1XD3

Crystal structure of UCHL3-UbVME complex

DOI: 10.2210/pdb1XD3/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-09-03 Released: 2004-11-23
Deposition Author(s): Misaghi, S., Galardy, P.J., Meester, W.J.N., Ovaa, H., Ploegh, H.L., Gaudet, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.192
R-Value Work: 0.166
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of the Ubiquitin Hydrolase UCH-L3 Complexed with a Suicide Substrate

Misaghi, S., Galardy, P.J., Meester, W.J.N., Ovaa, H., Ploegh, H.L., Gaudet, R.

(2005) J Biol Chem 280: 1512-1520

PubMed: 15531586 Search on PubMed
DOI: 10.1074/jbc.M410770200
Primary Citation of Related Structures:
1XD3

PubMed Abstract:

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.

Related Citations:

Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family
Borodovsky, A., Ovaa, H., Kolli, N., Gan-Erdene, T., Wilkinson, K.D., Ploegh, H.L., Kessler, B.M.
(2002) Chem Biol 9: 1149

A novel active site-directed probe specific for deubiquitinating enzymes reveals proteasome association of USP14
Borodovsky, A., Kessler, B.M., Casagrande, R., Overkleeft, H.S., Wilkinson, K.D., Ploegh, H.L.
(2001) EMBO J 20: 5187

Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution
Johnston, S.C., Larsen, C.N., Cook, W.J., Wilkinson, K.D., Hill, C.P.
(1997) EMBO J 16: 3787

Structural basis for the specificity of ubiquitin C-terminal hydrolases
Johnston, S.C., Riddle, S.M., Cohen, R.E., Hill, C.P.
(1999) EMBO J 18: 3877

Organizational Affiliation:

Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin Carboxyl-terminal esterase L3	A, C	230	Homo sapiens	Mutation(s): 0 Gene Names: UCHL3 EC: 3.4.19.12
Find proteins for P15374 (Homo sapiens) Explore P15374 Go to UniProtKB: P15374
NIH Common Fund Data Resources
PHAROS: P15374 GTEx: ENSG00000118939
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UBC protein	B, D	75	Homo sapiens	Mutation(s): 0 Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
NIH Common Fund Data Resources
PHAROS: P0CG48
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GVE Query on GVE Download Ideal Coordinates CCD File SDF format, chain H [B] SDF format, chain P [D] MOL2 format, chain H [B] MOL2 format, chain P [D]	B, D	METHYL 4-AMINOBUTANOATE C₅ H₁₁ N O₂ KVQGGLZHHFGHPU-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain F [A] SDF format, chain G [A] SDF format, chain I [C] SDF format, chain J [C] SDF format, chain K [C] SDF format, chain L [C] SDF format, chain M [C] SDF format, chain N [C] SDF format, chain O [C] MOL2 format, chain E [A] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain I [C] MOL2 format, chain J [C] MOL2 format, chain K [C] MOL2 format, chain L [C] MOL2 format, chain M [C] MOL2 format, chain N [C] MOL2 format, chain O [C]	A, C	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction