2BFD

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

• PDB DOI:  https://doi.org/10.2210/pdb2BFD/pdb

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


• Deposited: 2004-12-06 Released: 2006-02-16 
• Deposition Author(s): Machius, M., Wynn, R.M., Chuang, J.L., Tomchick, D.R., Brautigam, C.A., Chuang, D.T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.170 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Literature

A Versatile Conformational Switch Regulates Reactivity in Human Branched-Chain Alpha-Ketoacid Dehydrogenase.

Machius, M., Wynn, R.M., Chuang, J.L., Li, J., Kluger, R., Yu, D., Tomchick, D.R., Brautigam, C.A., Chuang, D.T.

(2006) Structure 14: 287

• PubMed: 16472748 
• DOI: https://doi.org/10.1016/j.str.2005.10.009
• Primary Citation of Related Structures:  
  1WCI, 2BEU, 2BEV, 2BEW, 2BFB, 2BFC, 2BFD, 2BFE, 2BFF


• PubMed Abstract: 
  

The dehydrogenase/decarboxylase (E1b) component of the 4 MD human branched-chain alpha-ketoacid dehydrogenase complex (BCKDC) is a thiamin diphosphate (ThDP)-dependent enzyme. We have determined the crystal structures of E1b with ThDP bound intermediates after decarboxylation of alpha-ketoacids. We show that a key tyrosine residue in the E1b active site functions as a conformational switch to reduce the reactivity of the ThDP cofactor through interactions with its thiazolium ring. The intermediates do not assume the often-postulated enamine state, but likely a carbanion state. The carbanion presumably facilitates the second E1b-catalyzed reaction, involving the transfer of an acyl moiety from the intermediate to a lipoic acid prosthetic group in the transacylase (E2b) component of the BCKDC. The tyrosine switch further remodels an E1b loop region to promote E1b binding to E2b. Our results illustrate the versatility of the tyrosine switch in coordinating the catalytic events in E1b by modulating the reactivity of reaction intermediates.

---

Related Citations: 

• Crosstalk between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine
  Li, J., Wynn, R.M., Machius, M., Chuang, J.L., Karthikeyan, S., Tomchick, D.R., Chuang, D.T.
  (2004) J Biol Chem 279: 32968

• Roles of His291-Alpha and His146-Beta in the Reductive Acylation Reaction Catalyzed by Human Branched-Chain Alpha-Ketoacid Dehydrogenase: Refined Phosphorylation Loop Structure in the Active Site
  Wynn, R., Machius, M., Chuang, J., Li, J., Tomchick, D., Chuang, D.
  (2003) J Biol Chem 278: 43402

• Roles of Active Site and Novel K+ Ion-Binding Site Residues in Human Mitochondrial Branched-Chain Alpha-Ketoacid Decarboxylase/Dehydrogenase
  Wynn, R.M., Ho, R., Chuang, J.L., Chuang, D.T.
  (2001) J Biol Chem 276: 4168

---

Organizational Affiliation: 

Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 84.1 kDa 
• Atom Count: 6,678 
• Modelled Residue Count: 706 
• Deposited Residue Count: 742 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT	A	400	Homo sapiens	Mutation(s): 1  Gene Names: BCKDHA EC: 1.2.4.4
UniProt & NIH Common Fund Data Resources
Find proteins for P12694 (Homo sapiens) Explore P12694  Go to UniProtKB:  P12694
PHAROS:  P12694

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT	B	342	Homo sapiens	Mutation(s): 0  Gene Names: BCKDHB EC: 1.2.4.4
UniProt & NIH Common Fund Data Resources
Find proteins for P21953 (Homo sapiens) Explore P21953  Go to UniProtKB:  P21953
PHAROS:  P21953

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	F [auth A]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
MPD	I [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL	H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
K	C [auth A], G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.170 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.839	α = 90
b = 144.839	β = 90
c = 69.247	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-16 
Deposition Author(s): Machius, M., Wynn, R.M., Chuang, J.L., Tomchick, D.R., Brautigam, C.A., Chuang, D.T.

Revision History  

• Version 1.0: 2006-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 2.0: 2021-08-04
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary