PDBsum entry 1t9h

Hydrolase

PDB id: 1t9h

Contents

Protein chain

287 a.a. *

Ligands

IUM ×8

ACT ×3

Metals

_ZN

_CA ×4

Waters ×303

* Residue conservation analysis

PDB id:

1t9h

Name:

Hydrolase

Title:

The crystal structure of yloq, a circularly permuted gtpase.

Structure:

Probable gtpase engc. Chain: a. Synonym: yloq. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: engc, bsu15780. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.60Å R-factor: 0.146 R-free: 0.178

Authors:

V.M.Levdikov,E.V.Blagova,J.A.Brannigan,L.Cladiere,A.A.Antson, M.N.Isupov,S.J.Seror,A.J.Wilkinson

Key ref:

V.M.Levdikov et al. (2004). The crystal structure of YloQ, a circularly permuted GTPase essential for Bacillus subtilis viability. J Mol Biol, 340, 767-782. PubMed id: 15223319 DOI: 10.1016/j.jmb.2004.05.029

Date:

17-May-04 Release date: 02-Nov-04

Protein chain

O34530  (RSGA_BACSU) -  Small ribosomal subunit biogenesis GTPase RsgA from Bacillus subtilis (strain 168)

Seq: 298 a.a.

Struc: 287 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.1.- - ?????

DOI no: 10.1016/j.jmb.2004.05.029

J Mol Biol 340:767-782 (2004)

PubMed id: 15223319

The crystal structure of YloQ, a circularly permuted GTPase essential for Bacillus subtilis viability.

V.M.Levdikov, E.V.Blagova, J.A.Brannigan, L.Cladière, A.A.Antson, M.N.Isupov, S.J.Séror, A.J.Wilkinson.

ABSTRACT

yloQ is one of 11 essential genes in Bacillus subtilis with unknown roles in the physiology of the cell. It encodes a polypeptide of 298 residues with motifs characteristic of GTPases. As a contribution to elucidating its indispensable cellular function, we have solved the crystal structure of YloQ to 1.6 A spacing, revealing a three-domain organisation. At the heart of the molecule is the putative GTPase domain, which exhibits a classical alpha/beta nucleotide-binding fold with a topology very similar to that of Ras and Era. However, as anticipated from the order in which the conserved G protein motifs appear in the sequence, the GTPase domain fold in YloQ is circularly permuted with respect to the classical GTPases. The nucleotide-binding pocket in YloQ is unoccupied, and analysis of the phosphate-binding (P) loop indicates that conformational changes in this region would be needed to accommodate GTP. The GTPase domain is flanked at its N terminus by a beta-barrel domain with an oligonucleotide/oligosaccharide-binding (OB) fold, and at its C terminus by an alpha-helical domain containing a coordinated zinc ion. This combination of protein modules is unique to YloQ and its orthologues. Sequence comparisons reveal a clustering of conserved basic and aromatic residues on one face of the OB domain, perhaps pointing to a role for YloQ in nucleic acid binding. The zinc ion in the alpha-helical domain is coordinated by three cysteine residues and a histidine residue in a novel ligand organisation. The juxtaposition of the switch I and switch II regions of the G domain and the OB and zinc-binding domains suggests that chemical events at the GTPase active site may be transduced into relative movements of these domains. The pattern of conserved residues and electrostatic surface potential calculations suggest that the OB and/or Zn-binding domains participate in nucleic acid binding consistent with a possible role for YloQ at some stage during mRNA translation.

Selected figure(s)

Figure 4.
Figure 4. Ribbon tracing of the GTPase domain of YloQ (A) and Era (B). The ribbons are colour-ramped from the N terminus (blue) to the C terminus (red). The secondary structure elements are labelled. In YloQ, the break in the ribbon connecting a4 to b12 is caused by residues 187-205 being disordered and absent from the model. Topology diagrams of YloQ (C) and Era (D) illustrating the circular permutation of the GTPase domain.

Figure 5.
Figure 5. Superimposition of the GTPase domains of YloQ and the Ras-GDPNP complex (PDB accession, 1LF0) as a stereo view. The ribbon tracing of YloQ is presented in cyan, that for Ras is in yellow. The guanine nucleotide bound in Ras is displayed in ball-and-stick format in magenta. The broken line indicates the disordered region in the YloQ molecule. The G1 (P-loop), G2 (Switch I), G3 (Switch II) and G4 (guanine specificity motif) segments of YloQ are coloured red. The structures were overlapped initially in the program MOLREP,[35.] and subsequently adjusted manually to emphasise similarities and differences in the P-loop region.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 340, 767-782) copyright 2004.

Figures were selected by an automated process.