4YDR

Crystal structure of oxidized homoserine dehydrogenase of Sulfolobus tokodaii

• PDB DOI: https://doi.org/10.2210/pdb4YDR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-23 Released: 2015-11-11 
• Deposition Author(s): Goto, M., Yoshimune, K., Kaneko, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

Literature

Structural insight into activation of homoserine dehydrogenase from the archaeonSulfolobus tokodaiivia reduction.

Tomonaga, Y., Kaneko, R., Goto, M., Ohshima, T., Yoshimune, K.

(2015) Biochem Biophys Rep 3: 14-17

• PubMed: 29124164 
• DOI: https://doi.org/10.1016/j.bbrep.2015.07.006
• Primary Citation of Related Structures:  
  4YDR, 5AVO


• PubMed Abstract: 
  

  Homoserine dehydrogenase (HSD; 305 amino acid residues) catalyzes an NAD(P)-dependent reversible reaction between l-homoserine and aspartate 4-semialdehyde and is involved in the aspartate pathway. HSD from the hyperthermophilic archaeon Sulfolobus tokodaii was markedly activated (2.5-fold) by the addition of 0.8 mM dithiothreitol. The crystal structure of the homodimer indicated that the activation was caused by cleavage of the disulfide bond formed between two cysteine residues (C303) in the C-terminal regions of the two subunits.

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Organizational Affiliation: 

Department of Applied Molecular Chemistry, Graduate School of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba 275-8575, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.85 kDa 
• Atom Count: 4,979 
• Modelled Residue Count: 604 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine dehydrogenase	A, B	304	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: hom, STK_15190 EC: 1.1.1.3
UniProt
Find proteins for F9VNG5 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore F9VNG5  Go to UniProtKB:  F9VNG5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.818	α = 90
b = 78.909	β = 105.79
c = 65.814	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Goto, M., Yoshimune, K., Kaneko, R.

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary