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Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase

Source organism: Homo sapiens
Biochemical function: protein binding
Biological process: proteasome-mediated ubiquitin-dependent protein catabolic process
Cellular component: nucleus

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EC 2.7.11.1: Non-specific serine/threonine protein kinase

Reaction catalysed:
ATP + a protein = ADP + a phosphoprotein
Systematic name:
ATP:protein phosphotransferase (non-specific)
Alternative Name(s):
  • A-kinase
  • AP50 kinase
  • ATP-protein transphosphorylase
  • Beta-IIPKC
  • Beta-adrenergic receptor kinase
  • CK-2
  • CKI
  • CKII
  • Calcium-dependent protein kinase C
  • Calcium/phospholipid-dependent protein kinase
  • Casein kinase
  • Casein kinase (phosphorylating)
  • Casein kinase 2
  • Casein kinase I
  • Casein kinase II
  • Cyclic AMP-dependent protein kinase
  • Cyclic AMP-dependent protein kinase A
  • Cyclic monophosphate-dependent protein kinase
  • Cyclic nucleotide-dependent protein kinase
  • Cyclin-dependent kinase
  • Cytidine 3',5'-cyclic monophosphate-responsive protein kinase
  • Dsk1
  • Epsilon PKC
  • Glycogen synthase A kinase
  • Glycogen synthase a kinase
  • Glycogen synthase kinase
  • HIPK2
  • Hpr kinase
  • Hydroxyalkyl-protein kinase
  • M phase-specific cdc2 kinase
  • MAPK
  • Mitogen-activated S6 kinase
  • Mitogen-activated protein kinase
  • P82 kinase
  • PKA
  • PKC
  • Phosphorylase B kinase kinase
  • Phosphorylase b kinase kinase
  • Phosphorylase b kinase kinase
  • Protein glutamyl kinase
  • Protein kinase (phosphorylating)
  • Protein kinase A
  • Protein kinase CK2
  • Protein kinase p58
  • Protein phosphokinase
  • Protein serine kinase
  • Protein serine-threonine kinase
  • Protein-aspartyl kinase
  • Protein-cysteine kinase
  • Protein-serine kinase
  • Prp4 protein kinase
  • Raf kinase
  • Raf-1
  • Ribosomal S6 protein kinase
  • Ribosomal protein S6 kinase II
  • STK32
  • Serine kinase
  • Serine protein kinase
  • Serine(threonine) protein kinase
  • Serine-specific protein kinase
  • Serine/threonine protein kinase
  • T-antigen kinase
  • Threonine-specific protein kinase
  • Twitchin kinase
  • Type-2 casein kinase
  • WEE1Hu
  • Wee 1-like kinase
  • Wee-kinase
  • cAMP-dependent protein kinase
  • cAMP-dependent protein kinase A
  • cGMP-dependent protein kinase

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF00069
Domain description: Protein kinase domain
Occurring in:
  1. Casein kinase I isoform alpha
The deposited structure of PDB entry 5fqd contains 2 copies of Pfam domain PF00069 (Protein kinase domain) in Casein kinase I isoform alpha. Showing 1 copy in chain C.

PF03226
Domain description: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly
Occurring in:
  1. Protein cereblon
The deposited structure of PDB entry 5fqd contains 2 copies of Pfam domain PF03226 (Yippee zinc-binding/DNA-binding /Mis18, centromere assembly) in Protein cereblon. Showing 1 copy in chain B.

PF02190
Domain description: ATP-dependent protease La (LON) substrate-binding domain
Occurring in:
  1. Protein cereblon
The deposited structure of PDB entry 5fqd contains 2 copies of Pfam domain PF02190 (ATP-dependent protease La (LON) substrate-binding domain ) in Protein cereblon. Showing 1 copy in chain B.

PF03178
Domain description: CPSF A subunit region
Occurring in:
  1. DNA damage-binding protein 1
The deposited structure of PDB entry 5fqd contains 2 copies of Pfam domain PF03178 (CPSF A subunit region) in DNA damage-binding protein 1. Showing 1 copy in chain D.

PF10433
Domain description: Mono-functional DNA-alkylating methyl methanesulfonate N-term
Occurring in:
  1. DNA damage-binding protein 1
The deposited structure of PDB entry 5fqd contains 2 copies of Pfam domain PF10433 (Mono-functional DNA-alkylating methyl methanesulfonate N-term) in DNA damage-binding protein 1. Showing 1 copy in chain D.

InterPro InterPro annotations
IPR000719
Domain description: Protein kinase domain
Occurring in:
  1. Casein kinase I isoform alpha
IPR034750
Domain description: CULT domain
Occurring in:
  1. Protein cereblon
IPR003111
Domain description: Lon protease, N-terminal domain
Occurring in:
  1. Protein cereblon
IPR015943
Domain description: WD40/YVTN repeat-like-containing domain superfamily
Occurring in:
  1. DNA damage-binding protein 1
IPR008271
Domain description: Serine/threonine-protein kinase, active site
Occurring in:
  1. Casein kinase I isoform alpha
IPR017441
Domain description: Protein kinase, ATP binding site
Occurring in:
  1. Casein kinase I isoform alpha
IPR011009
Domain description: Protein kinase-like domain superfamily
Occurring in:
  1. Casein kinase I isoform alpha
IPR004910
Domain description: Yippee/Mis18/Cereblon
Occurring in:
  1. Protein cereblon
IPR015947
Domain description: PUA-like superfamily
Occurring in:
  1. Protein cereblon
IPR046336
Domain description: Lon protease, N-terminal domain superfamily
Occurring in:
  1. Protein cereblon
IPR004871
Domain description: Cleavage/polyadenylation specificity factor, A subunit, C-terminal
Occurring in:
  1. DNA damage-binding protein 1
IPR011047
Domain description: Quinoprotein alcohol dehydrogenase-like superfamily
Occurring in:
  1. DNA damage-binding protein 1
IPR018846
Domain description: Cleavage/polyadenylation specificity factor, A subunit, N-terminal
Occurring in:
  1. DNA damage-binding protein 1

Structure domains

CATH CATH domains
2.130.10.10
Class: Mainly Beta
Architecture: 7 Propeller
Topology: Methylamine Dehydrogenase; Chain H
Homology: YVTN repeat-like/Quinoprotein amine dehydrogenase
Occurring in:
  1. DNA damage-binding protein 1
The deposited structure of PDB entry 5fqd contains 4 copies of CATH domain 2.130.10.10 (Methylamine Dehydrogenase; Chain H) in DNA damage-binding protein 1. Showing 2 copies in chain D.
3.30.200.20
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Phosphorylase Kinase; domain 1
Homology: Phosphorylase Kinase; domain 1
Occurring in:
  1. Casein kinase I isoform alpha
The deposited structure of PDB entry 5fqd contains 2 copies of CATH domain 3.30.200.20 (Phosphorylase Kinase; domain 1) in Casein kinase I isoform alpha. Showing 1 copy in chain C.
2.170.150.20
Class: Mainly Beta
Architecture: Beta Complex
Topology: Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homology: Peptide methionine sulfoxide reductase.
Occurring in:
  1. Protein cereblon
The deposited structure of PDB entry 5fqd contains 2 copies of CATH domain 2.170.150.20 (Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A) in Protein cereblon. Showing 1 copy in chain B.
1.10.510.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Transferase(Phosphotransferase); domain 1
Homology: Transferase(Phosphotransferase) domain 1
Occurring in:
  1. Casein kinase I isoform alpha
The deposited structure of PDB entry 5fqd contains 2 copies of CATH domain 1.10.510.10 (Transferase(Phosphotransferase); domain 1) in Casein kinase I isoform alpha. Showing 1 copy in chain C.
1.20.58.1480
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homology: Methane Monooxygenase Hydroxylase; Chain G, domain 1
Occurring in:
  1. Protein cereblon
The deposited structure of PDB entry 5fqd contains 2 copies of CATH domain 1.20.58.1480 (Methane Monooxygenase Hydroxylase; Chain G, domain 1) in Protein cereblon. Showing 1 copy in chain B.
2.30.130.40
Class: Mainly Beta
Architecture: Roll
Topology: Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homology: LON domain-like
Occurring in:
  1. Protein cereblon
The deposited structure of PDB entry 5fqd contains 2 copies of CATH domain 2.30.130.40 (Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4) in Protein cereblon. Showing 1 copy in chain B.
1.10.150.910
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: DNA polymerase; domain 1
Homology: DNA polymerase; domain 1
Occurring in:
  1. DNA damage-binding protein 1
The deposited structure of PDB entry 5fqd contains 2 copies of CATH domain 1.10.150.910 (DNA polymerase; domain 1) in DNA damage-binding protein 1. Showing 1 copy in chain D.

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