Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 228077.48 
• Atom Count: 15011 
• 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)

• DOI: 10.2210/pdb3RNM/pdb

• Classification: OXIDOREDUCTASE/PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.239 
• R-Value Work: 0.181 

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


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Dihydrolipoyl dehydrogenase, mitochondrial	A, B, C, D	495	Homo sapiens	Mutation(s): 0  Gene Names: DLD (GCSL, LAD, PHE3) EC: 1.8.1.4
Find proteins for P09622 (Homo sapiens) Go to Gene View: DLD Go to UniProtKB:  P09622

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
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
Find proteins for P11182 (Homo sapiens) Go to Gene View: DBT Go to UniProtKB:  P11182

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FAD	A, B, C, D	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NHE	A, B, C, D	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID N-CYCLOHEXYLTAURINE; CHES C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
BME	A, B, C, D	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.239 
• R-Value Work: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 84.136	α = 90.00
b = 112.308	β = 91.40
c = 122.545	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-20
  Type: Database references