PDBsum entry: 1rtw

Structural genomics, unknown function

PDB id: 1rtw

Contents

Protein chains

206 a.a. *

Ligands

MP5

PO4 ×3

Waters ×234

* Residue conservation analysis

PDB id:

1rtw

Name:

Structural genomics, unknown function

Title:

X-ray structure of pf1337, a tena homologue from pyrococcus northeast structural genomics research consortium (nesg) ta

Structure:

Transcriptional activator, putative. Chain: a, b, c, d. Engineered: yes

Source:

Pyrococcus furiosus. Organism_taxid: 186497. Strain: dsm 3638. Expressed in: escherichia coli. Expression_system_taxid: 562. Plasmid pmgk.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.35Å R-factor: 0.240 R-free: 0.281

Authors:

J.Benach,W.C.Edstrom,I.Lee,X.Rong,T.B.Acton,G.T.Montelione,J Northeast Structural Genomics Consortium (Nesg)

Key ref:

J.Benach et al. (2005). The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism. Acta Crystallogr D Biol Crystallogr, 61, 589-598. PubMed id: 15858269 DOI: 10.1107/S0907444905005147

Date:

10-Dec-03 Release date: 13-Jan-04

Protein chains

Q8U189  (Q8U189_PYRFU) -  Transcriptional activator, putative

Seq: 212 a.a.

Struc: 206 a.a.

DOI no: 10.1107/S0907444905005147

Acta Crystallogr D Biol Crystallogr 61:589-598 (2005)

PubMed id: 15858269

The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism.

J.Benach, W.C.Edstrom, I.Lee, K.Das, B.Cooper, R.Xiao, J.Liu, B.Rost, T.B.Acton, G.T.Montelione, J.F.Hunt.

ABSTRACT

TenA (transcriptional enhancer A) has been proposed to function as a transcriptional regulator based on observed changes in gene-expression patterns when overexpressed in Bacillus subtilis. However, studies of the distribution of proteins involved in thiamine biosynthesis in different fully sequenced genomes have suggested that TenA may be an enzyme involved in thiamine biosynthesis, with a function related to that of the ThiC protein. The crystal structure of PF1337, the TenA homolog from Pyrococcus furiosus, is presented here. The protomer comprises a bundle of alpha-helices with a similar tertiary structure and topology to that of human heme oxygenase-1, even though there is no significant sequence homology. A solvent-sequestered cavity lined by phylogenetically conserved residues is found at the core of this bundle in PF1337 and this cavity is observed to contain electron density for 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate, the product of the ThiC enzyme. In contrast, the modestly acidic surface of PF1337 shows minimal levels of sequence conservation and a dearth of the basic residues that are typically involved in DNA binding in transcription factors. Without significant conservation of its surface properties, TenA is unlikely to mediate functionally important protein-protein or protein-DNA interactions. Therefore, the crystal structure of PF1337 supports the hypothesis that TenA homologs have an indirect effect in altering gene-expression patterns and function instead as enzymes involved in thiamine metabolism.

Selected figure(s)

Figure 1.
Figure 1 Crystal structure of PF1337. (a) Stereo ribbon diagram (Carson, 1987 [Carson, M. (1987). J. Mol. Graph. 5, 103-106.]-[bluearr.gif] ) of PF1337 with a CPK representation of HMP-P (oxygen, red; nitrogen, blue; carbon, gray; phosphorus, green). (b) Topology diagram of PF1337. Red circles represent [alpha] -helices, oriented perpendicular to the plane of the page, with connections above the plane penetrating into the center of the circle and those below stopping at the boundary. (c) Stereo ribbon diagram of the PF1337 tetramer with CPK representations of HMP-P (magenta, subunit A) and inorganic phosphate (blue, subunits B-D). The different subunits are colored in cyan (A), red (B), yellow (C) and green (D).

Figure 5.
Figure 5 The putative active site and function of PF1337. (a) Stereo pair showing the environment of the crystallographically observed HMP-P molecule bound to PF1337. Residues within a 4 Å radius of HMP-P atoms are shown. The gray electron density is from an unbiased 2F[o] - F[c] map calculated prior to the inclusion of HMP-P in the refinement and contoured at 1 [sigma] . (b) Stereo pair of the electron density of an unbiased F[o] - F[c] map contoured at 1.8 [sigma] . (c) Schematic plot of the molecular interactions of the bound HMP-P. Distances are given in angstroms, and the values in parentheses represent the percentage identity among the TenA sequences in the COG in the case of protein residues or B factors in Å2 in the case of water molecules. The phosphate moiety of HMP-P is assumed to be in a protonated state, presumably reflecting a perturbation in its pK[a] caused by the chemical environment in the active site. (d) Reaction scheme for the biosynthesis of HMP-P from either HMP or AIR. TenA is hypothesized to catalyze a similar reaction to ThiC, consistent with the ability of the tenA gene to genetically complement a thiC deletion (Morett et al., 2003 [Morett, E., Korbel, J. O., Rajan, E., Saab-Rincon, G., Olvera, L., Olvera, M., Schmidt, S., Snel, B. & Bork, P. (2003). Nature Biotechnol. 21, 790-795.]-[bluearr.gif] ).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 589-598) copyright 2005.

Figures were selected by the author.