1KT8

HUMAN BRANCHED CHAIN AMINO ACID AMINOTRANSFERASE (MITOCHONDRIAL): THREE DIMENSIONAL STRUCTURE OF ENZYME IN ITS KETIMINE FORM WITH THE SUBSTRATE L-ISOLEUCINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.243 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structures of human mitochondrial branched chain aminotransferase reaction intermediates: ketimine and pyridoxamine phosphate forms

Yennawar, N.H.Conway, M.E.Yennawar, H.P.Farber, G.K.Hutson, S.M.

(2002) Biochemistry 41: 11592-11601

  • DOI: 10.1021/bi020221c
  • Primary Citation of Related Structures:  
    1KT8, 1KTA

  • PubMed Abstract: 
  • The three-dimensional structures of the isoleucine ketimine and the pyridoxamine phosphate forms of human mitochondrial branched chain aminotransferase (hBCATm) have been determined crystallographically at 1.9 A resolution. The hBCATm-catalyzed transamination can be described in molecular terms together with the earlier solved pyridoxal phosphate forms of the enzyme ...

    The three-dimensional structures of the isoleucine ketimine and the pyridoxamine phosphate forms of human mitochondrial branched chain aminotransferase (hBCATm) have been determined crystallographically at 1.9 A resolution. The hBCATm-catalyzed transamination can be described in molecular terms together with the earlier solved pyridoxal phosphate forms of the enzyme. The active site lysine, Lys202, undergoes large conformational changes, and the pyridine ring of the cofactor tilts by about 18 degrees during catalysis. A major determinant of the enzyme's substrate and stereospecificity for L-branched chain amino acids is a group of hydrophobic residues that form three hydrophobic surfaces and lock the side chain in place. Short-chain aliphatic amino acid side chains are unable to interact through van der Waals contacts with any of the surfaces whereas bulky aromatic side chains would result in significant steric hindrance. As shown by modeling, and in agreement with previous biochemical data, glutamate but not aspartate can form hydrogen bond interactions. The carboxylate group of the bound isoleucine is on the same side as the phosphate group of the cofactor. These active site interactions are largely retained in a model of the human cytosolic branched chain aminotransferase (hBCATc), suggesting that residues in the second tier of interactions are likely to determine the specificity of hBCATc for the drug gabapentin. Finally, the structures reveal a unique role for cysteine residues in the mammalian BCAT. Cys315 and Cys318, which immediately follow a beta-turn (residues 311-314) and are located just outside the active site, form an unusual thiol-thiolate hydrogen bond. This beta-turn positions Thr313 for its interaction with the pyridoxal phosphate oxygens and substrate alpha-carboxylate group.


    Related Citations: 
    • The Structure of Human Mitochondrial Branched-Chain Aminotransferase
      Yennawar, N.H., Dunbar, J., Conway, M., Hutson, S.M., Farber, G.K.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 506
    • Cloning of the Rat and Human Mitochondrial Branched Amino Acid Aminotransferase (Bcatm).
      Bledsoe, R.K., Dawson, P.A., Hutson, S.M.
      (1997) Biochim Biophys Acta 1339: 9

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Althouse Laboratory, The Pennsylvania State University, University Park, PA 16802, USA. nhy1@psu.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE, MITOCHONDRIALA, B365Homo sapiensMutation(s): 0 
Gene Names: BCAT2BCATMBCT2ECA40
EC: 2.6.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O15382 (Homo sapiens)
Explore O15382 
Go to UniProtKB:  O15382
PHAROS:  O15382
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15382
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ILP
Query on ILP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
N-[O-PHOSPHONO-PYRIDOXYL]-ISOLEUCINE
C14 H23 N2 O7 P
GZZDWFDWHXPWJK-QPUJVOFHSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.475α = 90
b = 105.457β = 90
c = 107.429γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance