2COI

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

PDB 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.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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

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.

Organizational Affiliation:

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for P54687 (Homo sapiens) Explore P54687 Go to UniProtKB: P54687
PHAROS: P54687
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54687
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A]	C [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Ligand Interaction
GBN Query on GBN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	[1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ACID C₉ H₁₇ N O₂ UGJMXCAKCUNAIE-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
GBN	Binding MOAD: 2COI	Ki: 3.50e+6 (nM) from 1 assay(s)

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2005-05-17
Released Date: 2005-08-30

Deposition Author(s):

Goto, M.

Revision History (Full details and data files)

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
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations