3O7W | pdb_00003o7w

The Crystal Structure of Human Leucine Carboxyl Methyltransferase 1

• PDB DOI: https://doi.org/10.2210/pdb3O7W/pdb
• Entry: 3O7W supersedes: 3MNT

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-01 Released: 2010-09-08 
• Deposition Author(s): Tsai, M.L., Cronin, N., Djordjevic, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

The structure of human leucine carboxyl methyltransferase 1 that regulates protein phosphatase PP2A

Tsai, M.L., Cronin, N., Djordjevic, S.

(2011) Acta Crystallogr D Biol Crystallogr 67: 14-24

• PubMed: 21206058 
• DOI: https://doi.org/10.1107/S0907444910042204
• Primary Citation of Related Structures:  
  3O7W


• PubMed Abstract: 
  

  Leucine carboxyl methyltransferase 1 (LCMT1) methylates the terminal carboxyl group of the leucine 309 residue of human protein phosphatase 2A (PP2A). PP2A, a key regulator of many cellular processes, has recently generated additional interest as a potential cancer-therapeutic target. The status of PP2A methylation impacts upon the selection of the regulatory subunit by the PP2A core enzyme, thus directing its activity and subcellular localization. An X-ray crystal structure of human LCMT1 protein in complex with the cofactor S-adenosylmethionine (AdoMet) has been solved to a resolution of 2 Å. The structure enables the postulation of a mode of interaction with protein phosphatase PP2A and provides a platform for further functional studies of the regulation of methylation of PP2A.

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Organizational Affiliation: 

Institute of Structural and Molecular Biology, University College London, England.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 34.42 kDa 
• Atom Count: 2,453 
• Modelled Residue Count: 282 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine carboxyl methyltransferase 1	A	294	Homo sapiens	Mutation(s): 0  Gene Names: LCMT1, LCMT, CGI-68 EC: 2.1.1 (PDB Primary Data), 2.1.1.233 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIC8 (Homo sapiens) Explore Q9UIC8  Go to UniProtKB:  Q9UIC8
PHAROS:  Q9UIC8 GTEx:  ENSG00000205629

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.086	α = 90
b = 63.296	β = 90
c = 81.77	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Tsai, M.L., Cronin, N., Djordjevic, S.
• This entry supersedes: 3MNT

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations