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Crystal structure of PRMT5:MEP50 with Compound 9 and sinefungin

Source organism: Homo sapiens
Biochemical function: methyl-CpG binding
Biological process: positive regulation of mRNA splicing, via spliceosome
Cellular component: methylosome

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EC 2.1.1.320: Type II protein arginine methyltransferase

Reaction catalysed:
(1a) S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-N(omega)-methyl-L-arginine
Systematic name:
S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-N(omega),N(omega)'-dimethyl-L-arginine-forming)
Alternative Name(s):
  • PRMT5 (gene name)
  • PRMT9 (gene name)

GO terms

Sequence families

Pfam Protein families (Pfam)
PF00400
Domain description: WD domain, G-beta repeat
Occurring in:
  1. Methylosome protein WDR77
The deposited structure of PDB entry 5emk contains 2 copies of Pfam domain PF00400 (WD domain, G-beta repeat) in Methylosome protein WDR77. Showing 2 copies in chain B.

PF17286
Domain description: PRMT5 oligomerisation domain
Occurring in:
  1. Protein arginine N-methyltransferase 5
The deposited structure of PDB entry 5emk contains 1 copy of Pfam domain PF17286 (PRMT5 oligomerisation domain) in Protein arginine N-methyltransferase 5. Showing 1 copy in chain A.

PF05185
Domain description: PRMT5 arginine-N-methyltransferase
Occurring in:
  1. Protein arginine N-methyltransferase 5
The deposited structure of PDB entry 5emk contains 1 copy of Pfam domain PF05185 (PRMT5 arginine-N-methyltransferase) in Protein arginine N-methyltransferase 5. Showing 1 copy in chain A.

PF17285
Domain description: PRMT5 TIM barrel domain
Occurring in:
  1. Protein arginine N-methyltransferase 5
The deposited structure of PDB entry 5emk contains 1 copy of Pfam domain PF17285 (PRMT5 TIM barrel domain) in Protein arginine N-methyltransferase 5. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR001680
Domain description: WD40 repeat
Occurring in:
  1. Methylosome protein WDR77
IPR029063
Domain description: S-adenosyl-L-methionine-dependent methyltransferase superfamily
Occurring in:
  1. Protein arginine N-methyltransferase 5
IPR025799
Domain description: Protein arginine N-methyltransferase
Occurring in:
  1. Protein arginine N-methyltransferase 5
IPR019775
Domain description: WD40 repeat, conserved site
Occurring in:
  1. Methylosome protein WDR77
IPR036322
Domain description: WD40-repeat-containing domain superfamily
Occurring in:
  1. Methylosome protein WDR77
IPR015943
Domain description: WD40/YVTN repeat-like-containing domain superfamily
Occurring in:
  1. Methylosome protein WDR77
IPR035248
Domain description: PRMT5, oligomerisation domain
Occurring in:
  1. Protein arginine N-methyltransferase 5
IPR035075
Domain description: PRMT5 arginine-N-methyltransferase
Occurring in:
  1. Protein arginine N-methyltransferase 5
IPR035247
Domain description: PRMT5, TIM barrel domain
Occurring in:
  1. Protein arginine N-methyltransferase 5
IPR007857
Domain description: Protein arginine N-methyltransferase PRMT5
Occurring in:
  1. Protein arginine N-methyltransferase 5

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. Methylosome protein WDR77
The deposited structure of PDB entry 5emk contains 1 copy of CATH domain 2.130.10.10 (Methylamine Dehydrogenase; Chain H) in Methylosome protein WDR77. Showing 1 copy in chain B.
2.70.160.11
Class: Mainly Beta
Architecture: Distorted Sandwich
Topology: Hnrnp arginine n-methyltransferase1
Homology: Hnrnp arginine n-methyltransferase1
Occurring in:
  1. Protein arginine N-methyltransferase 5
The deposited structure of PDB entry 5emk contains 1 copy of CATH domain 2.70.160.11 (Hnrnp arginine n-methyltransferase1) in Protein arginine N-methyltransferase 5. Showing 1 copy in chain A.
3.40.50.150
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: Vaccinia Virus protein VP39
Occurring in:
  1. Protein arginine N-methyltransferase 5
The deposited structure of PDB entry 5emk contains 1 copy of CATH domain 3.40.50.150 (Rossmann fold) in Protein arginine N-methyltransferase 5. Showing 1 copy in chain A.
3.20.20.150
Class: Alpha Beta
Architecture: Alpha-Beta Barrel
Topology: TIM Barrel
Homology: Divalent-metal-dependent TIM barrel enzymes
Occurring in:
  1. Protein arginine N-methyltransferase 5
The deposited structure of PDB entry 5emk contains 1 copy of CATH domain 3.20.20.150 (TIM Barrel) in Protein arginine N-methyltransferase 5. Showing 1 copy in chain A.

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