PDBsum entry 1wrn

RNA binding protein

PDB id: 1wrn

Contents

Protein chains

146 a.a. *

Ligands

HIS ×3

PEG ×6

Metals

_MN ×3

Waters ×367

* Residue conservation analysis

PDB id:

1wrn

Name:

RNA binding protein

Title:

Metal ion dependency of the antiterminator protein, hutp, for binding to the terminator region of hut mRNA- a structural basis

Structure:

Hut operon positive regulatory protein. Chain: a, b, c. Synonym: hutp. Engineered: yes. Mutation: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.30Å R-factor: 0.254 R-free: 0.305

Authors:

T.Kumarevel,H.Mizuno,P.K.R.Kumar

Key ref:

T.Kumarevel et al. (2005). Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis. Nucleic Acids Res, 33, 5494-5502. PubMed id: 16192572

Date:

25-Oct-04 Release date: 30-Aug-05

Protein chains

P10943  (HUTP_BACSU) -  Hut operon positive regulatory protein from Bacillus subtilis (strain 168)

Seq: 148 a.a.

Struc: 146 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

Nucleic Acids Res 33:5494-5502 (2005)

PubMed id: 16192572

Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis.

T.Kumarevel, H.Mizuno, P.K.Kumar.

ABSTRACT

HutP is an RNA-binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis, by binding to cis-acting regulatory sequences on hut mRNA. It requires L-histidine and an Mg2+ ion for binding to the specific sequence within the hut mRNA. In the present study, we show that several divalent cations can mediate the HutP-RNA interactions. The best divalent cations were Mn2+, Zn2+ and Cd2+, followed by Mg2+, Co2+ and Ni2+, while Cu2+, Yb2+ and Hg2+ were ineffective. In the HutP-RNA interactions, divalent cations cannot be replaced by monovalent cations, suggesting that a divalent metal ion is required for mediating the protein-RNA interactions. To clarify their importance, we have crystallized HutP in the presence of three different metal ions (Mg2+, Mn2+ and Ba2+), which revealed the importance of the metal ion binding site. Furthermore, these analyses clearly demonstrated how the metal ions cause the structural rearrangements that are required for the hut mRNA recognition.

Selected figure(s)

Figure 5.
Divalent metal ion coordinations in the complex structures. (A) A close up stereo view of the Ba^2+ ion binding site in the HutP-L-histidine-Ba^2+ complex. Hydrogen bonds are indicated by broken lines. The L-histidine ligand and the protein residues are represented by ball-and-stick models colored by atom type, as shown in Figure 4c. The Ba^2+ and water molecules are represented by cpk models in magenta and red, respectively. The electron density around the metal ion was contoured at 3 {sigma} level. (B) A close-up stereo view of the non-specific Ba^2+ ion binding site and its interactions. The electron density around the metal ions was contoured at 3 {sigma} level. Hydrogen bonds and the color scheme are described in Figure 5a.

Figure 6.
Divalent metal ion coordination distance comparison for different metal ions observed in the complex structures. A schematic hexa-coordination of the metal ions, drawn and numbered as in Figure 5a. The metal ion binding sites observed in the asymmetric unit were averaged individually and are depicted in the figures.

The above figures are reprinted from an Open Access publication published by Oxford University Press: Nucleic Acids Res (2005, 33, 5494-5502) copyright 2005.

Figures were selected by an automated process.