Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.92 kDa 
• Atom Count: 2349 
• Modelled Residue Count: 298 
• Deposited Residue Count: 303 
• Unique protein chains: 2

3KVF

Crystal structure of the I93M mutant of ubiquitin carboxy terminal hydrolase L1 bound to ubiquitin vinylmethylester

• DOI: 10.2210/pdb3KVF/pdb

• Classification: HYDROLASE/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-11-30 Released: 2010-06-16 
• Deposition Author(s): Davies, C.W., Maiti, T.K., Das, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.284 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 

Literature

Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation.

Boudreaux, D.A., Maiti, T.K., Davies, C.W., Das, C.

(2010) Proc Natl Acad Sci U S A 107: 9117-9122

• PubMed: 20439756 
• DOI: 10.1073/pnas.0910870107
• Primary Citation of Related Structures:  
  3KW5, 3KVF, 3IFW, 3IRT


• PubMed Abstract: 
  

Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a Parkinson disease-associated, putative cysteine protease found abundantly and selectively expressed in neurons. The crystal structure of apo UCHL1 showed that the active-site residues are not aligned in a canonical form, with the nucleophilic cysteine being 7.7 A from the general base histidine, an arrangement consistent with an inactive form of the enzyme. Here we report the crystal structures of the wild type and two Parkinson disease-associated variants of the enzyme, S18Y and I93M, bound to a ubiquitin-based suicide substrate, ubiquitin vinyl methyl ester. These structures reveal that ubiquitin vinyl methyl ester binds primarily at two sites on the enzyme, with its carboxy terminus at the active site and with its amino-terminal beta-hairpin at the distal site-a surface-exposed hydrophobic crevice 17 A away from the active site. Binding at the distal site initiates a cascade of side-chain movements in the enzyme that starts at a highly conserved, surface-exposed phenylalanine and is relayed to the active site resulting in the reorientation and proximal placement of the general base within 4 A of the catalytic cysteine, an arrangement found in productive cysteine proteases. Mutation of the distal-site, surface-exposed phenylalanine to alanine reduces ubiquitin binding and severely impairs the catalytic activity of the enzyme. These results suggest that the activity of UCHL1 may be regulated by its own substrate.

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Organizational Affiliation: 

Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase isozyme L1	A	228	Homo sapiens	Mutation(s): 1  Gene Names: PGP9.5, UCHL1 EC: 3.4.19.12 (PDB Primary Data), 6 (PDB Primary Data)
Find proteins for P09936 (Homo sapiens) Explore P09936  Go to UniProtKB:  P09936
NIH Common Fund Data Resources
PHAROS:  P09936 GTEx:  ENSG00000154277

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	75	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA52, UBA80, UBB, UBC, UBCEP1, UBCEP2, UBIQ_HUMAN
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS:  P0CG48

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GVE	B	METHYL 4-AMINOBUTANOATE C5 H11 N O2 KVQGGLZHHFGHPU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.284 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.089	α = 90
b = 87.089	β = 90
c = 193.476	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-30 
• Released Date: 2010-06-16 
Deposition Author(s): Davies, C.W., Maiti, T.K., Das, C.

Revision History  

• Version 1.0: 2010-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance