Escherichia coli K-12 substr. MG1655 Protein: nitrogen regulatory protein P-II 1

Gene: glnB Accession Numbers: EG10384 (EcoCyc), b2553, ECK2550

Synonyms: [protein PII], unmodified PII, PII

Regulation Summary Diagram: ?

Regulation summary diagram for glnB

Subunit composition of nitrogen regulatory protein P-II 1 = [GlnB]3
         PII = GlnB

Alternative forms of PII: uridylyl-[protein PII] (extended summary available)

The PII-1 protein plays a critical role in the regulation of nitrogen metabolism by controlling the level and activity of glutamine synthetase. At high nitrogen levels PII acts with adenylyltransferase to modify the glutamine synthetase subunits with adenylate and thus the enzyme is deactivated. At low nitrogen levels PII is uridylylated to form uridylyl-[protein PII]. PII-UMP interacts with adenylyltransferase to reconvert the modified glutamine synthetase to the active form. PII also has an effect on the transcription response activator, nitrogen regulator I-phosphate. The signalling role of PII in glutamine synthetase regulation involves at least five different protein-protein interactions [Vasudevan94, Liu95c]. E. coli possesses a second PII protein, PII-2, encoded by the glnK gene. Like PII, PII-2 protein can activate the adenylylation of glutamine synthetase in vitro and is itself uridylylated in vivo. Unlike PII, however, the expression of PII-2 depends upon the presence of uridylyltransferase, nitrogen regulator I, and the absence of ammonia [vanHeeswijk96, vanHeeswijk95]. PII and PII-2 are functionally equivalent; distinct expression of the two genes accounts for the distinct physiological effects [Blauwkamp02, Atkinson02a]. PII and PII-2 can heterotrimerize [vanHeeswijk00].

Gene Citations: [vanHeeswijk93, He93, Liu93a]

Locations: cytosol

Map Position: [2,685,092 <- 2,685,430] (57.87 centisomes, 208°)
Length: 339 bp / 112 aa

Molecular Weight of Polypeptide: 12.425 kD (from nucleotide sequence)

pI: 5.43

Isozyme Sequence Similarity:

Unification Links: ASAP:ABE-0008398 , CGSC:32933 , DIP:DIP-35005N , EchoBASE:EB0379 , EcoGene:EG10384 , EcoliWiki:b2553 , Mint:MINT-1235669 , ModBase:P0A9Z1 , OU-Microarray:b2553 , PortEco:glnB , PR:PRO_000022783 , Pride:P0A9Z1 , Protein Model Portal:P0A9Z1 , RegulonDB:EG10384 , SMR:P0A9Z1 , String:511145.b2553 , UniProt:P0A9Z1

Relationship Links: InterPro:IN-FAMILY:IPR002187 , InterPro:IN-FAMILY:IPR002332 , InterPro:IN-FAMILY:IPR011322 , InterPro:IN-FAMILY:IPR015867 , InterPro:IN-FAMILY:IPR017918 , PDB:Structure:1PIL , PDB:Structure:2PII , Pfam:IN-FAMILY:PF00543 , Prints:IN-FAMILY:PR00340 , Prosite:IN-FAMILY:PS00496 , Prosite:IN-FAMILY:PS00638 , Prosite:IN-FAMILY:PS51343 , Smart:IN-FAMILY:SM00938

Reactions known to consume the compound:

Nitrogen Regulation Two-Component System :
a PII protein + UTP → a uridylylated PII protein + diphosphate

Reactions known to produce the compound:

Nitrogen Regulation Two-Component System :
uridylyl-[protein PII] → PII + UMP

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for glnB

GO Terms:

Biological Process: GO:0006808 - regulation of nitrogen utilization Inferred from experiment Inferred by computational analysis [GOA01, Son87]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0050790 - regulation of catalytic activity Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05, Salinas03, Burillo04]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14, Burillo04]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0030234 - enzyme regulator activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks amino acids glutamine
regulation type of regulation posttranscriptional inhibition / activation of enzymes

Activates: NtrC-Pasp + H2O → NtrC + phosphate

Inhibits: ATP + NtrB sensory histidine kinase → ADP + NtrB-Phis

Essentiality data for glnB 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]

Sequence Features

Protein sequence of PII with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 19
[Son87, UniProt10]
UniProt: (in Ref. 1; AAA23883);
O-UMP-tyrosine-Modification 51
[Son87, UniProt15]
UniProt: O-UMP-tyrosine.
Sequence-Conflict 81 -> 82
[Son87, UniProt10]
UniProt: (in Ref. 1; AAA23883);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2553 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10384; confirmed by SwissProt match.


Atkinson02a: Atkinson MR, Blauwkamp TA, Ninfa AJ (2002). "Context-dependent functions of the PII and GlnK signal transduction proteins in Escherichia coli." J Bacteriol 2002;184(19);5364-75. PMID: 12218023

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

Blauwkamp02: Blauwkamp TA, Ninfa AJ (2002). "Physiological role of the GlnK signal transduction protein of Escherichia coli: survival of nitrogen starvation." Mol Microbiol 2002;46(1);203-14. PMID: 12366843

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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

He93: He B, Choi KY, Zalkin H (1993). "Regulation of Escherichia coli glnB, prsA, and speA by the purine repressor." J Bacteriol 1993;175(11);3598-606. PMID: 8388874

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Liu93a: Liu J, Magasanik B (1993). "The glnB region of the Escherichia coli chromosome." J Bacteriol 1993;175(22);7441-9. PMID: 8226691

Liu95c: Liu J, Magasanik B (1995). "Activation of the dephosphorylation of nitrogen regulator I-phosphate of Escherichia coli." J Bacteriol 1995;177(4);926-31. PMID: 7860602

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

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

Son87: Son HS, Rhee SG (1987). "Cascade control of Escherichia coli glutamine synthetase. Purification and properties of PII protein and nucleotide sequence of its structural gene." J Biol Chem 262(18);8690-5. PMID: 2885322

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

vanHeeswijk00: van Heeswijk WC, Wen D, Clancy P, Jaggi R, Ollis DL, Westerhoff HV, Vasudevan SG (2000). "The Escherichia coli signal transducers PII (GlnB) and GlnK form heterotrimers in vivo: fine tuning the nitrogen signal cascade." Proc Natl Acad Sci U S A 2000;97(8);3942-7. PMID: 10760266

vanHeeswijk93: van Heeswijk WC, Rabenberg M, Westerhoff HV, Kahn D (1993). "The genes of the glutamine synthetase adenylylation cascade are not regulated by nitrogen in Escherichia coli." Mol Microbiol 9(3);443-57. PMID: 8412694

vanHeeswijk95: van Heeswijk WC, Stegeman B, Hoving S, Molenaar D, Kahn D, Westerhoff HV (1995). "An additional PII in Escherichia coli: a new regulatory protein in the glutamine synthetase cascade." FEMS Microbiol Lett 1995;132(1-2);153-7. PMID: 7590157

vanHeeswijk96: van Heeswijk WC, Hoving S, Molenaar D, Stegeman B, Kahn D, Westerhoff HV (1996). "An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli." Mol Microbiol 1996;21(1);133-46. PMID: 8843440

Vasudevan94: Vasudevan SG, Gedye C, Dixon NE, Cheah E, Carr PD, Suffolk PM, Jeffrey PD, Ollis DL (1994). "Escherichia coli PII protein: purification, crystallization and oligomeric structure." FEBS Lett 1994;337(3);255-8. PMID: 8293810

Other References Related to Gene Regulation

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

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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