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J Mol Biol. 2014 Apr 3;426(7):1539-53. doi: 10.1016/j.jmb.2013.12.026. Epub 2013 Dec 31.

The NreA protein functions as a nitrate receptor in the staphylococcal nitrate regulation system.

Author information

  • 1Interfaculty Institute of Biochemistry, Universität Tübingen, Hoppe-Seyler-Strasse 4, D-72076 Tübingen, Germany.
  • 2Institute for Microbiology and Wine Research, Universität Mainz, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany.
  • 3Max Planck Institute for Developmental Biology, Spemannstrasse 35, D-72076 Tübingen, Germany.
  • 4Interfaculty Institute of Microbiology and Infection Medicine, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany.
  • 5Institute for Microbiology and Wine Research, Universität Mainz, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany. Electronic address: unden@uni-mainz.de.
  • 6Interfaculty Institute of Biochemistry, Universität Tübingen, Hoppe-Seyler-Strasse 4, D-72076 Tübingen, Germany; Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. Electronic address: thilo.stehle@uni-tuebingen.de.

Abstract

Staphylococci are able to use nitrate as an alternative electron acceptor during anaerobic respiration. The regulation of energy metabolism is dependent on the presence of oxygen and nitrate. Under anaerobic conditions, staphylococci employ the nitrate regulatory element (Nre) for transcriptional activation of genes involved in reduction and transport of nitrate and nitrite. Of the three proteins that constitute the Nre system, NreB has been characterized as an oxygen sensor kinase and NreC has been characterized as its cognate response regulator. Here, we present structural and functional data that establish NreA as a new type of nitrate receptor. The structure of NreA with bound nitrate was solved at 2.35Å resolution, revealing a GAF domain fold. Isothermal titration calorimetry experiments showed that NreA binds nitrate with low micromolar affinity (KD=22μM). Two crystal forms for NreA were obtained, with either bound nitrate or iodide. While the binding site is hydrophobic, two helix dipoles and polar interactions contribute to specific binding of the ions. The expression of nitrate reductase (NarGHI) was examined using a narG-lip (lipase) reporter gene assay in vivo. Expression was regulated by the presence of NreA and nitrate. Structure-guided mutations of NreA reduced its nitrate binding affinity and also affected the gene expression, thus providing support for the function of NreA as a nitrate receptor.

KEYWORDS:

GAF domain; Staphylococcus; X-ray structure; anaerobic respiration; nitrate binding

PMID:
24389349
DOI:
10.1016/j.jmb.2013.12.026
[PubMed - indexed for MEDLINE]
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