Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 74.15 kDa 
• Atom Count: 5159 
• Modelled Residue Count: 618 
• Deposited Residue Count: 638 
• Unique protein chains: 2

3P71

Crystal structure of the complex of LCMT-1 and PP2A

• PDB DOI: 10.2210/pdb3P71/pdb

• Classification: TRANSFERASE/HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Heliothis
• Mutation(s): Yes 


• Deposited: 2010-10-11 Released: 2011-02-16 
• Deposition Author(s): Xing, Y., Stanevich, V., Satyshur, K.A., Jiang, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Literature

The Structural Basis for Tight Control of PP2A Methylation and Function by LCMT-1.

Stanevich, V., Jiang, L., Satyshur, K.A., Li, Y., Jeffrey, P.D., Li, Z., Menden, P., Semmelhack, M.F., Xing, Y.

(2011) Mol Cell 41: 331-342

• PubMed: 21292165 
• DOI: 10.1016/j.molcel.2010.12.030
• Primary Citation of Related Structures:  
  3P71


• PubMed Abstract: 
  

Proper formation of protein phosphatase 2A (PP2A) holoenzymes is essential for the fitness of all eukaryotic cells. Carboxyl methylation of the PP2A catalytic subunit plays a critical role in regulating holoenzyme assembly; methylation is catalyzed by PP2A-specific methyltransferase LCMT-1, an enzyme required for cell survival. We determined crystal structures of human LCMT-1 in isolation and in complex with PP2A stabilized by a cofactor mimic. The structures show that the LCMT-1 active-site pocket recognizes the carboxyl terminus of PP2A, and, interestingly, the PP2A active site makes extensive contacts to LCMT-1. We demonstrated that activation of the PP2A active site stimulates methylation, suggesting a mechanism for efficient conversion of activated PP2A into substrate-specific holoenzymes, thus minimizing unregulated phosphatase activity or formation of inactive holoenzymes. A dominant-negative LCMT-1 mutant attenuates the cell cycle without causing cell death, likely by inhibiting uncontrolled phosphatase activity. Our studies suggested mechanisms of LCMT-1 in tight control of PP2A function, important for the cell cycle and cell survival.

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Organizational Affiliation: 

McArdle Laboratory, Department of Oncology, School of Medicine and Public Health, University of Wisconsin at Madison, Madison, WI 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine carboxyl methyltransferase 1	A [auth T]	334	Homo sapiens	Mutation(s): 4  Gene Names: CGI-68, LCMT, LCMT1 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform	B [auth C]	304	Homo sapiens	Mutation(s): 0  Gene Names: PPP2CA EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P67775 (Homo sapiens) Explore P67775  Go to UniProtKB:  P67775
PHAROS:  P67775

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AN6	D [auth C]	5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine C16 H25 N7 O5 GAMUFACDOHMHSZ-OPYVMVOTSA-N
PEG	C [auth T]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MN	E [auth C], F [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.802	α = 90
b = 65.305	β = 90
c = 193.092	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-10-11 
• Released Date: 2011-02-16 
Deposition Author(s): Xing, Y., Stanevich, V., Satyshur, K.A., Jiang, L.

Revision History  

• Version 1.0: 2011-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-10-08
  Changes: Database references
• Version 1.3: 2014-10-15
  Changes: Structure summary