1CMX

STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 3877-3887

  • DOI: https://doi.org/10.1093/emboj/18.14.3877
  • Primary Citation of Related Structures:  
    1CMX

  • PubMed Abstract: 

    The release of ubiquitin from attachment to other proteins and adducts is critical for ubiquitin biosynthesis, proteasomal degradation and other cellular processes. De-ubiquitination is accomplished in part by members of the UCH (ubiquitin C-terminal hydrolase) family of enzymes. We have determined the 2.25 A resolution crystal structure of the yeast UCH, Yuh1, in a complex with the inhibitor ubiquitin aldehyde (Ubal). The structure mimics the tetrahedral intermediate in the reaction pathway and explains the very high enzyme specificity. Comparison with a related, unliganded UCH structure indicates that ubiquitin binding is coupled to rearrangements which block the active-site cleft in the absence of authentic substrate. Remarkably, a 21-residue loop that becomes ordered upon binding Ubal lies directly over the active site. Efficiently processed substrates apparently pass through this loop, and constraints on the loop conformation probably function to control UCH specificity.


  • Organizational Affiliation

    Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (UBIQUITIN YUH1-UBAL)
A, C
235N/AMutation(s): 0 
EC: 3.1.2.15
UniProt
Find proteins for P35127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35127 
Go to UniProtKB:  P35127
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35127
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (UBIQUITIN YUH1-UBAL)
B, D
76N/AMutation(s): 0 
EC: 3.1.2.15
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
GTEx:  ENSG00000150991 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG48
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
GLZ
Query on GLZ
B, D
L-PEPTIDE LINKINGC2 H5 N OGLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.248 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.3α = 90
b = 199.3β = 90
c = 36.8γ = 120
Software Package:
Software NamePurpose
CCP4model building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-27
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations