1P0Y

Crystal structure of the SET domain of LSMT bound to MeLysine and AdoHcy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT

Trievel, R.C.Flynn, E.M.Houtz, R.L.Hurley, J.H.

(2003) Nat.Struct.Mol.Biol. 10: 545-552

  • DOI: 10.1038/nsb946
  • Primary Citation of Related Structures:  1OZV

  • PubMed Abstract: 
  • SET domain protein methyltransferases catalyze the transfer of methyl groups from the cofactor S-adenosylmethionine (AdoMet) to specific lysine residues of protein substrates, such as the N-terminal tails of histones H3 and H4 and the large subunit o ...

    SET domain protein methyltransferases catalyze the transfer of methyl groups from the cofactor S-adenosylmethionine (AdoMet) to specific lysine residues of protein substrates, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex. The crystal structures of pea Rubisco large subunit methyltransferase (LSMT) in ternary complexes with either lysine or epsilon-N-methyllysine (MeLys) and the product S-adenosylhomocysteine (AdoHcy) were determined to resolutions of 2.65 and 2.55 A, respectively. The zeta-methyl group of MeLys is bound to the enzyme via carbon-oxygen hydrogen bonds that play a key role in catalysis. The methyl donor and acceptor are aligned in a linear geometry for S(N)2 nucleophilic transfer of the methyl group during catalysis. Differences in hydrogen bonding between the MeLys epsilon-amino group and Rubisco LSMT and SET7/9 explain why Rubisco LSMT generates multiply methylated Lys, wheras SET7/9 generates only MeLys.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast
A, B, C
444Pisum sativumGene Names: RBCMT
EC: 2.1.1.127, 2.1.1.259
Find proteins for Q43088 (Pisum sativum)
Go to UniProtKB:  Q43088
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLZ
Query on MLZ

Download SDF File 
Download CCD File 
C
N-METHYL-LYSINE
C7 H16 N2 O2
PQNASZJZHFPQLE-LURJTMIESA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B, C
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MLZKi: 100800000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 130.410α = 90.00
b = 153.190β = 90.00
c = 266.320γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance