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TitleStructural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 9899, Year 2024
Publish dateNov 15, 2024
AuthorsDaniel C Scott / Sagar Chittori / Nicholas Purser / Moeko T King / Samuel A Maiwald / Kelly Churion / Amanda Nourse / Chan Lee / Joao A Paulo / Darcie J Miller / Stephen J Elledge / J Wade Harper / Gary Kleiger / Brenda A Schulman /
PubMed AbstractSpecificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the ...Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend on E3 ligases binding to peptide-like sequences - termed N- or C-degrons - at the termini of substrates. However, our knowledge of structural features distinguishing closely related C-degron substrate-E3 pairings is limited. Here, by systematically comparing ubiquitylation activities towards a suite of common model substrates, and defining interactions by biochemistry, crystallography, and cryo-EM, we reveal principles of C-degron recognition across the KLHDCX family of Cullin-RING ligases (CRLs). First, a motif common across these E3 ligases anchors a substrate's C-terminus. However, distinct locations of this C-terminus anchor motif in different blades of the KLHDC2, KLHDC3, and KLHDC10 β-propellers establishes distinct relative positioning and molecular environments for substrate C-termini. Second, our structural data show KLHDC3 has a pre-formed pocket establishing preference for an Arg or Gln preceding a C-terminal Gly, whereas conformational malleability contributes to KLHDC10's recognition of varying features adjacent to substrate C-termini. Finally, additional non-consensus interactions, mediated by C-degron binding grooves and/or by distal propeller surfaces and substrate globular domains, can substantially impact substrate binding and ubiquitylatability. Overall, the data reveal combinatorial mechanisms determining specificity and plasticity of substrate recognition by KLDCX-family C-degron E3 ligases.
External linksNat Commun / PubMed:39548056 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.88 - 3.3 Å
Structure data

EMDB-46644: Cryo-EM structure of a trapped ARIH1-diUB-CRL2-KLHDC10 complex - consensus map
Method: EM (single particle) / Resolution: 3.3 Å

46645

9d8p

EMDB-46645, PDB-9d8p:
Focused map of Cryo-EM structure of Ubiquitin C-degron bound to KLHDC10-EloB/C
Method: EM (single particle) / Resolution: 3.2 Å

PDB-9d1i:
Structure of Ubiquitin bound to KLHDC3-EloB/C
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-9d1y:
Structure of G75R Ubiquitin bound to KLHDC3-EloB/C
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-9d1z:
Structure of G75Q Ubiquitin bound to KLHDC3-EloB/C
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

Chemicals

ChemComp-GOL:
GLYCEROL

ChemComp-HOH:
WATER

ChemComp-MPD:
(4S)-2-METHYL-2,4-PENTANEDIOL / precipitant*YM

Source
  • homo sapiens (human)
KeywordsLIGASE / KLHDC3 / Ubiquitin / C-degron / Cullin-RING / E3 / KLHDC10

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