1OR8 | pdb_00001or8

Structure of the Predominant protein arginine methyltransferase PRMT1

• PDB DOI: https://doi.org/10.2210/pdb1OR8/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-03-12 Released: 2003-08-26 
• Deposition Author(s): Zhang, X., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.254 (Depositor) 
• R-Value Work: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Structure of the Predominant Protein Arginine Methyltransferase PRMT1 and Analysis of Its Binding to Substrate Peptides

Zhang, X., Cheng, X.

(2003) Structure 11: 509-520

• PubMed: 12737817 
• DOI: https://doi.org/10.1016/s0969-2126(03)00071-6
• Primary Citation Related Structures: 
  1OR8, 1ORH, 1ORI


• PubMed Abstract: 
  

  PRMT1 is the predominant type I protein arginine methyltransferase in mammals and highly conserved among all eukaryotes. It is essential for early postimplantation development in mouse. Here we describe the crystal structure of rat PRMT1 in complex with the reaction product AdoHcy and a 19 residue substrate peptide containing three arginines. The results reveal a two-domain structure-an AdoMet binding domain and a barrel-like domain-with the active site pocket located between the two domains. Mutagenesis studies confirmed that two active site glutamates are essential for enzymatic activity, and that dimerization of PRMT1 is essential for AdoMet binding. Three peptide binding channels are identified: two are between the two domains, and the third is on the surface perpendicular to the strands forming the beta barrel.

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Organizational Affiliation: 
• Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.53 kDa 
• Atom Count: 2,791 
• Modeled Residue Count: 356 
• Deposited Residue Count: 416 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 1	A	340	Rattus norvegicus	Mutation(s): 0  Gene Names: HRMT1L2 OR PRMT1 EC: 2.1.1.125 (PDB Primary Data), 2.1.1.319 (UniProt)
UniProt
Find proteins for Q63009 (Rattus norvegicus) Explore Q63009  Go to UniProtKB:  Q63009

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Substrate peptide	B, C, D, E	19	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	F [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNL	G [auth A]	Unknown ligand PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.254 (Depositor) 
• R-Value Work:  0.195 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.5	α = 90
b = 86.5	β = 90
c = 142.4	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-26 
Deposition Author(s): Zhang, X., Cheng, X.

Revision History  

• Version 1.0: 2003-08-26
  Type: Initial release
  
• Version 1.1: 2008-04-02
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary