Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Protein: NtrB sensory histidine kinase



Gene: glnL Accession Numbers: EG10387 (EcoCyc), b3869, ECK3862

Synonyms: glnR, ntrB, I, nitrogen regulator II, NRII

Regulation Summary Diagram: ?

Subunit composition of NtrB sensory histidine kinase = [GlnL]2
         NtrB = GlnL

Alternative forms of NtrB sensory histidine kinase: NtrB sensory histidine kinase - phosphorylated (summary available)

Summary:
NtrB (NRII), encoded by glnL, is a dual function cytoplasmic protein with both histidine kinase and phosphatase activity. Depending on nitrogen availability, NtrB can autophosphorylate and donate a phosphoryl group to its cognate response regulator, NtrC (NRI, product of glnG), or it may act as a phosphatase and catalyse the rapid dephosphorylation of NtrC-P [Ninfa86, Keener88]. The phosphatase and kinase activities of NtrB are regulated by the homologous signal proteins PII (GlnB) and PII2 (GlnK).

The NtrB protein consists of an N-terminal domain which contains a PAS motif and may be involved in binding regulatory ligands and intermolecular signal transduction, a central domain consisting of a four helix bundle (two helices contributed by each monomer) and a C-terminal domain which contains ATP and PII binding sites [Jiang00a, Pioszak00]. A crystal structure of the C-terminal ATP-binding domain of a mutant form of NtrB has been determined at 1.6 A resolution [Song04].

Citations: [Jiang99, Kramer99]

Gene Citations: [MirandaRios87, SasseDwight88, Magasanik, UenoNishio84, UenoNishio83]

Locations: inner membrane, cytosol

Map Position: [4,053,313 <- 4,054,362] (87.36 centisomes)
Length: 1050 bp / 349 aa

Molecular Weight of Polypeptide: 38.556 kD (from nucleotide sequence), 36.0 kD (experimental) [McFarland81 ]

Molecular Weight of Multimer: 68.0 kD (experimental) [Ninfa86a]

pI: 5.68

Unification Links: ASAP:ABE-0012634 , CGSC:701 , EchoBASE:EB0382 , EcoGene:EG10387 , EcoliWiki:b3869 , ModBase:P0AFB5 , OU-Microarray:b3869 , PortEco:glnL , PR:PRO_000022789 , Protein Model Portal:P0AFB5 , RefSeq:NP_418305 , RegulonDB:EG10387 , SMR:P0AFB5 , String:511145.b3869 , Swiss-Model:P0AFB5 , UniProt:P0AFB5

Relationship Links: InterPro:IN-FAMILY:IPR000014 , InterPro:IN-FAMILY:IPR003594 , InterPro:IN-FAMILY:IPR003661 , InterPro:IN-FAMILY:IPR004358 , InterPro:IN-FAMILY:IPR005467 , InterPro:IN-FAMILY:IPR009082 , InterPro:IN-FAMILY:IPR013767 , PDB:Structure:1R62 , Pfam:IN-FAMILY:PF00512 , Pfam:IN-FAMILY:PF00989 , Pfam:IN-FAMILY:PF02518 , Prints:IN-FAMILY:PR00344 , Prosite:IN-FAMILY:PS50109 , Prosite:IN-FAMILY:PS50112 , Smart:IN-FAMILY:SM00091 , Smart:IN-FAMILY:SM00387 , Smart:IN-FAMILY:SM00388

In Paralogous Gene Group: 122 (29 members)

Reactions known to consume the compound:

Nitrogen Regulation Two-Component System :
ATP + NtrB → ADP + NtrB-Phis

Reactions known to produce the compound:

Nitrogen Regulation Two-Component System :
NtrB-Phis + NtrC → NtrB + NtrC-Pasp

Reactions known to consume the compound:

NtrBC Two-Component Signal Transduction System, nitrogen-dependent :
ATP + NtrB sensory histidine kinase → ADP + NtrB-Phis

Reactions known to produce the compound:

NtrBC Two-Component Signal Transduction System, nitrogen-dependent :
NtrB-Phis + NtrC → NtrB sensory histidine kinase + NtrC-Pasp

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0000160 - phosphorelay signal transduction system Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Ninfa86]
GO:0016311 - dephosphorylation Inferred from experiment [Ninfa86]
GO:0023014 - signal transduction by phosphorylation Inferred by computational analysis Inferred from experiment [Ninfa86, GOA01a]
GO:0046777 - protein autophosphorylation Inferred from experiment [Ninfa93]
GO:0051171 - regulation of nitrogen compound metabolic process Inferred from experiment [McFarland81]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [GOA01a]
GO:0007165 - signal transduction Inferred by computational analysis [GOA01a]
GO:0009399 - nitrogen fixation Inferred by computational analysis [UniProtGOA11a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0018106 - peptidyl-histidine phosphorylation Inferred by computational analysis [GOA01]
Molecular Function: GO:0000155 - phosphorelay sensor kinase activity Inferred from experiment Inferred by computational analysis [GOA01a, Ninfa86]
GO:0004721 - phosphoprotein phosphatase activity Inferred from experiment [Ninfa86]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Burillo04, Salinas03]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Burillo04, Salinas03]
GO:0042803 - protein homodimerization activity Inferred from experiment [Ninfa86a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0004673 - protein histidine kinase activity Inferred by computational analysis [GOA01]
GO:0004871 - signal transducer activity Inferred by computational analysis [GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016772 - transferase activity, transferring phosphorus-containing groups Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005622 - intracellular Inferred from experiment [Ninfa86a]
GO:0005829 - cytosol
GO:0005886 - plasma membrane Inferred by computational analysis [DiazMejia09]
GO:0016020 - membrane Inferred by computational analysis [GOA01a]

MultiFun Terms: information transfer protein related posttranslational modification
metabolism biosynthesis of building blocks amino acids glutamine
regulation type of regulation posttranscriptional covalent modification, demodification, maturation
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)

Activates: NtrC-Pasp + H2O → NtrC + phosphate

Essentiality data for glnL knockouts: ?

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

Credits:
Last-Curated ? 21-Oct-2010 by Mackie A , Macquarie University


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 5 -> 78
[UniProt09]
UniProt: PAS;
Conserved-Region 136 -> 349
[UniProt09]
UniProt: Histidine kinase;
Phosphorylation-Modification 139
[Ninfa91, UniProt13]
UniProt: Phosphohistidine; by autocatalysis.
Amino-Acid-Sites-That-Bind 329
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
3/2/1998 (pkarp) Merged genes G256/b3869 and EG10387/glnL
10/20/97 Gene b3869 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10387; 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

Burillo04: Burillo S, Luque I, Fuentes I, Contreras A (2004). "Interactions between the nitrogen signal transduction protein PII and N-acetyl glutamate kinase in organisms that perform oxygenic photosynthesis." J Bacteriol 186(11);3346-54. PMID: 15150219

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

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Jiang00a: Jiang P, Atkinson MR, Srisawat C, Sun Q, Ninfa AJ (2000). "Functional dissection of the dimerization and enzymatic activities of Escherichia coli nitrogen regulator II and their regulation by the PII protein." Biochemistry 39(44);13433-49. PMID: 11063580

Jiang99: Jiang P, Ninfa AJ (1999). "Regulation of autophosphorylation of Escherichia coli nitrogen regulator II by the PII signal transduction protein." J Bacteriol 181(6);1906-11. PMID: 10074086

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

Keener88: Keener J, Kustu S (1988). "Protein kinase and phosphoprotein phosphatase activities of nitrogen regulatory proteins NTRB and NTRC of enteric bacteria: roles of the conserved amino-terminal domain of NTRC." Proc Natl Acad Sci U S A 85(14);4976-80. PMID: 2839825

Kramer99: Kramer G, Weiss V (1999). "Functional dissection of the transmitter module of the histidine kinase NtrB in Escherichia coli." Proc Natl Acad Sci U S A 96(2);604-9. PMID: 9892680

Magasanik: Magasanik B "Regulation of transcription of the glnALG operon of Escherichia coli by protein phosphorylation." Biochimie NIL;71(9-10);1005-12. PMID: 2574599

McFarland81: McFarland N, McCarter L, Artz S, Kustu S (1981). "Nitrogen regulatory locus "glnR" of enteric bacteria is composed of cistrons ntrB and ntrC: identification of their protein products." Proc Natl Acad Sci U S A 78(4);2135-9. PMID: 6113591

MirandaRios87: Miranda-Rios J, Sanchez-Pescador R, Urdea M, Covarrubias AA (1987). "The complete nucleotide sequence of the glnALG operon of Escherichia coli K12." Nucleic Acids Res 15(6);2757-70. PMID: 2882477

Ninfa86: Ninfa AJ, Magasanik B (1986). "Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli." Proc Natl Acad Sci U S A 1986;83(16);5909-13. PMID: 2874557

Ninfa86a: Ninfa AJ, Ueno-Nishio S, Hunt TP, Robustell B, Magasanik B (1986). "Purification of nitrogen regulator II, the product of the glnL (ntrB) gene of Escherichia coli." J Bacteriol 168(2);1002-4. PMID: 3536843

Ninfa91: Ninfa AJ, Bennett RL (1991). "Identification of the site of autophosphorylation of the bacterial protein kinase/phosphatase NRII." J Biol Chem 1991;266(11);6888-93. PMID: 2016302

Ninfa93: Ninfa EG, Atkinson MR, Kamberov ES, Ninfa AJ (1993). "Mechanism of autophosphorylation of Escherichia coli nitrogen regulator II (NRII or NtrB): trans-phosphorylation between subunits." J Bacteriol 1993;175(21);7024-32. PMID: 8226644

Pioszak00: Pioszak AA, Jiang P, Ninfa AJ (2000). "The Escherichia coli PII signal transduction protein regulates the activities of the two-component system transmitter protein NRII by direct interaction with the kinase domain of the transmitter module." Biochemistry 39(44);13450-61. PMID: 11063581

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Salinas03: Salinas P, Contreras A (2003). "Identification and analysis of Escherichia coli proteins that interact with the histidine kinase NtrB in a yeast two-hybrid system." Mol Genet Genomics 269(4);574-81. PMID: 12838411

SasseDwight88: Sasse-Dwight S, Gralla JD (1988). "Probing the Escherichia coli glnALG upstream activation mechanism in vivo." Proc Natl Acad Sci U S A 1988;85(23);8934-8. PMID: 2904147

Song04: Song Y, Peisach D, Pioszak AA, Xu Z, Ninfa AJ (2004). "Crystal structure of the C-terminal domain of the two-component system transmitter protein nitrogen regulator II (NRII; NtrB), regulator of nitrogen assimilation in Escherichia coli." Biochemistry 43(21);6670-8. PMID: 15157101

UenoNishio83: Ueno-Nishio S, Backman KC, Magasanik B (1983). "Regulation at the glnL-operator-promoter of the complex glnALG operon of Escherichia coli." J Bacteriol 153(3);1247-51. PMID: 6131062

UenoNishio84: Ueno-Nishio S, Mango S, Reitzer LJ, Magasanik B (1984). "Identification and regulation of the glnL operator-promoter of the complex glnALG operon of Escherichia coli." J Bacteriol 1984;160(1);379-84. PMID: 6148334

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

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

Other References Related to Gene Regulation

Atkinson02: Atkinson MR, Pattaramanon N, Ninfa AJ (2002). "Governor of the glnAp2 promoter of Escherichia coli." Mol Microbiol 46(5);1247-57. PMID: 12453212

ColladoVides91: Collado-Vides J, Magasanik B, Gralla JD (1991). "Control site location and transcriptional regulation in Escherichia coli." Microbiol Rev 1991;55(3);371-94. PMID: 1943993

Huo06: Huo YX, Nan BY, You CH, Tian ZX, Kolb A, Wang YP (2006). "FIS activates glnAp2 in Escherichia coli: role of a DNA bend centered at -55, upstream of the transcription start site." FEMS Microbiol Lett 257(1);99-105. PMID: 16553838

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

Ninfa87: Ninfa AJ, Reitzer LJ, Magasanik B (1987). "Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers." Cell 1987;50(7);1039-46. PMID: 3304660

Reitzer85: Reitzer LJ, Magasanik B (1985). "Expression of glnA in Escherichia coli is regulated at tandem promoters." Proc Natl Acad Sci U S A 1985;82(7);1979-83. PMID: 2858855

Reitzer86: Reitzer LJ, Magasanik B (1986). "Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter." Cell 45(6);785-92. PMID: 2871943

Reitzer89: Reitzer LJ, Movsas B, Magasanik B (1989). "Activation of glnA transcription by nitrogen regulator I (NRI)-phosphate in Escherichia coli: evidence for a long-range physical interaction between NRI-phosphate and RNA polymerase." J Bacteriol 1989;171(10);5512-22. PMID: 2571609

Rocha85: Rocha M, Vazquez M, Garciarrubio A, Covarrubias AA (1985). "Nucleotide sequence of the glnA-glnL intercistronic region of Escherichia coli." Gene 37(1-3);91-9. PMID: 2865194

Tian01a: Tian ZX, Li QS, Buck M, Kolb A, Wang YP (2001). "The CRP-cAMP complex and downregulation of the glnAp2 promoter provides a novel regulatory linkage between carbon metabolism and nitrogen assimilation in Escherichia coli." Mol Microbiol 41(4);911-24. PMID: 11532153


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 Nov 21, 2014, biocyc14.