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.

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

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F9VNG5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]