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Escherichia coli K-12 substr. MG1655 Enzyme: glucosamine-6-phosphate deaminase



Gene: nagB Accession Numbers: EG10633 (EcoCyc), b0678, ECK0666

Synonyms: glmD

Regulation Summary Diagram: ?

Subunit composition of glucosamine-6-phosphate deaminase = [NagB]6
         glucosamine-6-phosphate deaminase = NagB

Summary:
Glucosamine-6-phosphate deaminase (NagB) catalyzes the second cytoplasmic reaction in the metabolism of N-acetyl-D-glucosamine. The deamination of glucosamine-6-phosphate generates ammonia and fructose-6-phosphate, which can enter glycolysis directly. Both N-acetylglucosamine and glucosamine can serve as the sole source of carbon for E. coli.

Crystal structures of the enzyme have been solved [Oliva95, Horjales99, RudinoPinera02]. The enzyme is a trimer of dimers that are linked by an interchain disulfide bridge [Altamirano93]. The enzyme is allosterically activated by N-acetyl-D-glucosamine-6-phosphate [White67, Altamirano92]. Both substrate binding and the allosteric transition are entropy-driven processes [BustosJaimes01].

The growth rate on glucosamine is limited by the supply of substrate to NagB rather than the absence of the allosteric activator N-acetyl-D-glucosamine-6-phosphate [AlvarezAnorve09].

Extensive site-directed mutagenesis and analysis of the mutant enzymes has allowed identification of residues that play roles in catalysis, coupling binding in the active site to the allosteric pocket, and binding of the allosteric effector N-acetyl-D-glucosamine-6-phosphate [Altamirano92, Altamirano95, MonteroMoran98, MonteroMoran01, MonteroMoran01, BustosJaimes02, Cisneros04, LucumiMoreno05, BustosJaimes05]. A fluorescently labelled derivative allowed monitoring of the allosteric transition of the enzyme [SosaPeinado05].

nagB mutants are unable to grow on N-acetylglucosamine as the sole source of carbon and energy [White68, Holmes72a, Rolls72]. Several point mutants that affect N-acetyl-D-glucosamine-6-phosphate binding, the active site, and the active site lid in vitro were tested for their effect on the growth rate with glucosamine or N-acetylglucosamine as the source of carbon and energy in vivo [AlvarezAnorve05].

Overexpression of nagB can suppress the defect of a glmS mutant, showing that glucosamine-6-phosphate deaminase can act in the biosynthetic direction, supplying glucosamine-6-phosphate for the synthesis of UDP-GlcNAc. To avoid a futile cycle, proper regulation of both enzymes is thus essential [Vogler89], and it has been hypothesized that allosteric activation of NagB by N-acetyl-D-glucosamine-6-phosphate plays this role [AlvarezAnorve09].

NagB: "N-acetylglucosamine" [Holmes72a]

Gene Citations: [Plumbridge91, Plumbridge89, Vogler89a, Rogers88, Plumbridge91a]

Locations: cytosol

Map Position: [702,034 <- 702,834] (15.13 centisomes)
Length: 801 bp / 266 aa

Molecular Weight of Polypeptide: 29.774 kD (from nucleotide sequence), 29 kD (experimental) [Peri90 ]

pI: 6.83

Unification Links: ASAP:ABE-0002304 , CGSC:463 , DIP:DIP-35992N , EchoBASE:EB0627 , EcoGene:EG10633 , EcoliWiki:b0678 , ModBase:P0A759 , OU-Microarray:b0678 , PortEco:nagB , PR:PRO_000023337 , Pride:P0A759 , Protein Model Portal:P0A759 , RefSeq:NP_415204 , RegulonDB:EG10633 , SMR:P0A759 , String:511145.b0678 , UniProt:P0A759

Relationship Links: InterPro:IN-FAMILY:IPR004547 , InterPro:IN-FAMILY:IPR006148 , InterPro:IN-FAMILY:IPR018321 , Panther:IN-FAMILY:PTHR11280 , PDB:Structure:1CD5 , PDB:Structure:1DEA , PDB:Structure:1FQO , PDB:Structure:1FRZ , PDB:Structure:1FS5 , PDB:Structure:1FS6 , PDB:Structure:1FSF , PDB:Structure:1HOR , PDB:Structure:1HOT , PDB:Structure:1JT9 , PDB:Structure:2WU1 , Pfam:IN-FAMILY:PF01182 , Prosite:IN-FAMILY:PS01161

In Paralogous Gene Group: 498 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006046 - N-acetylglucosamine catabolic process Inferred from experiment [Rolls72]
GO:0006048 - UDP-N-acetylglucosamine biosynthetic process Inferred from experiment [Vogler89]
GO:0019262 - N-acetylneuraminate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Hopkins13]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006044 - N-acetylglucosamine metabolic process Inferred by computational analysis [GOA06, GOA01]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004342 - glucosamine-6-phosphate deaminase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Altamirano92]
GO:0042802 - identical protein binding Inferred from experiment [Altamirano93]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism central intermediary metabolism amino sugar conversions

Essentiality data for nagB 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]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 14-Aug-2013 by Keseler I , SRI International


Enzymatic reaction of: glucosamine-6-phosphate deaminase

Synonyms: glucosamine-6-phosphate isomerase, D-glucosamine 6-phosphate ketol-isomerase (deaminating), 2-amino-2-deoxy-D-glucose-6-phosphate ketol isomerase (deaminating), G6PD

EC Number: 3.5.99.6

α-D-glucosamine 6-phosphate + H2O <=> ammonium + β-D-fructofuranose 6-phosphate

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

This reaction is reversible.

In Pathways: superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation , N-acetylglucosamine degradation I

Summary:
The enzyme from E. coli B was first isolated and later purified to homogeneity and characterized [Comb58, Calcagno84, Altamirano87, Altamirano90].

Glucosamine-6-phosphate deaminase shows a preference for the α anomer of glucosamine-6-phosphate [Midelfort77].

Activators (Allosteric): N-acetyl-D-glucosamine 6-phosphate [White67, Altamirano92, Comment 5]

Inhibitors (Competitive): 2-deoxy-2-amino glucitol-6-phosphate [Midelfort77]

Primary Physiological Regulators of Enzyme Activity: N-acetyl-D-glucosamine 6-phosphate

Kinetic Parameters:

Substrate
Km (μM)
Citations
α-D-glucosamine 6-phosphate
400.0
[Midelfort77]
ammonium
31400.0, 35400.0
[Calcagno84, BRENDA14]

pH(opt): 7.8 [BRENDA14, Comb58], 7.0 [White67]


Sequence Features

Feature Class Location Common Name Citations Comment State
Sequence-Conflict 70  
[Peri90, UniProt10a]
Alternate sequence: N → NM; UniProt: (in Ref. 2; AAC09324);
 
Active-Site 72  
[MonteroMoran01, UniProt11]
UniProt: Proton acceptor; for enolization step.
 
Sequence-Conflict 91  
[Peri90, UniProt10a]
Alternate sequence: R → missing; UniProt: (in Ref. 2; AAC09324);
 
Mutagenesis-Variant 118  
[Altamirano92, UniProt11]
Alternate sequence: C → S; UniProt: 50% of wild-type activity, but 2- fold decrease in substrate affinity.
 
Mutagenesis-Variant 141  
[MonteroMoran01, UniProt11]
Alternate sequence: D → N; UniProt: Large decrease in activity.
 
Active-Site 141  
[MonteroMoran01, UniProt11]
UniProt: For ring-opening step.
 
Mutagenesis-Variant 143  
[MonteroMoran01, UniProt11]
Alternate sequence: H → Q; UniProt: Loss of activity for the deamination reaction but not for the reverse reaction; complete loss of the homotropic cooperativity.
 
Active-Site 143  
[MonteroMoran01, UniProt11]
UniProt: Proton acceptor; for ring-opening step.
 
Mutagenesis-Variant 148  
[MonteroMoran01, UniProt11]
Alternate sequence: E → Q; UniProt: Large decrease in activity.
 
Active-Site 148  
[MonteroMoran01, UniProt11]
UniProt: For ring-opening step.
 
Amino-Acid-Site 151  
[UniProt10a]
UniProt: Part of the allosteric site; Sequence Annotation Type: site;
 
Amino-Acid-Site 158  
[UniProt10a]
UniProt: Part of the allosteric site; Sequence Annotation Type: site;
 
Amino-Acid-Site 160  
[UniProt10a]
UniProt: Part of the allosteric site; Sequence Annotation Type: site;
 
Amino-Acid-Site 161  
[UniProt10a]
UniProt: Part of the allosteric site; Sequence Annotation Type: site;
 
Mutagenesis-Variant 174  
[UniProt10a]
Alternate sequence: F → A; UniProt: Loss of activity in the absence of the allosteric activator;
 
Interchain-Disulfide-Bond 219 interchain disulfide bond, not required for activity
[Altamirano93]
  Linked
Mutagenesis-Variant 239  
[Altamirano92, UniProt11]
Alternate sequence: C → S; UniProt: 50% of wild-type activity, but 2- fold decrease in substrate affinity; decrease in allosteric interaction energy.
 
Amino-Acid-Site 254  
[UniProt10a]
UniProt: Part of the allosteric site; Sequence Annotation Type: site;
 


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0678 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10633; confirmed by SwissProt match.


References

Altamirano87: Altamirano MM, Mulliert G, Calcagno M (1987). "Sulfhydryl groups of glucosamine-6-phosphate isomerase deaminase from Escherichia coli." Arch Biochem Biophys 1987;258(1);95-100. PMID: 2821923

Altamirano90: Altamirano MM, Calcagno M (1990). "Zinc binding and its trapping by allosteric transition in glucosamine-6-phosphate deaminase from Escherichia coli." Biochim Biophys Acta 1038(3);291-4. PMID: 2111170

Altamirano92: Altamirano MM, Plumbridge JA, Calcagno ML (1992). "Identification of two cysteine residues forming a pair of vicinal thiols in glucosamine-6-phosphate deaminase from Escherichia coli and a study of their functional role by site-directed mutagenesis." Biochemistry 31(4);1153-8. PMID: 1734962

Altamirano93: Altamirano MM, Plumbridge JA, Barba HA, Calcagno ML (1993). "Glucosamine-6-phosphate deaminase from Escherichia coli has a trimer of dimers structure with three intersubunit disulphides." Biochem J 295 ( Pt 3);645-8. PMID: 8240271

Altamirano94: Altamirano MM, Hernandez-Arana A, Tello-Solis S, Calcagno ML (1994). "Spectrochemical evidence for the presence of a tyrosine residue in the allosteric site of glucosamine-6-phosphate deaminase from Escherichia coli." Eur J Biochem 1994;220(2);409-13. PMID: 8125098

Altamirano95: Altamirano MM, Plumbridge JA, Horjales E, Calcagno ML (1995). "Asymmetric allosteric activation of Escherichia coli glucosamine-6-phosphate deaminase produced by replacements of Tyr 121." Biochemistry 34(18);6074-82. PMID: 7742311

AlvarezAnorve05: Alvarez-Anorve LI, Calcagno ML, Plumbridge J (2005). "Why does Escherichia coli grow more slowly on glucosamine than on N-acetylglucosamine? Effects of enzyme levels and allosteric activation of GlcN6P deaminase (NagB) on growth rates." J Bacteriol 187(9);2974-82. PMID: 15838023

AlvarezAnorve09: Alvarez-Anorve LI, Bustos-Jaimes I, Calcagno ML, Plumbridge J (2009). "Allosteric regulation of glucosamine-6-phosphate deaminase (NagB) and growth of Escherichia coli on glucosamine." J Bacteriol 191(20);6401-7. PMID: 19700525

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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

BustosJaimes01: Bustos-Jaimes I, Calcagno ML (2001). "Allosteric transition and substrate binding are entropy-driven in glucosamine-6-phosphate deaminase from Escherichia coli." Arch Biochem Biophys 394(2);156-60. PMID: 11594728

BustosJaimes02: Bustos-Jaimes I, Sosa-Peinado A, Rudino-Pinera E, Horjales E, Calcagno ML (2002). "On the role of the conformational flexibility of the active-site lid on the allosteric kinetics of glucosamine-6-phosphate deaminase." J Mol Biol 319(1);183-9. PMID: 12051945

BustosJaimes05: Bustos-Jaimes I, Ramirez-Costa M, De Anda-Aguilar L, Hinojosa-Ocana P, Calcagno ML (2005). "Evidence for two different mechanisms triggering the change in quaternary structure of the allosteric enzyme, glucosamine-6-phosphate deaminase." Biochemistry 44(4);1127-35. PMID: 15667206

Calcagno84: Calcagno M, Campos PJ, Mulliert G, Suastegui J (1984). "Purification, molecular and kinetic properties of glucosamine-6-phosphate isomerase (deaminase) from Escherichia coli." Biochim Biophys Acta 1984;787(2);165-73. PMID: 6375729

Cisneros04: Cisneros DA, Montero-Moran GM, Lara-Gonzalez S, Calcagno ML (2004). "Inversion of the allosteric response of Escherichia coli glucosamine-6-P deaminase to N-acetylglucosamine 6-P, by single amino acid replacements." Arch Biochem Biophys 421(1);77-84. PMID: 14678787

Comb58: Comb DG, Roseman S (1958). "Glucosamine metabolism. IV. Glucosamine-6-phosphate deaminase." J Biol Chem 232(2);807-27. PMID: 13549465

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

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."

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."

Holmes72a: Holmes RP, Russell RR (1972). "Mutations affecting amino sugar metabolism in Escherichia coli K-12." J Bacteriol 111(1);290-1. PMID: 4591481

Hopkins13: Hopkins AP, Hawkhead JA, Thomas GH (2013). "Transport and catabolism of the sialic acids N-glycolylneuraminic acid and 3-keto-3-deoxy-D-glycero-D-galactonononic acid by Escherichia coli K-12." FEMS Microbiol Lett 347(1);14-22. PMID: 23848303

Horjales99: Horjales E, Altamirano MM, Calcagno ML, Garratt RC, Oliva G (1999). "The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3 A resolution." Structure 7(5);527-37. PMID: 10378272

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

LaraGonzalez00: Lara-Gonzalez S, Dixon HB, Mendoza-Hernandez G, Altamirano MM, Calcagno ML (2000). "On the role of the N-terminal group in the allosteric function of glucosamine-6-phosphate deaminase from Escherichia coli." J Mol Biol 301(1);219-27. PMID: 10926504

LucumiMoreno05: Lucumi-Moreno A, Calcagno ML (2005). "On the functional role of Arg172 in substrate binding and allosteric transition in Escherichia coli glucosamine-6-phosphate deaminase." Arch Biochem Biophys 442(1);41-8. PMID: 16168949

Midelfort77: Midelfort CF, Rose IA (1977). "Studies on the mechanism of Escherichia coli glucosamine-6-phosphate isomerase." Biochemistry 16(8);1590-6. PMID: 322702

MonteroMoran01: Montero-Moran GM, Lara-Gonzalez S, Alvarez-Anorve LI, Plumbridge JA, Calcagno ML (2001). "On the multiple functional roles of the active site histidine in catalysis and allosteric regulation of Escherichia coli glucosamine 6-phosphate deaminase." Biochemistry 40(34);10187-96. PMID: 11513596

MonteroMoran98: Montero-Moran GM, Horjales E, Calcagno ML, Altamirano MM (1998). "Tyr254 hydroxyl group acts as a two-way switch mechanism in the coupling of heterotropic and homotropic effects in Escherichia coli glucosamine-6-phosphate deaminase." Biochemistry 37(21);7844-9. PMID: 9601045

Oliva95: Oliva G, Fontes MR, Garratt RC, Altamirano MM, Calcagno ML, Horjales E (1995). "Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 A resolution." Structure 3(12);1323-32. PMID: 8747459

Peri90: Peri KG, Goldie H, Waygood EB (1990). "Cloning and characterization of the N-acetylglucosamine operon of Escherichia coli." Biochem Cell Biol 68(1);123-37. PMID: 2190615

Plumbridge89: Plumbridge JA (1989). "Sequence of the nagBACD operon in Escherichia coli K12 and pattern of transcription within the nag regulon." Mol Microbiol 1989;3(4);505-15. PMID: 2668691

Plumbridge91: Plumbridge J, Kolb A (1991). "CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli." J Mol Biol 1991;217(4);661-79. PMID: 1848637

Plumbridge91a: Plumbridge JA (1991). "Repression and induction of the nag regulon of Escherichia coli K-12: the roles of nagC and nagA in maintenance of the uninduced state." Mol Microbiol 1991;5(8);2053-62. PMID: 1766379

Rogers88: Rogers MJ, Ohgi T, Plumbridge J, Soll D (1988). "Nucleotide sequences of the Escherichia coli nagE and nagB genes: the structural genes for the N-acetylglucosamine transport protein of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and for glucosamine-6-phosphate deaminase." Gene 1988;62(2);197-207. PMID: 3284790

Rolls72: Rolls JP, Shuster CW (1972). "Amino sugar assimilation by Escherichia coli." J Bacteriol 112(2);894-902. PMID: 4563983

RudinoPinera02: Rudino-Pinera E, Morales-Arrieta S, Rojas-Trejo SP, Horjales E (2002). "Structural flexibility, an essential component of the allosteric activation in Escherichia coli glucosamine-6-phosphate deaminase." Acta Crystallogr D Biol Crystallogr 58(Pt 1);10-20. PMID: 11752775

SosaPeinado05: Sosa-Peinado A, Gonzalez-Andrade M (2005). "Site-directed fluorescence labeling reveals differences on the R-conformer of glucosamine 6-phosphate deaminase of Escherichia coli induced by active or allosteric site ligands at steady state." Biochemistry 44(46);15083-92. PMID: 16285712

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Vogler89: Vogler AP, Trentmann S, Lengeler JW (1989). "Alternative route for biosynthesis of amino sugars in Escherichia coli K-12 mutants by means of a catabolic isomerase." J Bacteriol 1989;171(12);6586-92. PMID: 2687246

Vogler89a: Vogler AP, Lengeler JW (1989). "Analysis of the nag regulon from Escherichia coli K12 and Klebsiella pneumoniae and of its regulation." Mol Gen Genet 219(1-2);97-105. PMID: 2693951

White67: White RJ, Pasternak CA (1967). "The purification and properties of N-acetylglucosamine 6-phosphate deacetylase from Escherichia coli." Biochem J 1967;105(1);121-5. PMID: 4861885

White68: White RJ (1968). "Control of amino sugar metabolism in Escherichia coli and isolation of mutants unable to degrade amino sugars." Biochem J 106(4);847-58. PMID: 4866432

Other References Related to Gene Regulation

Plumbridge01: Plumbridge J (2001). "DNA binding sites for the Mlc and NagC proteins: regulation of nagE, encoding the N-acetylglucosamine-specific transporter in Escherichia coli." Nucleic Acids Res 29(2);506-14. PMID: 11139621

Plumbridge93: Plumbridge J, Kolb A (1993). "DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo." Mol Microbiol 10(5);973-81. PMID: 7934873

Plumbridge98a: Plumbridge J, Kolb A (1998). "DNA bending and expression of the divergent nagE-B operons." Nucleic Acids Res 26(5);1254-60. PMID: 9469834


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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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