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Escherichia coli K-12 substr. MG1655 Protein: Zur-Zn2+ DNA-binding transcriptional repressor



Gene: zur Accession Numbers: EG11929 (EcoCyc), b4046, ECK4038

Synonyms: yjbK, znuR

Regulation Summary Diagram: ?

Subunit composition of Zur-Zn2+ DNA-binding transcriptional repressor = [(Zur)2][Zn2+]4
         Zur transcriptional repressor = (Zur)2

Summary:
Zur, "zinc uptake regulator," regulates genes involved in the Zn2+ ABC transporter uptake system and genes involved in the expression of alternative ribosomal proteins [Patzer98, Patzer00, Panina03].

The active conformation of Zur is observed when it is in a reduced form and when it is bound to Zn(II). The oxidized form of Zur does not bind to DNA or zinc. [Patzer98, Patzer00, Hantke02]. Zur is not autoregulated [Hantke02].

Zur, which belongs to the Fur family [Patzer98], appears to have a DNA-binding site in the N-terminal domain, around residue 65, and a signal-recognition site in the C-terminal domain. This protein has two Zn(II)-binding sites: site A, which only binds to Zn(II), and site B (the sensor site), which binds to Zn(II) and Co(II) with high and low affinities, respectively [Outten01]. Zur is able to form dimers, even in the absence of zinc [Patzer00].

The 23-bp palindrome consensus sequence for Zur-binding sites of gamma-proteobacteria, including Escherichia coli, has been determined by computational analysis [Panina03].

Map Position: [4,257,511 <- 4,258,026] (91.76 centisomes)
Length: 516 bp / 171 aa

Unification Links: ASAP:ABE-0013249 , EchoBASE:EB1873 , EcoGene:EG11929 , OU-Microarray:b4046 , PortEco:zur , RegulonDB:EG11929

In Paralogous Gene Group: 178 (2 members)

In Reactions of unknown directionality:

Not in pathways:
Zur + Zn2+ = Zur transcriptional repressor

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0071580 - regulation of zinc ion transmembrane transport Inferred from experiment [Patzer98]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment [Patzer00]
GO:0044212 - transcription regulatory region DNA binding Inferred from experiment [Patzer00]

MultiFun Terms: information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation DNA structure level
regulation type of regulation transcriptional level repressor

DNA binding site length: 23 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: GaaaTGTtAtAatATAACAtttC

Regulated Transcription Units (4 total): ?

Notes:

Credits:
Last-Curated ? 25-Mar-2008 by Gama-Castro S , UNAM


Subunit of Zur-Zn2+ DNA-binding transcriptional repressor: Zur transcriptional repressor

Synonyms: yjbK, znuR

Gene: zur Accession Numbers: EG11929 (EcoCyc), b4046, ECK4038

Locations: cytosol

Subunit composition of Zur transcriptional repressor = [Zur]2

Map Position: [4,257,511 <- 4,258,026] (91.76 centisomes)
Length: 516 bp / 171 aa

Molecular Weight of Polypeptide: 19.254 kD (from nucleotide sequence), 19 kD (experimental) [Patzer00 ]

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Patzer00]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation DNA structure level
regulation type of regulation transcriptional level repressor

Unification Links: EcoliWiki:b4046 , ModBase:P0AC51 , PR:PRO_000024259 , Protein Model Portal:P0AC51 , RefSeq:NP_418470 , SMR:P0AC51 , String:511145.b4046 , UniProt:P0AC51

Relationship Links: InterPro:IN-FAMILY:IPR002481 , InterPro:IN-FAMILY:IPR011991 , Pfam:IN-FAMILY:PF01475

In Reactions of unknown directionality:

Not in pathways:
Zur + Zn2+ = Zur transcriptional repressor

Citations: [Hantke02, Panina03, Hantke01, Outten01]

Essentiality data for zur knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b4046 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11929; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Hantke01: Hantke K (2001). "Bacterial zinc transporters and regulators." Biometals 14(3-4);239-49. PMID: 11831459

Hantke02: Hantke K (2002). "Members of the Fur protein family regulate iron and zinc transport in E. coli and characteristics of the Fur-regulated fhuF protein." J Mol Microbiol Biotechnol 2002;4(3);217-22. PMID: 11931550

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Outten01: Outten CE, Tobin DA, Penner-Hahn JE, O'Halloran TV (2001). "Characterization of the metal receptor sites in Escherichia coli Zur, an ultrasensitive zinc(II) metalloregulatory protein." Biochemistry 40(35);10417-23. PMID: 11523983

Panina03: Panina EM, Mironov AA, Gelfand MS (2003). "Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins." Proc Natl Acad Sci U S A 100(17);9912-7. PMID: 12904577

Patzer00: 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. PMID: 10816566

Patzer98: Patzer SI, Hantke K (1998). "The ZnuABC high-affinity zinc uptake system and its regulator Zur in Escherichia coli." Mol Microbiol 1998;28(6);1199-210. PMID: 9680209

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 26, 2014, BIOCYC13A.