PDBsum entry 1z3e

Transcription

PDB id: 1z3e

Contents

Protein chains

119 a.a. *

67 a.a. *

Ligands

SO4 ×4

Waters ×143

* Residue conservation analysis

PDB id:

1z3e

Name:

Transcription

Title:

Crystal structure of spx in complex with thE C-terminal domain of the RNA polymerase alpha subunit

Structure:

Regulatory protein spx. Chain: a. Fragment: transcription regulator. Engineered: yes. DNA-directed RNA polymerase alpha chain. Chain: b. Fragment: c-terminal domain of RNA polymerase alpha subunit. Synonym: rnap alpha subunit, transcriptase alpha chain, RNA polymerase alpha subunit.

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: spxa. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: rpoa.

Resolution:

1.50Å R-factor: 0.196 R-free: 0.220

Authors:

K.J.Newberry,S.Nakano,P.Zuber,R.G.Brennan

Key ref:

K.J.Newberry et al. (2005). Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the alpha C-terminal domain of RNA polymerase. Proc Natl Acad Sci U S A, 102, 15839-15844. PubMed id: 16249335 DOI: 10.1073/pnas.0506592102

Date:

11-Mar-05 Release date: 11-Oct-05

Protein chain

O31602  (SPX_BACSU) -  Global transcriptional regulator Spx from Bacillus subtilis (strain 168)

Seq: 131 a.a.

Struc: 119 a.a.

Protein chain

P20429  (RPOA_BACSU) -  DNA-directed RNA polymerase subunit alpha from Bacillus subtilis (strain 168)

Seq: 314 a.a.

Struc: 67 a.a.

Enzyme reactions

• Enzyme class: Chain B: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1073/pnas.0506592102

Proc Natl Acad Sci U S A 102:15839-15844 (2005)

PubMed id: 16249335

Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the alpha C-terminal domain of RNA polymerase.

K.J.Newberry, S.Nakano, P.Zuber, R.G.Brennan.

ABSTRACT

Spx, a global transcription regulator in Bacillus subtilis, interacts with the C-terminal domain of the alpha subunit (alphaCTD) of RNA polymerase to control gene expression under conditions of disulfide stress, which is sensed by disulfide bond formation between Spx residues C10 and C13. Here, we describe the crystal structure of the B. subtilis alphaCTD bound to oxidized Spx. Analysis of the complex reveals interactions between three regions of "anti-alpha" Spx and helix alpha1 and the "261" determinant of alphaCTD. The former contact could disrupt the interaction between alphaCTD and activator proteins or alter the DNA-bound conformation of alphaCTD, thereby repressing activator-stimulated transcription. Binding to the 261 determinant would prevent interaction between alphaCTD and region 4 of sigma(A). Intriguingly, the Spx disulfide bond is far from the alphaCTD-Spx interface, suggesting that Spx regulates transcription allosterically or through the redox-dependent creation or destruction of binding sites for additional components of the transcription machinery.

Selected figure(s)

Figure 2.
Fig. 2. Disulfide bridge and sulfate binding sites of oxidized Spx. (A) The disulfide bridge is shown as yellow sticks. The sulfate, which is found in both Spx and ArsC, and may be involved in transcription regulation by Spx, is bound by the guanidinium moiety of residue R92 and the main chain carbonyl oxygen of S12. A second sulfate ion, which is found only in the Spx- CTD structure, is shown to the left of R92. Interactions between the sulfates and protein are depicted by dashed line. (B) A representative 2F[o] - F[c] simulated annealing composite omit map contoured at 1 shows the electron density for the disulfide bridge of Spx.

Figure 3.
Fig. 3. The Spx- CTD heterodimer interface. (A and B) Hydrogen bonding interactions at the dimer interface. The backbones of Spx and CTD are colored pink and green, respectively. Interacting residues are depicted as sticks and are colored according to atom type. Hydrogen bonds are depicted as dashes. (C) Interactions of cxs mutants of CTD (V260 and Y263) and Spx (G52). These residues cluster and are shown as blue sticks.

Figures were selected by an automated process.