PDBsum entry 2fcj

Structural genomics, unknown function

PDB id: 2fcj

Contents

Protein chains

114 a.a. *

Ligands

GOL ×2

SO4 ×2

MES

Waters ×393

* Residue conservation analysis

PDB id:

2fcj

Name:

Structural genomics, unknown function

Title:

Structure of small toprim domain protein from bacillus stearothermophilus.

Structure:

Small toprim domain protein. Chain: a, b, c. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: rbstp2199. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.30Å R-factor: 0.192 R-free: 0.214

Authors:

P.Rezacova,Y.Chen,D.Borek,F.Collart,A.Joachimiak,Z.Otwinowski,Midwest Center For Structural Genomics (Mcsg)

Key ref:

P.Rezácová et al. (2008). Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilus. Proteins, 70, 311-319. PubMed id: 17705269 DOI: 10.1002/prot.21511

Date:

12-Dec-05 Release date: 24-Jan-06

Protein chains

Q5KVJ9  (Q5KVJ9_GEOKA) -  Hypothetical conserved protein from Geobacillus kaustophilus (strain HTA426)

Seq: 119 a.a.

Struc: 114 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1002/prot.21511

Proteins 70:311-319 (2008)

PubMed id: 17705269

Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilus.

P.Rezácová, D.Borek, S.F.Moy, A.Joachimiak, Z.Otwinowski.

ABSTRACT

The crystal structure of the Midwest Center for Structural Genomics target APC35832, a 14.7-kDa cytosolic protein from Bacillus stearothermophilus, has been determined at 1.3 A resolution by the single anomalous diffraction method from a mercury soaked crystal. The APC35832 protein is a representative of large group of bacterial and archeal proteins entirely consisting of the Toprim (topoisomerase-primase) domain. This domain is found in the catalytic centers of many enzymes catalyzing phosphodiester bond formation or cleavage, but the function of small Toprim domain proteins remains unknown. Consistent with the sequence analysis, the APC35832 structure shows a conserved Toprim fold, with a central 4-stranded parallel beta-sheet surrounded by four alpha-helixes. Comparison of the APC35832 structure with its closest structural homolog, the catalytic core of bacteriophage T7 primase, revealed structural conservation of a metal binding site and isothermal titration calorimetry indicates that APC35832 binds Mg2+ with a sub-millimolar dissociation constant (K(d)). The APC35832-Mg2+ complex structure was determined at 1.65 A and reveals the role of conserved acidic residues in Mg2+ ion coordination. The structural similarities to other Toprim domain containing proteins and potential function and substrates of APC35832 are discussed in this article.

Selected figure(s)

Figure 2.
Figure 2. A: A stereo diagram showing the overall APC35832 structure. B: Superimposition of APC35832 and the Toprim domain of T7 DNA primase (PDB entry 1NUI), showing conserved acidic residue positions. APC35832 is colored pink, 1NUI is blue and conserved acidic residues are highlighted in green and yellow. C: The solvent-accessible surface colored according to electrostatic potential (blue positive, red negative, calculated with DS ViewerPro 6.0 [Accelerys Software]). The acidic surface pocket is visible, with the MES molecule shown as sticks.

Figure 4.
Figure 4. A: Detail of octahedral coordination of Mg^2+ ion with 2F[o]-F[c] electron density map contoured at the 1.3 level of the map. B: Schematic of Mg^2+ ion binding by APC35832. Mg^2+ is shown as a yellow sphere, water molecules are represented with turquoise spheres, ion coordination is shown by violet lines, and hydrogen bonds as green dotted lines with their length in Å. Figure was prepared using the program Ligplot.[20] C: A stereo view of the superimposed Mg^2+ binding sites in APC35832 (pink) and T7 primase, PDB entry 1NUI (blue), Mg^2+ ions are colored accordingly. Residues numbers are for the APC35832 protein.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 70, 311-319) copyright 2008.

Figures were selected by an automated process.