1MLV | pdb_00001mlv

Structure and Catalytic Mechanism of a SET Domain Protein Methyltransferase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.277 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.232 (DCC) 

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This is version 1.5 of the entry. See complete history. 

Literature

Structure and catalytic mechanism of a SET domain protein methyltransferase.

Trievel, R.C., Beach, B.M., Dirk, L.M., Houtz, R.L., Hurley, J.H.

(2002) Cell 111: 91-103

  • DOI: https://doi.org/10.1016/s0092-8674(02)01000-0
  • Primary Citation Related Structures: 
    1MLV

  • PubMed Abstract: 

    Protein lysine methylation by SET domain enzymes regulates chromatin structure, gene silencing, transcriptional activation, plant metabolism, and other processes. The 2.6 A resolution structure of Rubisco large subunit methyltransferase in a pseudo-bisubstrate complex with S-adenosylhomocysteine and a HEPES ion reveals an all-beta architecture for the SET domain embedded within a larger alpha-helical enzyme fold. Conserved regions of the SET domain bind S-adenosylmethionine and substrate lysine at two sites connected by a pore. We propose that methyl transfer is catalyzed by a conserved Tyr at a narrow pore connecting the sites. The cofactor enters by a "back door" on the opposite side of the enzyme from substrate, promoting highly specific protein recognition and allowing addition of multiple methyl groups.

    • Organizational Affiliation: 
    • Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 153.76 kDa 
  • Atom Count: 11,270 
  • Modeled Residue Count: 1,302 
  • Deposited Residue Count: 1,332 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
A, B, C
444Lathyrus oleraceusMutation(s): 6 
EC: 2.1.1.127 (PDB Primary Data), 2.1.1.259 (UniProt)
UniProt
Find proteins for Q43088 (Pisum sativum)
Explore Q43088 
Go to UniProtKB:  Q43088
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ43088
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.277 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.232 (DCC) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.16α = 90
b = 156.68β = 90
c = 268.44γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-14
    Changes: Data collection