3WST

Crystal structure of C.elegans PRMT7 in complex with SAH(P31)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

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This is version 1.1 of the entry. See complete history


Literature

Protein arginine methyltransferase 7 has a novel homodimer-like structure formed by tandem repeats

Hasegawa, M.Toma-fukai, S.Kim, J.D.Fukamizu, A.Shimizu, T.

(2014) FEBS Lett 588: 1942-1948

  • DOI: 10.1016/j.febslet.2014.03.053
  • Primary Citation of Related Structures:  
    3WST, 3X0D

  • PubMed Abstract: 
  • Protein arginine methyltransferase 7 (PRMT7) is a member of a family of enzymes that catalyze the transfer of methyl groups from S-adenosyl-l-methionine to nitrogen atoms on arginine residues. Here, we describe the crystal structure of Caenorhabditis elegans PRMT7 in complex with its reaction product S-adenosyl-L-homocysteine ...

    Protein arginine methyltransferase 7 (PRMT7) is a member of a family of enzymes that catalyze the transfer of methyl groups from S-adenosyl-l-methionine to nitrogen atoms on arginine residues. Here, we describe the crystal structure of Caenorhabditis elegans PRMT7 in complex with its reaction product S-adenosyl-L-homocysteine. The structural data indicated that PRMT7 harbors two tandem repeated PRMT core domains that form a novel homodimer-like structure. S-adenosyl-L-homocysteine bound to the N-terminal catalytic site only; the C-terminal catalytic site is occupied by a loop that inhibits cofactor binding. Mutagenesis demonstrated that only the N-terminal catalytic site of PRMT7 is responsible for cofactor binding.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; CREST, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan. Electronic address: shimizu@mol.f.u-tokyo.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 7655Caenorhabditis elegansMutation(s): 0 
Gene Names: pmrt-2prmt-7W06D4.4
EC: 2.1.1
UniProt
Find proteins for Q9XW42 (Caenorhabditis elegans)
Explore Q9XW42 
Go to UniProtKB:  Q9XW42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XW42
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
AA [auth F],
AB [auth L],
CA [auth E],
EA [auth G],
GA [auth H],
AA [auth F],
AB [auth L],
CA [auth E],
EA [auth G],
GA [auth H],
IA [auth I],
KA [auth M],
MA [auth N],
OA [auth O],
QA [auth P],
S [auth A],
SA [auth Q],
U [auth D],
UA [auth R],
W [auth B],
WA [auth J],
Y [auth C],
YA [auth K]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
BA [auth F],
BB [auth L],
DA [auth E],
FA [auth G],
HA [auth H],
BA [auth F],
BB [auth L],
DA [auth E],
FA [auth G],
HA [auth H],
JA [auth I],
LA [auth M],
NA [auth N],
PA [auth O],
RA [auth P],
T [auth A],
TA [auth Q],
V [auth D],
VA [auth R],
X [auth B],
XA [auth J],
Z [auth C],
ZA [auth K]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.703α = 90
b = 190.703β = 90
c = 373.088γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references