Function and Biology

The 1.9A crystal structure of humanized Xenopus Mdm2 with nutlin-3a

Source organism: Xenopus laevis
Biochemical function: not assigned
Biological process: negative regulation of transcription from RNA polymerase II promoter
Cellular component: nucleus

EC 2.3.2.27: RING-type E3 ubiquitin transferase

Reaction catalysed:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)- ubiquitinyl-[acceptor protein]-L-lysine.
Comments:
  • The RING domain of E3 ubiquitin transferase serves as a mediator bringing the ubiquitin-charged E2 ubiquitin-conjugating enzyme and the acceptor protein together to enable the direct transfer of ubiquitin through the formation of an isopeptide bond between the C-terminal glycine residue of ubiquitin an the epsilon-amino group of an L-lysine residue of the acceptor protein.
  • The RING-E3 domain does not form a catalytic thioester intermediate with ubiquitin (unlike the HECT domain, EC 2.3.2.26).
  • RING-type ubiquitin transferases may occur as single-chain enzymes but also in dimeric forms or in multi-subunit assemblies.
  • Formerly EC 6.3.2.19 and EC 6.3.2.21.
Systematic name:
S-ubiquitinyl-[ubiquitin-conjugating E2 enzyme]-L-cysteine:acceptor protein ubiquitin transferase (isopeptide bond-forming; RING-type)
Alternative Name(s):
  • RING E3 ligase
  • Ubiquitin transferase RING E3

Sequence family

Pfam Protein family (Pfam)
PF02201
Domain description: SWIB/MDM2 domain
Occurring in:
  1. E3 ubiquitin-protein ligase Mdm2
1 copy of Pfam domain PF02201 (SWIB/MDM2 domain) in E3 ubiquitin-protein ligase Mdm2 in PDB 4j3e.

InterPro InterPro annotations
IPR036885
Domain description: SWIB/MDM2 domain superfamily
Occurring in:
  1. E3 ubiquitin-protein ligase Mdm2
IPR015459
Domain description: Ubiquitin-protein ligase E3 MDM2
Occurring in:
  1. E3 ubiquitin-protein ligase Mdm2
IPR003121
Domain description: SWIB/MDM2 domain
Occurring in:
  1. E3 ubiquitin-protein ligase Mdm2
IPR016495
Domain description: p53 negative regulator Mdm2/Mdm4
Occurring in:
  1. E3 ubiquitin-protein ligase Mdm2

Structure domain

CATH CATH domain
1.10.245.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: MDM2
Homology: MDM2
Occurring in:
  1. E3 ubiquitin-protein ligase Mdm2
1 copy of CATH domain 1.10.245.10 (MDM2) in E3 ubiquitin-protein ligase Mdm2 in PDB 4j3e.