIUM ION, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: lys6, lys63, nf-kb, ubiquitin, nuclear protein, signal transduction, signaling protein
• Biological source: HOMO SAPIENS (HUMAN)
• Total number of polymer chains: 2
• Total formula weight: 17556.11

Authors

Komander, D.,Odenwaelder, P.,Barford, D. (deposition date: 2007-01-26, release date: 2008-02-05, Last modification date: 2023-12-13)

Primary citation

Komander, D.,Reyes-Turcu, F.,Licchesi, J.D.F.,Odenwaelder, P.,Wilkinson, K.D.,Barford, D.
Molecular Discrimination of Structurally Equivalent Lys 63-Linked and Linear Polyubiquitin Chains.
Embo Rep., 10:466-, 2009

PubMed Abstract: At least eight types of ubiquitin chain exist, and individual linkages affect distinct cellular processes. The only distinguishing feature of differently linked ubiquitin chains is their structure, as polymers of the same unit are chemically identical. Here, we have crystallized Lys 63-linked and linear ubiquitin dimers, revealing that both adopt equivalent open conformations, forming no contacts between ubiquitin molecules and thereby differing significantly from Lys 48-linked ubiquitin chains. We also examined the specificity of various deubiquitinases (DUBs) and ubiquitin-binding domains (UBDs). All analysed DUBs, except CYLD, cleave linear chains less efficiently compared with other chain types, or not at all. Likewise, UBDs can show chain specificity, and are able to select distinct linkages from a ubiquitin chain mixture. We found that the UBAN (ubiquitin binding in ABIN and NEMO) motif of NEMO (NF-kappaB essential modifier) binds to linear chains exclusively, whereas the NZF (Npl4 zinc finger) domain of TAB2 (TAK1 binding protein 2) is Lys 63 specific. Our results highlight remarkable specificity determinants within the ubiquitin system.

PubMed: 19373254
DOI: 10.1038/EMBOR.2009.55

Experimental method

X-RAY DIFFRACTION (1.95 Å)