1xd3

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1xd3, resolution 1.45Å ()
Ligands: ,
Activity: Ubiquitinyl hydrolase 1, with EC number 3.4.19.12
Related: 1cmx, 1ubq, 1uch
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



Crystal structure of UCHL3-UbVME complex

Publication Abstract from PubMed

Ubiquitin C-terminal hydrolases (UCHs) comprise a family of small ubiquitin-specific proteases of uncertain function. Although no cellular substrates have been identified for UCHs, their highly tissue-specific expression patterns and the association of UCH-L1 mutations with human disease strongly suggest a critical role. The structure of the yeast UCH Yuh1-ubiquitin aldehyde complex identified an active site crossover loop predicted to limit the size of suitable substrates. We report the 1.45 A resolution crystal structure of human UCH-L3 in complex with the inhibitor ubiquitin vinylmethylester, an inhibitor that forms a covalent adduct with the active site cysteine of ubiquitin-specific proteases. This structure confirms the predicted mechanism of the inhibitor and allows the direct comparison of a UCH family enzyme in the free and ligand-bound state. We also show the efficient hydrolysis by human UCH-L3 of a 13-residue peptide in isopeptide linkage with ubiquitin, consistent with considerable flexibility in UCH substrate size. We propose a model for the catalytic cycle of UCH family members which accounts for the hydrolysis of larger ubiquitin conjugates.

Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate., Misaghi S, Galardy PJ, Meester WJ, Ovaa H, Ploegh HL, Gaudet R, J Biol Chem. 2005 Jan 14;280(2):1512-20. Epub 2004 Nov 5. PMID:15531586

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

1xd3 is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA.

Reference

  • Misaghi S, Galardy PJ, Meester WJ, Ovaa H, Ploegh HL, Gaudet R. Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate. J Biol Chem. 2005 Jan 14;280(2):1512-20. Epub 2004 Nov 5. PMID:15531586 doi:http://dx.doi.org/10.1074/jbc.M410770200
  • Borodovsky A, Ovaa H, Kolli N, Gan-Erdene T, Wilkinson KD, Ploegh HL, Kessler BM. Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family. Chem Biol. 2002 Oct;9(10):1149-59. PMID:12401499
  • Borodovsky A, Kessler BM, Casagrande R, Overkleeft HS, Wilkinson KD, Ploegh HL. A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14. EMBO J. 2001 Sep 17;20(18):5187-96. PMID:11566882 doi:http://dx.doi.org/10.1093/emboj/20.18.5187
  • Johnston SC, Larsen CN, Cook WJ, Wilkinson KD, Hill CP. Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution. EMBO J. 1997 Jul 1;16(13):3787-96. PMID:9233788 doi:http://dx.doi.org/10.1093/emboj/16.13.3787
  • Johnston SC, Riddle SM, Cohen RE, Hill CP. Structural basis for the specificity of ubiquitin C-terminal hydrolases. EMBO J. 1999 Jul 15;18(14):3877-87. PMID:10406793 doi:http://dx.doi.org/10.1093/emboj/18.14.3877
  • Virnau P, Mirny LA, Kardar M. Intricate knots in proteins: Function and evolution. PLoS Comput Biol. 2006 Sep 15;2(9):e122. Epub 2006 Jul 28. PMID:16978047 doi:10.1371/journal.pcbi.0020122

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