2HDK

Crystal Structure of Cys315Ala-Cys318Ala Mutant of Human Mitochondrial Branched Chain Aminotransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.320 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Human Mitochondrial Branched Chain Aminotransferase Isozyme: STRUCTURAL ROLE OF THE CXXC CENTER IN CATALYSIS.

Yennawar, N.H.Islam, M.M.Conway, M.Wallin, R.Hutson, S.M.

(2006) J Biol Chem 281: 39660-39671

  • DOI: 10.1074/jbc.M607552200
  • Primary Citation of Related Structures:  
    2HDK, 2HG8, 2HHF, 2HGX, 2HGW

  • PubMed Abstract: 
  • Mammalian branched chain aminotransferases (BCATs) have a unique CXXC center. Kinetic and structural studies of three CXXC center mutants (C315A, C318A, and C315A/C318A) of human mitochondrial (hBCATm) isozyme and the oxidized hBCATm enzyme (hBCATm-O ...

    Mammalian branched chain aminotransferases (BCATs) have a unique CXXC center. Kinetic and structural studies of three CXXC center mutants (C315A, C318A, and C315A/C318A) of human mitochondrial (hBCATm) isozyme and the oxidized hBCATm enzyme (hBCATm-Ox) have been used to elucidate the role of this center in hBCATm catalysis. X-ray crystallography revealed that the CXXC motif, through its network of hydrogen bonds, plays a crucial role in orienting the substrate optimally for catalysis. In all structures, there were changes in the structure of the beta-turn preceding the CXXC motif when compared with wild type protein. The N-terminal loop between residues 15 and 32 is flexible in the oxidized and mutant enzymes, the disorder greater in the oxidized protein. Disordering of the N-terminal loop disrupts the integrity of the side chain binding pocket, particularly for the branched chain side chain, less so for the dicarboxylate substrate side chain. The kinetic studies of the mutant and oxidized enzymes support the structural analysis. The kinetic results showed that the predominant effect of oxidation was on the second half-reaction rather than the first half-reaction. The oxidized enzyme was completely inactive, whereas the mutants showed limited activity. Model building of the second half-reaction substrate alpha-ketoisocaproate in the pyridoxamine 5'-phosphate-hBCATm structure suggests that disruption of the CXXC center results in altered substrate orientation and deprotonation of the amino group of pyridoxamine 5'-phosphate, which inhibits catalysis.


    Organizational Affiliation

    Departments of Biochemistry and Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Branched-chain-amino-acid aminotransferase, mitochondrialAB365Homo sapiensMutation(s): 2 
Gene Names: BCAT2BCATMBCT2ECA40
EC: 2.6.1.42
Find proteins for O15382 (Homo sapiens)
Explore O15382 
Go to UniProtKB:  O15382
NIH Common Fund Data Resources
PHAROS  O15382
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
COI
Query on COI

Download CCD File 
B
2-OXO-4-METHYLPENTANOIC ACID
C6 H10 O3
BKAJNAXTPSGJCU-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
COIKd:  6100000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.320 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.48α = 90
b = 112.187β = 96.16
c = 60.265γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description