5D2M image
Deposition Date 2015-08-05
Release Date 2015-11-04
Last Version Date 2024-11-20
Entry Detail
PDB ID:
5D2M
Title:
Complex between human SUMO2-RANGAP1, UBC9 and ZNF451
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:SUMO-conjugating enzyme UBC9
Gene (Uniprot):UBE2I
Mutations:K14R
Chain IDs:A, D
Chain Length:161
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Small ubiquitin-related modifier 2
Gene (Uniprot):SUMO2
Chain IDs:B, E
Chain Length:83
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Ran GTPase-activating protein 1
Gene (Uniprot):RANGAP1
Chain IDs:C, F
Chain Length:171
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Zinc finger protein 451
Gene (Uniprot):ZNF451
Chain IDs:G
Chain Length:65
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structural basis for catalytic activation by the human ZNF451 SUMO E3 ligase.
Nat.Struct.Mol.Biol. 22 968 975 (2015)
PMID: 26524494 DOI: 10.1038/nsmb.3116

Abstact

E3 protein ligases enhance transfer of ubiquitin-like (Ubl) proteins from E2 conjugating enzymes to substrates by stabilizing the thioester-charged E2~Ubl in a closed configuration optimally aligned for nucleophilic attack. Here, we report biochemical and structural data that define the N-terminal domain of the Homo sapiens ZNF451 as the catalytic module for SUMO E3 ligase activity. The ZNF451 catalytic module contains tandem SUMO-interaction motifs (SIMs) bridged by a Pro-Leu-Arg-Pro (PLRP) motif. The first SIM and PLRP motif engage thioester-charged E2~SUMO while the next SIM binds a second molecule of SUMO bound to the back side of E2. We show that ZNF451 is SUMO2 specific and that SUMO modification of ZNF451 may contribute to activity by providing a second molecule of SUMO that interacts with E2. Our results are consistent with ZNF451 functioning as a bona fide SUMO E3 ligase.

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Primary Citation of related structures