Function and Biology

Crystal Structure of the Uba1-Ubiquitin Complex

Source organism: Saccharomyces cerevisiae S288C
Biochemical function: ATP binding
Biological process: cellular protein modification process
Cellular component: nucleus

EC 6.2.1.45: E1 ubiquitin-activating enzyme

Reaction catalysed:
ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine.
Comments:
  • Catalyzes the ATP-dependent activation of ubiquitin through the formation of a thioester bond between the C-terminal glycine of ubiquitin and the sulfhydryl side group of a cysteine residue in the E1 protein.
  • The two-step reaction consists of the ATP-dependent formation of an E1-ubiquitin adenylate intermediate in which the C-terminal glycine of ubiquitin is bound to AMP via an acyl-phosphate linkage, then followed by the conversion to an E1-ubiquitin thioester bond via the cysteine residue on E1 in the second step.
  • Formerly EC 6.3.2.19 and EC 6.3.2.21.
Systematic name:
Ubiquitin:[E1 ubiquitin-activating enzyme] ligase (AMP-forming)
Alternative Name(s):
  • Ubiquitin activating enzyme
  • E1
  • Ubiquitin-activating enzyme E1

Sequence families

Pfam Protein families (Pfam)
PF00899
Domain description: ThiF family
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
2 copies of Pfam domain PF00899 (ThiF family) in Ubiquitin-activating enzyme E1 1 in PDB 3cmm.

PF00240
Domain description: Ubiquitin family
Occurring in:
  1. Ubiquitin
1 copy of Pfam domain PF00240 (Ubiquitin family) in Ubiquitin in PDB 3cmm.

PF16190
Domain description: Ubiquitin-activating enzyme E1 FCCH domain
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
1 copy of Pfam domain PF16190 (Ubiquitin-activating enzyme E1 FCCH domain) in Ubiquitin-activating enzyme E1 1 in PDB 3cmm.

PF16191
Domain description: Ubiquitin-activating enzyme E1 four-helix bundle
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
1 copy of Pfam domain PF16191 (Ubiquitin-activating enzyme E1 four-helix bundle) in Ubiquitin-activating enzyme E1 1 in PDB 3cmm.

PF09358
Domain description: Ubiquitin fold domain
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
1 copy of Pfam domain PF09358 (Ubiquitin fold domain) in Ubiquitin-activating enzyme E1 1 in PDB 3cmm.

PF10585
Domain description: Ubiquitin-activating enzyme active site
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
1 copy of Pfam domain PF10585 (Ubiquitin-activating enzyme active site) in Ubiquitin-activating enzyme E1 1 in PDB 3cmm.

InterPro InterPro annotations
IPR000011
Domain description: Ubiquitin/SUMO-activating enzyme E1
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
IPR019956
Domain description: Ubiquitin
Occurring in:
  1. Ubiquitin
IPR000626
Domain description: Ubiquitin domain
Occurring in:
  1. Ubiquitin
IPR018965
Domain description: Ubiquitin-activating enzyme E1, C-terminal
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
IPR023318
Domain description: Ubiquitin activating enzyme, alpha domain superfamily
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
IPR035985
Domain description: Ubiquitin-activating enzyme
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
IPR000594
Domain description: THIF-type NAD/FAD binding fold
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
IPR018075
Domain description: Ubiquitin-activating enzyme E1
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
IPR033127
Domain description: Ubiquitin-activating enzyme E1, Cys active site
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
IPR019954
Domain description: Ubiquitin conserved site
Occurring in:
  1. Ubiquitin
IPR018074
Domain description: Ubiquitin-activating enzyme E1, conserved site
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
IPR032418
Domain description: Ubiquitin-activating enzyme E1, FCCH domain
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
IPR029071
Domain description: Ubiquitin-like domain superfamily
Occurring in:
  1. Ubiquitin
IPR032420
Domain description: Ubiquitin-activating enzyme E1, four-helix bundle
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
IPR019572
Domain description: Ubiquitin-activating enzyme, catalytic cysteine domain
Occurring in:
  1. Ubiquitin-activating enzyme E1 1

Structure domains

CATH CATH domains
3.40.50.720
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: NAD(P)-binding Rossmann-like Domain
Occurring in:
  1. Ubiquitin-activating enzyme E1 1
1 copy of CATH domain 3.40.50.720 (Rossmann fold) in Ubiquitin-activating enzyme E1 1 in PDB 3cmm.
3.10.20.90
Class: Alpha Beta
Architecture: Roll
Topology: Ubiquitin-like (UB roll)
Homology: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Occurring in:
  1. Ubiquitin
1 copy of CATH domain 3.10.20.90 (Ubiquitin-like (UB roll)) in Ubiquitin in PDB 3cmm.
SCOP SCOP annotation
54237
Class: Alpha and beta proteins (a+b)
Fold: beta-Grasp (ubiquitin-like)
Superfamily: Ubiquitin-like
Occurring in:
  1. Ubiquitin
1 copy of SCOP domain 54237 (Ubiquitin-related) in Ubiquitin in PDB 3cmm.