6DV2

Crystal Structure of Human Mitochondrial Trifunctional Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of human mitochondrial trifunctional protein, a fatty acid beta-oxidation metabolon.

Xia, C.Fu, Z.Battaile, K.P.Kim, J.P.

(2019) Proc. Natl. Acad. Sci. U.S.A. 116: 6069-6074

  • DOI: 10.1073/pnas.1816317116

  • PubMed Abstract: 
  • Membrane-bound mitochondrial trifunctional protein (TFP) catalyzes β-oxidation of long chain fatty acyl-CoAs, employing 2-enoyl-CoA hydratase (ECH), 3-hydroxyl-CoA dehydrogenase (HAD), and 3-ketothiolase (KT) activities consecutively. Inherited defic ...

    Membrane-bound mitochondrial trifunctional protein (TFP) catalyzes β-oxidation of long chain fatty acyl-CoAs, employing 2-enoyl-CoA hydratase (ECH), 3-hydroxyl-CoA dehydrogenase (HAD), and 3-ketothiolase (KT) activities consecutively. Inherited deficiency of TFP is a recessive genetic disease, manifesting in hypoketotic hypoglycemia, cardiomyopathy, and sudden death. We have determined the crystal structure of human TFP at 3.6-Å resolution. The biological unit of the protein is α 2 β 2 The overall structure of the heterotetramer is the same as that observed by cryo-EM methods. The two β-subunits make a tightly bound homodimer at the center, and two α-subunits are bound to each side of the β 2 dimer, creating an arc, which binds on its concave side to the mitochondrial innermembrane. The catalytic residues in all three active sites are arranged similarly to those of the corresponding, soluble monofunctional enzymes. A structure-based, substrate channeling pathway from the ECH active site to the HAD and KT sites is proposed. The passage from the ECH site to the HAD site is similar to those found in the two bacterial TFPs. However, the passage from the HAD site to the KT site is unique in that the acyl-CoA intermediate can be transferred between the two sites by passing along the mitochondrial inner membrane using the hydrophobic nature of the acyl chain. The 3'-AMP-PPi moiety is guided by the positively charged residues located along the "ceiling" of the channel, suggesting that membrane integrity is an essential part of the channel and is required for the activity of the enzyme.


    Organizational Affiliation

    Industrial Macromolecular Crystallography Association-Collaborative Access Team, Hauptman-Woodward Medical Research Institute, Argonne, IL 60439.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226; jjkim@mcw.edu.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trifunctional enzyme subunit beta, mitochondrial
A, B, C, D, E, F
457Homo sapiensMutation(s): 0 
Gene Names: HADHB
Membrane protein
mpstruc
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Oxidoreductases (Monotopic)
Protein: 
mitochondrial trifunctional protein
Find proteins for P55084 (Homo sapiens)
Go to Gene View: HADHB
Go to UniProtKB:  P55084
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Trifunctional enzyme subunit alpha, mitochondrial
G, H, I, J, K, L
727Homo sapiensMutation(s): 0 
Gene Names: HADHA (HADH)
Membrane protein
mpstruc
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Oxidoreductases (Monotopic)
Protein: 
mitochondrial trifunctional protein
Find proteins for P40939 (Homo sapiens)
Go to Gene View: HADHA
Go to UniProtKB:  P40939
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 136.536α = 90.00
b = 237.938β = 105.61
c = 141.319γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Health & Human Services (HHS)United StatesGM29076

Revision History 

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2019-03-06
    Type: Data collection, Database references
  • Version 1.2: 2019-03-20
    Type: Data collection, Database references
  • Version 1.3: 2019-04-10
    Type: Data collection, Database references
  • Version 1.4: 2020-01-01
    Type: Author supporting evidence