PDBsum entry: 1roz

Transferase

PDB id: 1roz

Contents

Protein chains

336 a.a. *

Ligands

NAD ×2

Waters ×423

* Residue conservation analysis

PDB id:

1roz

Name:

Transferase

Title:

Deoxyhypusine synthase holoenzyme in its low ionic strength, crystal form

Structure:

Deoxyhypusine synthase. Chain: a, b. Synonym: dhs. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: dhps, ds. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.21Å R-factor: 0.178 R-free: 0.200

Authors:

T.C.Umland,E.C.Wolff,M.-H.Park,D.R.Davies

Key ref:

T.C.Umland et al. (2004). A new crystal structure of deoxyhypusine synthase reveals the configuration of the active enzyme and of an enzyme.NAD.inhibitor ternary complex. J Biol Chem, 279, 28697-28705. PubMed id: 15100216 DOI: 10.1074/jbc.M404095200

Date:

02-Dec-03 Release date: 13-Jul-04

Protein chains

P49366  (DHYS_HUMAN) -  Deoxyhypusine synthase

Seq: 369 a.a.

Struc: 336 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.46 - Deoxyhypusine synthase.
• Pathway: EC 2.5.1.46
• Reaction: [eIF5A-precursor]-lysine + spermidine = [eIF5A-precursor]-deoxyhypusine + propane-1,3-diamine
• Cofactor: NAD(+)

NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytosol (1 term)
• Biological process: positive regulation of cell proliferation (7 terms)
• Biochemical function: protein binding (3 terms)

reference

DOI no: 10.1074/jbc.M404095200

J Biol Chem 279:28697-28705 (2004)

PubMed id: 15100216

A new crystal structure of deoxyhypusine synthase reveals the configuration of the active enzyme and of an enzyme.NAD.inhibitor ternary complex.

T.C.Umland, E.C.Wolff, M.H.Park, D.R.Davies.

ABSTRACT

Deoxyhypusine synthase catalyzes the first step in the two-step post-translational synthesis of hypusine, which is uniquely present in eukaryotic initiation factor 5A (eIF5A). Deoxyhypusine synthase and eIF5A are conserved throughout the eukaryotic kingdom, and both are essential for cell proliferation and survival. A previous study (Liao, D. I., Wolff, E. C., Park, M. H., and Davies, D. R. (1998) Structure 6, 23-32) of human deoxyhypusine synthase revealed four active sites of the homotetrameric enzyme located within deep tunnels. These Form I crystals were obtained under conditions of acidic pH and high ionic strength and likely contain an inactive enzyme. Each active-site entrance is blocked by a ball-and-chain motif composed of a region of extended structure capped by a two-turn alpha-helix. We report here at 2.2 A a new Form II crystal of the deoxyhypusine synthase:NAD holoenzyme grown at low ionic strength and pH 8.0, near the optimal pH for enzymatic activity. The ball-and-chain motif could not be detected in the electron density, suggesting that it swings freely and thus it no longer obstructs the active-site entrance. The deoxyhypusine synthase competitive inhibitor N(1)-guanyl-1,7-diaminoheptane (GC(7))is observed bound within the putative active site of the enzyme in the new crystal form (Form II) after exposure to the inhibitor. This first structure of a deoxyhypusine synthase.NAD.inhibitor ternary complex under physiological conditions now provides a structural context to discuss the results of previous biochemical investigations of the deoxyhypusine synthase reaction mechanism. This structure also provides a basis for the development of improved inhibitors and antiproliferative agents.

Selected figure(s)

Figure 1.
FIG. 1. Human DHS crystal structures. A, stereoview of the Form II DHS·NAD tetramer, with each monomer indicated by a different color and label, and NAD in red. The black diamonds indicate the general location of the active sites, and the blue spheres denote Ser28. B, the DHS Form I structure (this study), emphasizing the ball-and-chain motif obstructing an active-site entrance. C, the Rossmann fold of the DHS monomer is green, the mobile ball-and-chain is magenta, and the secondary structure labeling scheme is from Ref. 15.

Figure 4.
FIG. 4. Representations of the electrostatic surfaces surrounding an active-site tunnel entrance of the Form II human DHS crystal structure (A) and the homology model of HSS from a plant (S. vulgaris) (B). Positively and negatively charged regions are denoted as blue and red, respectively.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 28697-28705) copyright 2004.

Figures were selected by an automated process.