Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 87.02 kDa 
• Atom Count: 6258 
• Modelled Residue Count: 714 
• Deposited Residue Count: 772 
• Unique protein chains: 1

2COI

Crystal structure of oxidized human cytosolic branched-chain aminotransferase complexed with gabapentin

• DOI: 10.2210/pdb2COI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-05-17 Released: 2005-08-30 
• Deposition Author(s): Goto, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.272 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 

Literature

Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin

Goto, M., Miyahara, I., Hirotsu, K., Conway, M., Yennawar, N., Islam, M.M., Hutson, S.M.

(2005) J Biol Chem 280: 37246-37256

• PubMed: 16141215 
• DOI: 10.1074/jbc.M506486200
• Primary Citation of Related Structures:  
  2A1H, 2COJ, 2COI, 2COG


• PubMed Abstract: 
  

This study presents the first three-dimensional structures of human cytosolic branched-chain aminotransferase (hBCATc) isozyme complexed with the neuroactive drug gabapentin, the hBCATc Michaelis complex with the substrate analog, 4-methylvalerate, and the mitochondrial isozyme (hBCATm) complexed with gabapentin. The branched-chain aminotransferases (BCAT) reversibly catalyze transamination of the essential branched-chain amino acids (leucine, isoleucine, valine) to alpha-ketoglutarate to form the respective branched-chain alpha-keto acids and glutamate. The cytosolic isozyme is the predominant BCAT found in the nervous system, and only hBCATc is inhibited by gabapentin. Pre-steady state kinetics show that 1.3 mm gabapentin can completely inhibit the binding of leucine to reduced hBCATc, whereas 65.4 mm gabapentin is required to inhibit leucine binding to hBCATm. Structural analysis shows that the bulky gabapentin is enclosed in the active-site cavity by the shift of a flexible loop that enlarges the active-site cavity. The specificity of gabapentin for the cytosolic isozyme is ascribed at least in part to the location of the interdomain loop and the relative orientation between the small and large domain which is different from these relationships in the mitochondrial isozyme. Both isozymes contain a CXXC center and form a disulfide bond under oxidizing conditions. The structure of reduced hBCATc was obtained by soaking the oxidized hBCATc crystals with dithiothreitol. The close similarity in active-site structures between cytosolic enzyme complexes in the oxidized and reduced states is consistent with the small effect of oxidation on pre-steady state kinetics of the hBCATc first half-reaction. However, these kinetic data do not explain the inactivation of hBCATm by oxidation of the CXXC center. The structural data suggest that there is a larger effect of oxidation on the interdomain loop and residues surrounding the CXXC center in hBCATm than in hBCATc.

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Organizational Affiliation: 

Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
branched chain aminotransferase 1, cytosolic	A, B	386	Homo sapiens	Mutation(s): 1  Gene Names: BCAT1, BCT1, ECA39 EC: 2.6.1.42
Find proteins for P54687 (Homo sapiens) Explore P54687  Go to UniProtKB:  P54687
NIH Common Fund Data Resources
PHAROS:  P54687 GTEx:  ENSG00000060982

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GBN	D [auth A], G [auth B]	[1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ACID C9 H17 N O2 UGJMXCAKCUNAIE-UHFFFAOYSA-N
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GBN	Ki:  3500000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.272 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.72	α = 90
b = 107.69	β = 90
c = 110.3	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-17 
• Released Date: 2005-08-30 
Deposition Author(s): Goto, M.

Revision History  

• Version 1.0: 2005-08-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance