6QML

UCHL3 in complex with synthetic, K27-linked diubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

K27-Linked Diubiquitin Inhibits UCHL3 via an Unusual Kinetic Trap.

van Tilburg, G.B.A.Murachelli, A.G.Fish, A.van der Heden van Noort, G.J.Ovaa, H.Sixma, T.K.

(2021) Cell Chem Biol 28: 191-201.e8

  • DOI: 10.1016/j.chembiol.2020.11.005
  • Primary Citation of Related Structures:  
    6QML

  • PubMed Abstract: 
  • Functional analysis of lysine 27-linked ubiquitin chains ( K27 Ub) is difficult due to the inability to make them through enzymatic methods and due to a lack of model tools and substrates. Here we generate a series of ubiquitin (Ub) tools to study how the deubiquitinase UCHL3 responds to K27 Ub chains in comparison to lysine 63-linked chains and mono-Ub ...

    Functional analysis of lysine 27-linked ubiquitin chains ( K27 Ub) is difficult due to the inability to make them through enzymatic methods and due to a lack of model tools and substrates. Here we generate a series of ubiquitin (Ub) tools to study how the deubiquitinase UCHL3 responds to K27 Ub chains in comparison to lysine 63-linked chains and mono-Ub. From a crystal structure of a complex between UCHL3 and synthetic K27 Ub 2 , we unexpectedly discover that free K27 Ub 2 and K27 Ub 2 -conjugated substrates are natural inhibitors of UCHL3. Using our Ub tools to profile UCHL3's activity, we generate a quantitative kinetic model of the inhibitory mechanism and we find that K27 Ub 2 can inhibit UCHL3 covalently, by binding to its catalytic cysteine, and allosterically, by locking its catalytic loop tightly in place. Based on this inhibition mechanism, we propose that UCHL3 and K27 Ub chains likely sense and regulate each other in cells.


    Organizational Affiliation

    Department of Biochemistry and Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Electronic address: t.sixma@nki.nl.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase isozyme L3A, D227Homo sapiensMutation(s): 0 
Gene Names: UCHL3
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P15374 (Homo sapiens)
Explore P15374 
Go to UniProtKB:  P15374
PHAROS:  P15374
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-BB, E76Homo sapiensMutation(s): 1 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-CC, F76Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download Ideal Coordinates CCD File 
DA [auth F], I [auth A], O [auth B], R [auth C]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D] , BA [auth D] , EA [auth F] , FA [auth F] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , 
AA [auth D], BA [auth D], EA [auth F], FA [auth F], J [auth A], K [auth A], L [auth A], M [auth A], P [auth B], Q [auth B], S [auth C], T [auth C], U [auth C], Y [auth D], Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], V [auth D], W [auth D], X [auth D]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth D], N [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE
B, EL-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.29α = 90
b = 81.206β = 90
c = 159.858γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Oncode InstituteNetherlands--
CancerGenomiCs.nlNetherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Advisory, Derived calculations
  • Version 1.2: 2021-03-10
    Changes: Database references, Derived calculations