6O60

Crystal structure of GGTase3-FBXL2-SKP1 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


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


Literature

GGTase3 is a newly identified geranylgeranyltransferase targeting a ubiquitin ligase.

Kuchay, S., Wang, H., Marzio, A., Jain, K., Homer, H., Fehrenbacher, N., Philips, M.R., Zheng, N., Pagano, M.

(2019) Nat Struct Mol Biol 26: 628-636

  • DOI: 10.1038/s41594-019-0249-3
  • Primary Citation of Related Structures:  
    6O60

  • PubMed Abstract: 

    • Protein prenylation is believed to be catalyzed by three heterodimeric enzymes: FTase, GGTase1 and GGTase2. Here we report the identification of a previously unknown human prenyltransferase complex consisting of an orphan prenyltransferase α-subunit, PTAR1, and the catalytic β-subunit of GGTase2, RabGGTB ...

    Protein prenylation is believed to be catalyzed by three heterodimeric enzymes: FTase, GGTase1 and GGTase2. Here we report the identification of a previously unknown human prenyltransferase complex consisting of an orphan prenyltransferase α-subunit, PTAR1, and the catalytic β-subunit of GGTase2, RabGGTB. This enzyme, which we named GGTase3, geranylgeranylates FBXL2 to allow its localization at cell membranes, where this ubiquitin ligase mediates the polyubiquitylation of membrane-anchored proteins. In cells, FBXL2 is specifically recognized by GGTase3 despite having a typical carboxy-terminal CaaX prenylation motif that is predicted to be recognized by GGTase1. Our crystal structure analysis of the full-length GGTase3-FBXL2-SKP1 complex reveals an extensive multivalent interface specifically formed between the leucine-rich repeat domain of FBXL2 and PTAR1, which unmasks the structural basis of the substrate-enzyme specificity. By uncovering a missing prenyltransferase and its unique mode of substrate recognition, our findings call for a revision of the 'prenylation code'.

    Organizational Affiliation: 

    Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA. michele.pagano@nyumc.org.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein prenyltransferase alpha subunit repeat-containing protein 1A407Homo sapiensMutation(s): 0 
Gene Names: PTAR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z6K3 (Homo sapiens)
Explore Q7Z6K3 
Go to UniProtKB:  Q7Z6K3
PHAROS:  Q7Z6K3
GTEx:  ENSG00000188647
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Geranylgeranyl transferase type-2 subunit betaB332Homo sapiensMutation(s): 0 
Gene Names: RABGGTB, GGTB
EC: 2.5.1.60
UniProt & NIH Common Fund Data Resources
Find proteins for P53611 (Homo sapiens)
Explore P53611 
Go to UniProtKB:  P53611
PHAROS:  P53611
GTEx:  ENSG00000137955
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
F-box/LRR-repeat protein 2C424Homo sapiensMutation(s): 0 
Gene Names: FBXL2, FBL2, FBL3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKC9 (Homo sapiens)
Explore Q9UKC9 
Go to UniProtKB:  Q9UKC9
PHAROS:  Q9UKC9
GTEx:  ENSG00000153558
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1D164Homo sapiensMutation(s): 0 
Gene Names: SKP1, EMC19, OCP2, SKP1A, TCEB1L
UniProt & NIH Common Fund Data Resources
Find proteins for P63208 (Homo sapiens)
Explore P63208 
Go to UniProtKB:  P63208
PHAROS:  P63208
GTEx:  ENSG00000113558
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
 E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.843α = 90
b = 99.318β = 90
c = 151.202γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-04 
  • Released Date: 2019-06-26 
    • Deposition Author(s): Wang, H., Zheng, N.
Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Database references
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence