Escherichia coli K-12 substr. MG1655 Enzyme: [protein-PII] uridylyltransferase

Gene: glnD Accession Numbers: EG11411 (EcoCyc), b0167, ECK0165

Synonyms: glnD5

Regulation Summary Diagram: ?

Regulation summary diagram for glnD

Uridylyltransferase is a single polypeptide chain. The purified enzyme catalyzes the uridylylation as well as the de-uridylylation of the regulatory protein PII, demonstrating that a single bifunctional enzyme is involved in the covalent interconversion of PII [Garcia83]. The present data show that UTase and UR co-purify to a homogeneous preparation and that molecular weights determined under denaturing and native conditions are identical. This shows unequivocally that UTase and UR are contained in single polypeptide [Garcia83].
ArcA appears to activate glnD gene expression under anaerobiosis. A putative ArcA binding site was identified 560 bp upstream of this gene, but no promoter upstream of it has been identified [Salmon05].

Gene Citations: [vanHeeswijk93]

Locations: cytosol

Map Position: [185,978 <- 188,650] (4.01 centisomes, 14°)
Length: 2673 bp / 890 aa

Molecular Weight of Polypeptide: 102.39 kD (from nucleotide sequence)

pI: 6.68

Unification Links: ASAP:ABE-0000568 , CGSC:704 , DIP:DIP-9779N , EchoBASE:EB1383 , EcoGene:EG11411 , EcoliWiki:b0167 , Mint:MINT-1252261 , ModBase:P27249 , OU-Microarray:b0167 , PortEco:glnD , PR:PRO_000022784 , Pride:P27249 , Protein Model Portal:P27249 , RefSeq:NP_414709 , RegulonDB:EG11411 , SMR:P27249 , String:511145.b0167 , UniProt:P27249

Relationship Links: InterPro:IN-FAMILY:IPR002912 , InterPro:IN-FAMILY:IPR002934 , InterPro:IN-FAMILY:IPR003607 , InterPro:IN-FAMILY:IPR006674 , InterPro:IN-FAMILY:IPR010043 , InterPro:IN-FAMILY:IPR013546 , Panther:IN-FAMILY:PTHR13734:SF1 , Pfam:IN-FAMILY:PF01842 , Pfam:IN-FAMILY:PF01909 , Pfam:IN-FAMILY:PF01966 , Pfam:IN-FAMILY:PF08335 , Prosite:IN-FAMILY:PS51671 , Smart:IN-FAMILY:SM00471

In Paralogous Gene Group: 57 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for glnD

GO Terms:

Biological Process: GO:0006464 - cellular protein modification process Inferred from experiment [Garcia83]
GO:0006807 - nitrogen compound metabolic process Inferred by computational analysis [GOA01]
GO:0006808 - regulation of nitrogen utilization Inferred by computational analysis [GOA06]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Burillo04]
GO:0008773 - [protein-PII] uridylyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Garcia83]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11]
GO:0008081 - phosphoric diester hydrolase activity Inferred by computational analysis [GOA06]
GO:0016597 - amino acid binding Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016779 - nucleotidyltransferase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred by curator
GO:0005829 - cytosol

MultiFun Terms: information transfer protein related posttranslational modification
metabolism biosynthesis of building blocks amino acids glutamine
metabolism metabolism of other compounds nitrogen metabolism

Essentiality data for glnD 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]

Enzymatic reaction of: [protein-PII] uridylyltransferase

Synonyms: protein PII uridylyltransferase, PII uridylyltransferase

a PII protein + UTP <=> a uridylylated PII protein + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: Nitrogen Regulation Two-Component System

High intracellular levels of 2-oxoglutarate activate the uridylyltransferase portion of the bifunctional enzyme. Uridylyltransferase transfers a UMP group to each subunit of PII to form PII-UMP or PIID. PII-UMP in turn interacts with adenylyltransferase which catalyzes the removal of AMP from glutamine synthetase, activating the enzyme. Interconversion of the two forms of PII involves the covalent attachment of UMP to, and its removal from, a specific tyrosyl residue in PII, in reactions catalyzed by a uridylyltransferase and a uridylyl-removing activity, respectively [Garcia83]. In the absence of UTase there is very little activation of glutamine synthetase production in response to nitrogen deprivation. The loss of the ability to produce PII, the product of glnB, enhances activation of glutamine synthetase formation in the absence of UTase. This indicates that the presence of PII, which cannot be converted to PII-UMP in the absence of UTase, is responsible for the failure to activate the synthesis of glutamine synthetase [Bueno85]. The loss of UTase results in the inability to activate transcription from glnAp2 [Ninfa86]. The de-uridylylation reaction is not a reversal of the uridylylation reaction.

ATP and alpha-ketoglutarate are required for UTase activity. 3-ketoglutarate and oxaloacetate will also activate the enzyme but much less effectively [Adler75, Atkinson94a, Kamberov95].

Cofactors or Prosthetic Groups: Mg2+

Activators (Allosteric): 2-oxoglutarate , ATP

Inhibitors (Unknown Mechanism): L-glutamine [Adler75, Atkinson94a, Kamberov95]

Sequence Features

Protein sequence of [protein-PII] uridylyltransferase with features indicated

Feature Class Location Citations Comment
Protein-Segment 1 -> 349
UniProt: Uridylyltransferase; Sequence Annotation Type: region of interest.
Sequence-Conflict 47
[Park92a, UniProt15]
UniProt: (in Ref. 1; AAA23878).
Mutagenesis-Variant 93
[Zhang10d, UniProt15]
G → L or V: Loss of UTase activity, while no significant effect on UR activity.
Mutagenesis-Variant 94
[Zhang10d, UniProt15]
UniProt: Loss of UTase activity, while no significant effect on UR activity.
Mutagenesis-Variant 107
[Zhang10d, UniProt15]
D → A, V or Y: Loss of UTase activity, while no significant effect on UR activity.
Sequence-Conflict 225
[Fujita94, UniProt10]
UniProt: (in Ref. 3);
Protein-Segment 350 -> 708
UniProt: Uridylyl-removing; Sequence Annotation Type: region of interest.
Sequence-Conflict 357 -> 358
[Park92a, UniProt15]
UniProt: (in Ref. 1; AAA23878).
Conserved-Region 468 -> 601
UniProt: HD.
Mutagenesis-Variant 514 -> 515
[Zhang10d, UniProt15]
HD → AA or QN: Loss of UR activity, while no significant effect on UTase activity.
Sequence-Conflict 523
[Park92a, UniProt15]
UniProt: (in Ref. 1; AAA23878).
Sequence-Conflict 703
[vanHeeswijk93, UniProt10]
UniProt: (in Ref. 2; CAA79887);
Conserved-Region 709 -> 789
UniProt: ACT 1.
Conserved-Region 816 -> 890
UniProt: ACT 2.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b0167 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11411; confirmed by SwissProt match.


Adler75: Adler SP, Purich D, Stadtman ER (1975). "Cascade control of Escherichia coli glutamine synthetase. Properties of the PII regulatory protein and the uridylyltransferase-uridylyl-removing enzyme." J Biol Chem 1975;250(16);6264-72. PMID: 239942

Atkinson94a: Atkinson MR, Kamberov ES, Weiss RL, Ninfa AJ (1994). "Reversible uridylylation of the Escherichia coli PII signal transduction protein regulates its ability to stimulate the dephosphorylation of the transcription factor nitrogen regulator I (NRI or NtrC)." J Biol Chem 1994;269(45);28288-93. PMID: 7961766

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

Bueno85: Bueno R, Pahel G, Magasanik B (1985). "Role of glnB and glnD gene products in regulation of the glnALG operon of Escherichia coli." J Bacteriol 1985;164(2);816-22. PMID: 2865248

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

Fujita94: Fujita N, Mori H, Yura T, Ishihama A (1994). "Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region." Nucleic Acids Res 22(9);1637-9. PMID: 8202364

Garcia83: Garcia E, Rhee SG (1983). "Cascade control of Escherichia coli glutamine synthetase. Purification and properties of PII uridylyltransferase and uridylyl-removing enzyme." J Biol Chem 1983;258(4);2246-53. PMID: 6130097

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

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Kamberov95: Kamberov ES, Atkinson MR, Ninfa AJ (1995). "The Escherichia coli PII signal transduction protein is activated upon binding 2-ketoglutarate and ATP." J Biol Chem 1995;270(30);17797-807. PMID: 7629080

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

Park92a: Park S.-C., Kim I.H., Rhee S.G. (1992). "Molecular cloning and sequencing of gldD, the gene for uridylyl transferase and uridyl removing enzyme of E. coli." Data submission to EMBL/GenBank/DDBJ databases on 1992-07.

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

Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038

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

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

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-14 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."

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

Zhang10d: Zhang Y, Pohlmann EL, Serate J, Conrad MC, Roberts GP (2010). "Mutagenesis and functional characterization of the four domains of GlnD, a bifunctional nitrogen sensor protein." J Bacteriol 192(11);2711-21. PMID: 20363937

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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