PDBsum entry 3ec1

Hydrolase, signaling protein

PDB id: 3ec1

Contents

Protein chains

311 a.a. *

Ligands

GDP ×2

Waters ×335

* Residue conservation analysis

PDB id:

3ec1

Name:

Hydrolase, signaling protein

Title:

Structure of yqeh gtpase from geobacillus stearothermophilus (an atnos1 / atnoa1 ortholog)

Structure:

Gtp-binding protein yqeh required for biosis of 30s ribosome subunit. Chain: a, b. Synonym: ribosome biogenesis gtpase yqeh,yqeh gtpase. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: yqeh, b4114_2212, d9548_03520, tgs27_0162. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.36Å R-factor: 0.254 R-free: 0.287

Authors:

J.Sudhamsu,B.R.Crane

Key ref:

J.Sudhamsu et al. (2008). The structure of YqeH. An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition. J Biol Chem, 283, 32968-32976. PubMed id: 18801747 DOI: 10.1074/jbc.M804837200

Date:

28-Aug-08 Release date: 21-Oct-08

Protein chains

D0VWU7  (D0VWU7_GEOSE) -  Ribosome biogenesis GTPase YqeH from Geobacillus stearothermophilus

Seq: 369 a.a.

Struc: 311 a.a.

DOI no: 10.1074/jbc.M804837200

J Biol Chem 283:32968-32976 (2008)

PubMed id: 18801747

The structure of YqeH. An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition.

J.Sudhamsu, G.I.Lee, D.F.Klessig, B.R.Crane.

ABSTRACT

AtNOS1/AtNOA1 was identified as a nitric oxide-generating enzyme in plants, but that function has recently been questioned. To resolve issues surrounding AtNOA1 activity, we report the biochemical properties and a 2.36 A resolution crystal structure of a bacterial AtNOA1 ortholog (YqeH). Geobacillus YqeH fused to a putative AtNOA1 leader peptide complements growth and morphological defects of Atnoa1 mutant plants. YqeH does not synthesize nitric oxide from L-arginine but rather hydrolyzes GTP. The YqeH structure reveals a circularly permuted GTPase domain and an unusual C-terminal beta-domain. A small N-terminal domain, disordered in the structure, binds zinc. Structural homology among the C-terminal domain, the RNA-binding regulator TRAP, and the hypoxia factor pVHL define a recognition module for peptides and nucleic acids. TRAP residues important for RNA binding are conserved by the YqeH C-terminal domain, whose positioning is coupled to GTP hydrolysis. YqeH and AtNOA1 probably act as G-proteins that regulate nucleic acid recognition and not as nitric-oxide synthases.

Selected figure(s)

Figure 1.
Crystal structure of GsYqeH. A, the CPG domain (right) has a central seven-stranded β-sheet surrounded by α-helices and binds GDP, which is exposed to the solvent on one side. The C-terminal domain (left) has a 2-fold pseudosymmetric β-fold. B, alternate view of the C-terminal domain. The domain starts (bottom) with a 3[10]-helix (dark orange), followed by a coil (purple), α-helix (purple), five β-strands (blue), a 3[10]-helix (yellow), an α-helix (magenta), coil (magenta), and five β-strands (green).

Figure 4.
GTP hydrolysis may change orientation of C-terminal domain. Superpositions the CPG domains of GsYqeH (blue) and BsYlqF (pink) with the C-terminal domains of either BsYlqF (A) or GsYqeH (B) removed for clarity. Comparison of GTP-bound YlqF and GDP-bound YqeH indicates that GTP binding displaces the conserved Ile from the phosphate pocket and thereby reorients the C-terminal domain.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 32968-32976) copyright 2008.

Figures were selected by an automated process.