Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 100.93 kDa 
• Atom Count: 7385 
• Modelled Residue Count: 928 
• Deposited Residue Count: 928 
• Unique protein chains: 1

2A8X

Crystal Structure of Lipoamide Dehydrogenase from Mycobacterium tuberculosis

• DOI: 10.2210/pdb2A8X/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-07-10 Released: 2005-08-16 
• Deposition Author(s): Rajashankar, K.R., Bryk, R., Kniewel, R., Buglino, J.A., Nathan, C.F., Lima, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

Crystal structure and functional analysis of lipoamide dehydrogenase from Mycobacterium tuberculosis

Rajashankar, K.R., Bryk, R., Kniewel, R., Buglino, J.A., Nathan, C.F., Lima, C.D.

(2005) J Biol Chem 280: 33977-33983

• PubMed: 16093239 
• DOI: 10.1074/jbc.M507466200
• Primary Citation of Related Structures:  
  2A8X


• PubMed Abstract: 
  

We report the 2.4 A crystal structure for lipoamide dehydrogenase encoded by lpdC from Mycobacterium tuberculosis. Based on the Lpd structure and sequence alignment between bacterial and eukaryotic Lpd sequences, we generated single point mutations in Lpd and assayed the resulting proteins for their ability to catalyze lipoamide reduction/oxidation alone and in complex with other proteins that participate in pyruvate dehydrogenase and peroxidase activities. The results suggest that amino acid residues conserved in mycobacterial species but not conserved in eukaryotic Lpd family members modulate either or both activities and include Arg-93, His-98, Lys-103, and His-386. In addition, Arg-93 and His-386 are involved in forming both "open" and "closed" active site conformations, suggesting that these residues play a role in dynamically regulating Lpd function. Taken together, these data suggest protein surfaces that should be considered while developing strategies for inhibiting this enzyme.

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Organizational Affiliation: 

Structural Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase	A, B	464	Mycobacterium tuberculosis	Mutation(s): 7  Gene Names: Rv0462, MT0478, lpdC EC: 1.8.1.4
UniProt
Find proteins for P9WHH9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHH9  Go to UniProtKB:  P9WHH9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.246 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.582	α = 90
b = 96.677	β = 90
c = 122.889	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2005-07-10 
• Released Date: 2005-08-16 
Deposition Author(s): Rajashankar, K.R., Bryk, R., Kniewel, R., Buglino, J.A., Nathan, C.F., Lima, C.D.

Revision History  

• Version 1.0: 2005-08-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance