RegulonDB

TRANSCRIPTION FACTOR:

Name:

OxyR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

DNA-binding transcriptional dual regulator OxyR, MomR, Mor, bifunctional regulatory protein sensor for oxidative stress

Gene name(s):

oxyR

Functional conformation(s):

OxyR

Coregulator(s):

CRP, DksA, ExuR, FNR, Fis, Fur, H-NS, HypT, IHF, IscR, MarA, MetJ, MetR, MntR, NarL, NarP, NsrR, OxyR, PdhR, Rob, SoxS, UxuR, YdcI, Zur, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

Zur	Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional repressor Zur, YjbK, ZnuR

Gene name(s):

zur

Functional conformation(s):

Zur-Zn²⁺ , Zur

Coregulator(s):

Fur, OxyR, SoxS, Zur

Summary:

TF Summary ...[more]

REGULATION EXERTED BY OxyR,Zur

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
OxyR activator Zur repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
Zur-Zn²⁺	repressor	znuCp	znuC , znuB	1942613	1942636	-10.0	atgaatatgaGAAGTGTGATATTATAACATTTCAtgactactgc	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [2] [3]
Zur-Zn²⁺	repressor	znuAp	znuA	1942613	1942636	38.0	gcagtagtcaTGAAATGTTATAATATCACACTTCtcatattcat	[COMP-HINF-SIMILAR-TO-CONSENSUS] [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] [EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [2] [3] [4]
OxyR	activator	znuAp	znuA	1942598	1942614	55.5	atatcacactTCTCATATTCATTACGAttattggtcg	[COMP-HINF] [EXP-CHIP-EXO-MANUAL] [EXP-IEP-RNA-SEQ]	[5]
OxyR	activator	znuCp	znuC , znuB	1942598	1942614	-27.5	cgaccaataaTCGTAATGAATATGAGAagtgtgatat	[EXP-IEP-RNA-SEQ]	[5]

Evidence:

[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins
[COMP-HINF] Inferred by a human based on computational evidence
[EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion
[EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

Reference(s):

[1] Outten CE., et al., 2001
[2] Patzer SI., et al., 2000
[3] Patzer SI., et al., 1998
[4] Warner DM., et al., 2012
[5] Seo SW., et al., 2015

Reference(s)
[1] Outten CE., O'Halloran TV., 2001, Femtomolar sensitivity of metalloregulatory proteins controlling zinc homeostasis., Science 292(5526):2488-92
[2] Patzer SI., Hantke K., 2000, The zinc-responsive regulator Zur and its control of the znu gene cluster encoding the ZnuABC zinc uptake system in Escherichia coli., J Biol Chem 275(32):24321-32
[3] Patzer SI., Hantke K., 1998, The ZnuABC high-affinity zinc uptake system and its regulator Zur in Escherichia coli., Mol Microbiol 28(6):1199-210
[4] Warner DM., Levy SB., 2012, SoxS increases the expression of the zinc uptake system ZnuACB in an Escherichia coli murine pyelonephritis model., J Bacteriol 194(5):1177-85
[5] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99