2DEB | pdb_00002deb

Crystal structure of rat carnitine palmitoyltransferase 2 in space group C2221

• PDB DOI: https://doi.org/10.2210/pdb2DEB/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-02-10 Released: 2007-02-10 
• Deposition Author(s): Rufer, A.C., Thoma, R., Benz, J., Stihle, M., Gsell, B., De Roo, E., Banner, D.W., Mueller, F., Chomienne, O., Hennig, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.194 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

The crystal structure of carnitine palmitoyltransferase 2 and implications for diabetes treatment

Rufer, A.C., Thoma, R., Benz, J., Stihle, M., Gsell, B., De Roo, E., Banner, D.W., Mueller, F., Chomienne, O., Hennig, M.

(2006) Structure 14: 713-723

• PubMed: 16615901 
• DOI: https://doi.org/10.1016/j.str.2006.03.002
• Primary Citation Related Structures: 
  2DEB, 2FW3, 2FYO


• PubMed Abstract: 
  

  Carnitine palmitoyltransferases (CPTs) are part of the enzymatic system that imports fatty acids into mitochondria. The crystal structure of rat CPT-2 by Rufer et al. (2006) (this issue of Structure) reveals a Y-shaped tunnel for binding the CoA and acyl-carnitine substrates and a hydrophobic insert mediating membrane association.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 150.6 kDa 
• Atom Count: 11,542 
• Modeled Residue Count: 1,253 
• Deposited Residue Count: 1,306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carnitine O-palmitoyltransferase II, mitochondrial	A, B	653	Rattus norvegicus	Mutation(s): 12  EC: 2.3.1.21
UniProt
Find proteins for P18886 (Rattus norvegicus) Explore P18886  Go to UniProtKB:  P18886

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	C [auth A], F [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
BOG	E [auth B]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PLM	D [auth A], G [auth B]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.194 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.18	α = 90
b = 97.29	β = 90
c = 310.44	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-10 
Deposition Author(s): Rufer, A.C., Thoma, R., Benz, J., Stihle, M., Gsell, B., De Roo, E., Banner, D.W., Mueller, F., Chomienne, O., Hennig, M.

Revision History  

• Version 1.0: 2007-02-10
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Structure summary