Bacterial gene regulators with transition metal cofactors

 

Criteria for inclusion in this database:

 

Cases where a metal ion functions exclusively as an inducer or co-repressor (for example nickel binding to NikR) are excluded

 

Only proteins that regulate gene expression are included.  So, proteins that are components of other types of signaling pathway (for example chemotaxis or dcGMP signaling) are, for the time being, excluded

 

Gene regulation can be either direct (by DNA binding proteins) or indirect (by histidine kinases, proteins that interact with histidine kinases, anti-repressors and anti-sigma factors)

 

Some biochemical or physiological support for the presence of a metal cofactor is required, so there are no inferences based solely on sequence information

 

Abbreviations.  HK: histidine kinase; R-HK: regulator of a histidine kinase; AR: anti-repressor; AS: anti-sigma factor

 

Acknowledgements: I am grateful to Mark Buttner, Chris den Hengst, Ray Dixon and Matt Hutchings for helping to ensure the completeness of this database.  Any errors or omissions remain the responsibility of the author.  If you have additions or corrections to make please e-mail me.  Support of the NSF (award MCB-0702858) is gratefully acknowledged.

 

© Stephen Spiro, 2010

 

 

Protein

Cofactor

Primary Signal

Secondary signals

Comments

References

Links

FNR

[4Fe-4S]

Oxygen

NO

 

Khoroshilova et al. (1995)

Cruz-Ramos et al. (2002)

Uniprot

NreB (HK)

[4Fe-4S]

Oxygen

 

 

Kamps et al. (2004)

Uniprot

ArnR

[Fe-S]

Oxygen

 

 

Nishimura et al. (2008)

 

IscR

[2Fe-2S]

Iron depletion?

Oxygen, NO, hydrogen peroxide

 

Zheng et al. (2001)

Schwartz et al. (2001)

Outten et al. (2004)

Giel et al. (2006)

Hyduke et al. (2007)

Uniprot

Pfam

SoxR

[2Fe-2S]

Superoxide or guanine radicals?

NO, singlet oxygen, hydrogen peroxide

 

Hidalgo & Demple (1994)

Ding & Demple (2000)

Agnez-Lima et al. (2001)

Zheng et al. (2001)

Lee et al. (2009)

Uniprot

PDB

PDB

NsrR

[Fe-S]

NO

 

 

Bodenmiller & Spiro (2006)

Nakano et al. (2006)

Uniprot

Pfam

SufR

[4Fe-4S]

?

 

 

Shen at al. (2007)

Uniprot

PqrR

[Fe-S]

Superoxide

 

 

Rungrassamee et al. (2009)

 

RsmA (AS)

[2Fe-2S]

?

 

 

Gaskell et al. (2007)

 

FixL (HK)

Heme

Oxygen

 

 

Gilles-Gonzalez et al. (1991)

Rodgers & Lukat-Rodgers (2005)

Uniprot

AppA (AR)

Heme

Oxygen

 

 

Moskvin et al. (2007)

Uniprot

DosS/DosT (HK)

Heme

Oxygen

 

NO binds to DosS/DosT, preventing oxygen from binding and so mimicking anoxia

Sousa et al. (2007)

Kumar et al. (2007)

Uniprot

CooA

Heme

CO

 

 

Lanzilotta et al. (2000)

Roberts et al. (2005)

Borjigin et al. (2007)

Uniprot

RcoM

Heme

CO

NO?

 

Kerby et al. (2008)

 

DNR

Heme

NO

 

 

Giardina et al. (2008)

Uniprot

H-NOX (R-HK)

Heme

Oxygen and NO

 

The H-NOX family contains some members that bind oxygen and some that bind NO

Boon & Marletta (2005)

Boon et al. (2006)

Price et al. (2007)

 

PerR

(CatR)

Iron, zinc

Peroxide

NO

PerR contains a structural zinc, and a second site that can be occupied by Fe or Mn.  The Fe protein is a peroxide sensor, the zinc site is sensitive to severe oxidative stress

Lee & Helmann (2006a)

Lee & Helmann (2006b)

Uniprot

PDB

Fur

Iron, zinc

Iron

NO, peroxide

Fur is an iron sensor; Fe functions both as a co-repressor and as a cofactor that can be modified by NO.  A structural zinc site is sensitive to severe oxidative stress

D’Autreaux et al. (2002)

Mukhopadhyay et al. (2004)

D’Autreaux et al. (2007)

 

Uniprot

PDB

NorR

Iron

NO

 

 

D’Autreaux et al. (2005)

Klink et al. (2007)

Tucker et al. (2008)

Uniprot

ChrR (AS)

Zinc

Singlet oxygen

 

 

Anthony et al. (2005)

Campbell et al. (2007)

Uniprot

PDB

NmlR

Zinc

NO/nitrosative stress

 

Zinc is required for NmlR activity in vivo; zinc binding to the protein has not been shown directly

Kidd et al. (2005)

 

RsrA (AS)

Zinc

Thiol oxidation

 

 

Li et al. (2003)

Zdanowski et al. (2006)

Uniprot

Ada

Zinc

Thiol methylation

 

 

He et al. (2005)

Uniprot

NrdR

Zinc

ATP/dATP

 

Zinc site is structural

Grinberg et al. (2006)

 

HoxBC (R-HK)

Nickel, iron

Hydrogen

 

 

Gebler et al. (2007)

Uniprot