6QRQ

Apo conformation of chemotaxis sensor ODP

  • Classification: SIGNALING PROTEIN
  • Organism(s): Thermotoga maritima
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2019-02-19 Released: 2019-06-19 
  • Deposition Author(s): Muok, A.R., Crane, B.R.
  • Funding Organization(s): National Institutes of Health/Office of the Director, National Institutes of Health/National Institute of General Medical Sciences, National Science Foundation (United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A di-iron protein recruited as an Fe[II] and oxygen sensor for bacterial chemotaxis functions by stabilizing an iron-peroxy species.

Muok, A.R.Deng, Y.Gumerov, V.M.Chong, J.E.DeRosa, J.R.Kurniyati, K.Coleman, R.E.Lancaster, K.M.Li, C.Zhulin, I.B.Crane, B.R.

(2019) Proc Natl Acad Sci U S A 116: 14955-14960

  • DOI: 10.1073/pnas.1904234116
  • Primary Citation of Related Structures:  
    6QNM, 6QRQ, 6QWO, 6R9N

  • PubMed Abstract: 
  • Many bacteria contain cytoplasmic chemoreceptors that lack sensor domains. Here, we demonstrate that such cytoplasmic receptors found in 8 different bacterial and archaeal phyla genetically couple to metalloproteins related to β-lactamases and nitric oxide reductases ...

    Many bacteria contain cytoplasmic chemoreceptors that lack sensor domains. Here, we demonstrate that such cytoplasmic receptors found in 8 different bacterial and archaeal phyla genetically couple to metalloproteins related to β-lactamases and nitric oxide reductases. We show that this oxygen-binding di-iron protein (ODP) acts as a sensor for chemotactic responses to both iron and oxygen in the human pathogen Treponema denticola ( Td ). The ODP di-iron site binds oxygen at high affinity to reversibly form an unusually stable μ-peroxo adduct. Crystal structures of ODP from Td and the thermophile Thermotoga maritima ( Tm ) in the Fe[III] 2 -O 2 2- , Zn[II], and apo states display differences in subunit association, conformation, and metal coordination that indicate potential mechanisms for sensing. In reconstituted systems, iron-peroxo ODP destabilizes the phosphorylated form of the receptor-coupled histidine kinase CheA, thereby providing a biochemical link between oxygen sensing and chemotaxis in diverse prokaryotes, including anaerobes of ancient origin.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; bc69@cornell.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxygen-binding diiron proteinB [auth A], A [auth B], C, D253Thermotoga maritimaMutation(s): 0 
Gene Names: Tmari_0010
UniProt
Find proteins for Q9S5W7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9S5W7 
Go to UniProtKB:  Q9S5W7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.65α = 90
b = 110.725β = 90
c = 110.964γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesR35GM122535
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP30 GM124165
National Institutes of Health/National Institute of General Medical SciencesUnited StatesS10 RR029205
National Science Foundation (United States)United States2014155468

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-31
    Changes: Data collection, Database references