Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 228.08 kDa 
• Atom Count: 15358 
• Modelled Residue Count: 1974 
• Deposited Residue Count: 2096 
• Unique protein chains: 2

3RNM

The crystal structure of the subunit binding of human dihydrolipoamide transacylase (E2b) bound to human dihydrolipoamide dehydrogenase (E3)

• PDB DOI: 10.2210/pdb3RNM/pdb

• Classification: OXIDOREDUCTASE/PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-04-22 Released: 2011-05-04 
• Deposition Author(s): Brautigam, C.A., Wynn, R.M., Chuang, J.C., Young, B.B., Chuang, D.T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.239 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Literature

Structural and Thermodynamic Basis for Weak Interactions between Dihydrolipoamide Dehydrogenase and Subunit-binding Domain of the Branched-chain {alpha}-Ketoacid Dehydrogenase Complex.

Brautigam, C.A., Wynn, R.M., Chuang, J.L., Naik, M.T., Young, B.B., Huang, T.H., Chuang, D.T.

(2011) J Biol Chem 286: 23476-23488

• PubMed: 21543315 
• DOI: 10.1074/jbc.M110.202960
• Primary Citation of Related Structures:  
  3RNM


• PubMed Abstract: 
  

The purified mammalian branched-chain α-ketoacid dehydrogenase complex (BCKDC), which catalyzes the oxidative decarboxylation of branched-chain α-keto acids, is essentially devoid of the constituent dihydrolipoamide dehydrogenase component (E3). The absence of E3 is associated with the low affinity of the subunit-binding domain of human BCKDC (hSBDb) for hE3. In this work, sequence alignments of hSBDb with the E3-binding domain (E3BD) of the mammalian pyruvate dehydrogenase complex show that hSBDb has an arginine at position 118, where E3BD features an asparagine. Substitution of Arg-118 with an asparagine increases the binding affinity of the R118N hSBDb variant (designated hSBDb*) for hE3 by nearly 2 orders of magnitude. The enthalpy of the binding reaction changes from endothermic with the wild-type hSBDb to exothermic with the hSBDb* variant. This higher affinity interaction allowed the determination of the crystal structure of the hE3/hSBDb* complex to 2.4-Å resolution. The structure showed that the presence of Arg-118 poses a unique, possibly steric and/or electrostatic incompatibility that could impede E3 interactions with the wild-type hSBDb. Compared with the E3/E3BD structure, the hE3/hSBDb* structure has a smaller interfacial area. Solution NMR data corroborated the interactions of hE3 with Arg-118 and Asn-118 in wild-type hSBDb and mutant hSBDb*, respectively. The NMR results also showed that the interface between hSBDb and hE3 does not change significantly from hSBDb to hSBDb*. Taken together, our results represent a starting point for explaining the long standing enigma that the E2b core of the BCKDC binds E3 far more weakly relative to other α-ketoacid dehydrogenase complexes.

---

Organizational Affiliation: 

Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase, mitochondrial	A, B, C, D	495	Homo sapiens	Mutation(s): 0  Gene Names: DLD, GCSL, LAD, PHE3 EC: 1.8.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for P09622 (Homo sapiens) Explore P09622  Go to UniProtKB:  P09622
PHAROS:  P09622 GTEx:  ENSG00000091140

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial	E, F	58	Homo sapiens	Mutation(s): 1  Gene Names: DBT, BCATE2 EC: 2.3.1.168
UniProt & NIH Common Fund Data Resources
Find proteins for P11182 (Homo sapiens) Explore P11182  Go to UniProtKB:  P11182
PHAROS:  P11182 GTEx:  ENSG00000137992

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	H [auth A], K [auth B], N [auth C], Q [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NHE	I [auth A], L [auth B], O [auth C], R [auth D]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
BME	G [auth A], J [auth B], M [auth C], P [auth D]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.239 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.136	α = 90
b = 112.308	β = 91.4
c = 122.545	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-22 
• Released Date: 2011-05-04 
Deposition Author(s): Brautigam, C.A., Wynn, R.M., Chuang, J.C., Young, B.B., Chuang, D.T.

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-20
  Changes: Database references