Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: evolved β-D-galactosidase, α subunit; cryptic gene



Gene: ebgA Accession Numbers: EG10252 (EcoCyc), b3076, ECK3066

Regulation Summary Diagram: ?

Component of: evolved β-D-galactosidase (summary available)

Gene Citations: [Elliott92]

Map Position: [3,220,655 -> 3,223,747] (69.42 centisomes)
Length: 3093 bp / 1030 aa

Molecular Weight of Polypeptide: 117.88 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010104 , CGSC:830 , DIP:DIP-2893N , EchoBASE:EB0248 , EcoGene:EG10252 , EcoliWiki:b3076 , ModBase:P06864 , OU-Microarray:b3076 , PortEco:ebgA , PR:PRO_000022497 , Protein Model Portal:P06864 , RefSeq:YP_026199 , RegulonDB:EG10252 , SMR:P06864 , String:511145.b3076 , UniProt:P06864

Relationship Links: CAZy:IN-FAMILY:GH2 , InterPro:IN-FAMILY:IPR004199 , InterPro:IN-FAMILY:IPR006101 , InterPro:IN-FAMILY:IPR006102 , InterPro:IN-FAMILY:IPR006103 , InterPro:IN-FAMILY:IPR006104 , InterPro:IN-FAMILY:IPR008979 , InterPro:IN-FAMILY:IPR011013 , InterPro:IN-FAMILY:IPR013781 , InterPro:IN-FAMILY:IPR013812 , InterPro:IN-FAMILY:IPR014718 , InterPro:IN-FAMILY:IPR017853 , InterPro:IN-FAMILY:IPR023230 , InterPro:IN-FAMILY:IPR023232 , Pfam:IN-FAMILY:PF00703 , Pfam:IN-FAMILY:PF02836 , Pfam:IN-FAMILY:PF02837 , Pfam:IN-FAMILY:PF02929 , Prints:IN-FAMILY:PR00132 , Prosite:IN-FAMILY:PS00608 , Prosite:IN-FAMILY:PS00719 , Smart:IN-FAMILY:SM01038

In Paralogous Gene Group: 108 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds Inferred by computational analysis [GOA01a]
GO:0004565 - beta-galactosidase activity Inferred by computational analysis [GOA01, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016798 - hydrolase activity, acting on glycosyl bonds Inferred by computational analysis [UniProtGOA11a]
GO:0030246 - carbohydrate binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0009341 - beta-galactosidase complex Inferred by computational analysis [GOA01a]

MultiFun Terms: All-Genes Pseudo-Genes Cryptic-Genes
MultiFun metabolism carbon utilization carbon compounds

Essentiality data for ebgA 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]

Subunit of: evolved β-D-galactosidase

Subunit composition of evolved β-D-galactosidase = [EbgA]4[EbgC]4
         evolved β-D-galactosidase, α subunit; cryptic gene = EbgA
         evolved β-D-galactosidase, β subunit; cryptic gene = EbgC

Summary:
The EbgA-EbgC complex represents the second β-D-galactosidase enzyme in E. coli. The wild-type enzyme is too catalytically feeble to allow growth on lactose as the sole carbon source. Spontaneous mutations that enable growth on lactose occur under selective conditions in the absence of LacZ [Campbell73].

The ebg and lac operons are homologous and probably descended from a common ancestor [Stokes85, Stokes85a]. The EbgAC enzyme is a heterooctamer [Elliott92]. Catalytic activity of the large (EbgA) subunit alone suggests that the small subunit is associated with the optimal positioning of the electrophilic Mg2+ ions in the enzyme [Calugaru95]. Various types of evolved, catalytically active enzymes have been studied in detail [Elliott92, Hall89, Calugaru97].

Reviews: [Hall99, Hall03]

Credits:
Created 05-Jan-2006 by Keseler I , SRI International
Last-Curated ? 05-Jan-2006 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Extrinsic-Sequence-Variant 92
[UniProt10]
Alternate sequence: D → N; UniProt: (improve activity);
Extrinsic-Sequence-Variant 93
[UniProt10]
Alternate sequence: E → K; UniProt: (improve activity);
Sequence-Conflict 275
[Stokes85, Hall89, Blattner97, UniProt10]
Alternate sequence: S → T; UniProt: (in Ref. 1, 2 and 3; AAA57877);
Active-Site 449
[Fowler83, UniProt11]
UniProt: Proton donor.
Sequence-Conflict 465
[Stokes85, Hall89, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 1 and 2);
Active-Site 512
[UniProt10a]
UniProt: Nucleophile; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 640
[Stokes85, Hall89, UniProt10]
Alternate sequence: T → S; UniProt: (in Ref. 1 and 2);
Sequence-Conflict 649
[Stokes85, Hall89, UniProt10]
Alternate sequence: R → P; UniProt: (in Ref. 1 and 2);
Sequence-Conflict 767
[Stokes85, Hall89, UniProt10]
Alternate sequence: M → MM; UniProt: (in Ref. 1 and 2);
Sequence-Conflict 891 -> 892
[Stokes85, Hall89, Blattner97, UniProt10]
Alternate sequence: ST → QA; UniProt: (in Ref. 1, 2 and 3; AAA57877);
Extrinsic-Sequence-Variant 976
[UniProt10]
Alternate sequence: W → C; UniProt: (improve activity);
Extrinsic-Sequence-Variant 978
[UniProt10]
Alternate sequence: S → G; UniProt: (improve activity);
Sequence-Conflict 1026
[Stokes85, Hall89, UniProt10]
Alternate sequence: S → T; UniProt: (in Ref. 1 and 2);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
10/20/97 Gene b3076 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10252; 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

Blattner97: Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997). "The complete genome sequence of Escherichia coli K-12." Science 277(5331);1453-74. PMID: 9278503

Calugaru95: Calugaru SV, Hall BG, Sinnott ML (1995). "Catalysis by the large subunit of the second beta-galactosidase of Escherichia coli in the absence of the small subunit." Biochem J 312 ( Pt 1);281-6. PMID: 7492325

Calugaru97: Calugaru SV, Krishnan S, Chany CJ, Hall BG, Sinnott ML (1997). "Larger increases in sensitivity to paracatalytic inactivation than in catalytic competence during experimental evolution of the second beta-galactosidase of Escherichia coli." Biochem J 325 ( Pt 1);117-21. PMID: 9224636

Campbell73: Campbell JH, Lengyel JA, Langridge J (1973). "Evolution of a second gene for beta-galactosidase in Escherichia coli." Proc Natl Acad Sci U S A 70(6);1841-5. PMID: 4124306

Elliott92: Elliott AC, K S, Sinnott ML, Smith PJ, Bommuswamy J, Guo Z, Hall BG, Zhang Y (1992). "The catalytic consequences of experimental evolution. Studies on the subunit structure of the second (ebg) beta-galactosidase of Escherichia coli, and on catalysis by ebgab, an experimental evolvant containing two amino acid substitutions." Biochem J 1992;282 ( Pt 1);155-64. PMID: 1540130

Fowler83: Fowler AV, Smith PJ (1983). "The active site regions of lacZ and ebg beta-galactosidases are homologous." J Biol Chem 258(17);10204-7. PMID: 6411710

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, 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."

Hall03: Hall BG (2003). "The EBG system of E. coli: origin and evolution of a novel beta-galactosidase for the metabolism of lactose." Genetica 118(2-3);143-56. PMID: 12868605

Hall89: Hall BG, Betts PW, Wootton JC (1989). "DNA sequence analysis of artificially evolved ebg enzyme and ebg repressor genes." Genetics 1989;123(4);635-48. PMID: 2515108

Hall99: Hall BG (1999). "Experimental evolution of Ebg enzyme provides clues about the evolution of catalysis and to evolutionary potential." FEMS Microbiol Lett 174(1);1-8. PMID: 10234816

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

Stokes85: Stokes HW, Betts PW, Hall BG (1985). "Sequence of the ebgA gene of Escherichia coli: comparison with the lacZ gene." Mol Biol Evol 2(6);469-77. PMID: 3939707

Stokes85a: Stokes HW, Hall BG (1985). "Sequence of the ebgR gene of Escherichia coli: evidence that the EBG and LAC operons are descended from a common ancestor." Mol Biol Evol 1985;2(6);478-83. PMID: 3939708

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

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

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

Beisel11: Beisel CL, Storz G (2011). "The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli." Mol Cell 41(3);286-97. PMID: 21292161

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615


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 Sat Dec 20, 2014, biocyc13.