Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 73515.10 
• Atom Count: 5060 
• Residue Count: 634 
• Unique protein chains: 1

3A4V

Crystal structure of pyruvate bound L-Threonine dehydrogenase from Hyperthermophilic Archaeon Thermoplasma volcanium

• DOI: 10.2210/pdb3A4V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)
• Expression System: Escherichia coli


• Deposited: 2009-07-20 Released: 2010-07-28 
• Deposition Author(s): Yoneda, K., Sakuraba, H., Ohshima, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.209 
• R-Value Work: 0.203 

Literature

Crystal Structure of Binary and Ternary Complexes of Archaeal UDP-galactose 4-Epimerase-like L-Threonine Dehydrogenase from Thermoplasma volcanium.

Yoneda, K., Sakuraba, H., Araki, T., Ohshima, T.

(2012) J.Biol.Chem. 287: 12966-12974

• PubMed: 22374996 
• DOI: 10.1074/jbc.M111.336958
• Primary Citation of Related Structures:  
  3AJR, 3A9W, 3A1N


• PubMed Abstract: 
  

A gene from the thermophilic archaeon Thermoplasma volcanium encoding an L-threonine dehydrogenase (L-ThrDH) with a predicted amino acid sequence that was remarkably similar to the sequence of UDP-galactose 4-epimerase (GalE) was overexpressed in Escherichia coli, and its product was purified and characterized. The expressed enzyme was moderately thermostable, retaining more than 90% of its activity after incubation for 10 min at up to 70 °C. The catalytic residue was assessed using site-directed mutagenesis, and Tyr(137) was found to be essential for catalysis. To clarify the structural basis of the catalytic mechanism, four different crystal structures were determined using the molecular replacement method: L-ThrDH-NAD(+), L-ThrDH in complex with NAD(+) and pyruvate, Y137F mutant in complex with NAD(+) and L-threonine, and Y137F in complex with NAD(+) and L-3-hydroxynorvaline. Each monomer consisted of a Rossmann-fold domain and a C-terminal catalytic domain, and the fold of the catalytic domain showed notable similarity to that of the GalE-like L-ThrDH from the psychrophilic bacterium Flavobacterium frigidimaris KUC-1. The substrate binding model suggests that the reaction proceeds through abstraction of the β-hydroxyl hydrogen of L-threonine via direct proton transfer driven by Tyr(137). The factors contributing to the thermostability of T. volcanium L-ThrDH were analyzed by comparing its structure to that of F. frigidimaris L-ThrDH. This comparison showed that the presence of extensive inter- and intrasubunit ion pair networks are likely responsible for the thermostability of T. volcanium L-ThrDH. This is the first description of the molecular basis for the substrate recognition and thermostability of a GalE-like L-ThrDH.

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Organizational Affiliation: 

Department of Bioscience, School of Agriculture, Tokai University, Aso, Kumamoto, 869-1404, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NDP-sugar epimerase	A, B	317	Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)	Mutation(s): 0
Find proteins for Q97BK3 (Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)) Go to UniProtKB:  Q97BK3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PYR	A, B	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N
NAD	A, B	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MPD	A, B	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PYR	Ki: 23200000 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.209 
• R-Value Work: 0.203 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 149.803	α = 90.00
b = 45.988	β = 113.37
c = 89.778	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
HKL-2000	data collection
HKL-2000	data reduction
CNS	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-20 
• Released Date: 2010-07-28 
• Deposition Author(s): Yoneda, K., Sakuraba, H., Ohshima, T.

Revision History 

• Version 1.0: 2010-07-28
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2012-05-02
  Type: Database references