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Escherichia coli K-12 substr. MG1655 Enzyme: galactose-1-epimerase



Gene: galM Accession Numbers: EG11698 (EcoCyc), b0756, ECK0745

Regulation Summary Diagram: ?

Summary:
Epimerization of the β anomer of galactose to the α anomer links the metabolism of lactose and galactose. Although the interconversion of α- and β-galactose is spontaneous in vitro, the reaction is largely dependent on the presence of galactose-1-epimerase in vivo [Bouffard94].

The enzymatic reaction appears to follow a bifunctional mechanism, a simultaneous attack of a nucleophilic and electrophilic group of the enzyme on the substrate. The reaction proceeds from the pyranose form via the open chain intermediate, producing either pyranose or furanose products [Wallenfels65a, Hucho71]. The histidine residues H104 and H175 are essential for catalytic activity [Beebe98]. A catalytic mechanism has been proposed [Beebe03b].

When overexpressed, a small amount of galactose-1-epimerase also appears in the periplasm and cell supernatant [Bouffard94].

galM is required for utilization of galactose generated from lactose, but is not required for utilization of extracellular galactose [Bouffard94].

Gene Citations: [Sur01, Queen81]

Locations: cytosol

Map Position: [787,020 <- 788,060] (16.96 centisomes)
Length: 1041 bp / 346 aa

Molecular Weight of Polypeptide: 38.19 kD (from nucleotide sequence), 38.0 kD (experimental) [Bouffard94 ]

Unification Links: ASAP:ABE-0002566 , CGSC:35171 , DIP:DIP-35901N , EchoBASE:EB1649 , EcoGene:EG11698 , EcoliWiki:b0756 , Mint:MINT-1249454 , ModBase:P0A9C3 , OU-Microarray:b0756 , PortEco:galM , Pride:P0A9C3 , Protein Model Portal:P0A9C3 , RefSeq:NP_415277 , RegulonDB:EG11698 , SMR:P0A9C3 , String:511145.b0756 , UniProt:P0A9C3

Relationship Links: InterPro:IN-FAMILY:IPR008183 , InterPro:IN-FAMILY:IPR011013 , InterPro:IN-FAMILY:IPR013458 , InterPro:IN-FAMILY:IPR014718 , InterPro:IN-FAMILY:IPR015443 , InterPro:IN-FAMILY:IPR018052 , Panther:IN-FAMILY:PTHR10091 , Pfam:IN-FAMILY:PF01263 , Prosite:IN-FAMILY:PS00545

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0033499 - galactose catabolic process via UDP-galactose Inferred from experiment [Bouffard94]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006012 - galactose metabolic process Inferred by computational analysis [GOA01a]
GO:0019318 - hexose metabolic process Inferred by computational analysis [UniProtGOA12, GOA01a]
Molecular Function: GO:0004034 - aldose 1-epimerase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Hucho71]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0030246 - carbohydrate binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, Wallenfels65]
GO:0005829 - cytosol [Wallenfels65]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for galM 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 ? 01-Jul-2009 by Keseler I , SRI International


Enzymatic reaction of: galactose-1-epimerase

Synonyms: galactose mutarotase, aldose-1-epimerase, mutarotase

β-D-galactose <=> α-D-galactose

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.

Alternative Substrates for α-D-galactose [Comment 5 ]: D-glucose [Wallenfels65a , Hucho71 ] , α-D-xylopyranose [Wallenfels65a , Hucho71 ] , α-lactose [Wallenfels65a , Hucho71 ] , D-fucose [Wallenfels65a , Hucho71 ]

In Pathways: galactose degradation I (Leloir pathway)

Summary:
The enzyme accepts a variety of substrates [Hucho71].

Inhibitors (Competitive): 2-deoxy-D-glucose [Hucho71] , D-mannose [Hucho71]

Kinetic Parameters:

Substrate
Km (μM)
Citations
α-D-galactose
4000.0
[Beebe03b]

pH(opt): 6.6 [Wallenfels65a]


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 79
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Active-Site 175
[UniProt10a]
UniProt: Proton donor; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 245
[UniProt10a]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Active-Site 309
[UniProt10a]
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0756 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11698; 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

Beebe03b: Beebe JA, Arabshahi A, Clifton JG, Ringe D, Petsko GA, Frey PA (2003). "Galactose mutarotase: pH dependence of enzymatic mutarotation." Biochemistry 42(15);4414-20. PMID: 12693937

Beebe98: Beebe JA, Frey PA (1998). "Galactose mutarotase: purification, characterization, and investigations of two important histidine residues." Biochemistry 37(42);14989-97. PMID: 9778377

Bouffard94: Bouffard GG, Rudd KE, Adhya SL (1994). "Dependence of lactose metabolism upon mutarotase encoded in the gal operon in Escherichia coli." J Mol Biol 1994;244(3);269-78. PMID: 7966338

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, 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."

Hucho71: Hucho F, Wallenfels K (1971). "The enzymatically catalyzed mutarotaton. The mechanism of action of mutarotase (aldose 1-epimerase) from Escherichia coli." Eur J Biochem 1971;23(3);489-96. PMID: 4945113

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

Queen81: Queen C, Rosenberg M (1981). "Differential translation efficiency explains discoordinate expression of the galactose operon." Cell 25(1);241-9. PMID: 7023696

Sur01: Sur R, Debnath D, Mukhopadhyay J, Parrack P (2001). "A novel RNA polymerase binding site upstream of the galactose promoter in Escherichia coli exhibits promoter-like activity." Eur J Biochem 268(8);2344-50. PMID: 11298753

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

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

UniProtGOA11a: 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."

Wallenfels65: Wallenfels K, Herrmann K (1965). "[Aldose-1-epimerase (mutarotase) from E. coli. Purification and preliminary molecular characterization]." Biochem Z 343(3);294-306. PMID: 5337146

Wallenfels65a: Wallenfels K, Hucho F, Herrmann K (1965). "[Enzymatically catalyzed mutarotation of aldoses. Studies on aldose-1-epimerase from E. coli]." Biochem Z 1965;343(3);307-25. PMID: 4290293

Other References Related to Gene Regulation

Aiba81: Aiba H, Adhya S, de Crombrugghe B (1981). "Evidence for two functional gal promoters in intact Escherichia coli cells." J Biol Chem 256(22);11905-10. PMID: 6271763

Aki97: Aki T, Adhya S (1997). "Repressor induced site-specific binding of HU for transcriptional regulation." EMBO J 16(12);3666-74. PMID: 9218807

Bennik00: Bennik MH, Pomposiello PJ, Thorne DF, Demple B (2000). "Defining a rob regulon in Escherichia coli by using transposon mutagenesis." J Bacteriol 182(13);3794-801. PMID: 10850996

Bown00: Bown JA, Kolb A, Meares CF, Ishihama A, Minchin SD, Busby SJ (2000). "Positioning of region 4 of the Escherichia coli RNA polymerase sigma(70) subunit by a transcription activator." J Bacteriol 182(10);2982-4. PMID: 10781573

Busby83: Busby S, Kotlarz D, Buc H (1983). "Deletion mutagenesis of the Escherichia coli galactose operon promoter region." J Mol Biol 167(2);259-74. PMID: 6408264

Choy97: Choy HE, Hanger RR, Aki T, Mahoney M, Murakami K, Ishihama A, Adhya S (1997). "Repression and activation of promoter-bound RNA polymerase activity by Gal repressor." J Mol Biol 272(3);293-300. PMID: 9325090

Colland99: Colland F, Fujita N, Kotlarz D, Bown JA, Meares CF, Ishihama A, Kolb A (1999). "Positioning of sigma(S), the stationary phase sigma factor, in Escherichia coli RNA polymerase-promoter open complexes." EMBO J 1999;18(14);4049-59. PMID: 10406809

Csiszovszki12: Csiszovszki Z, Lewis DE, Le P, Sneppen K, Semsey S (2012). "Specific contacts of the -35 region of the galP1 promoter by RNA polymerase inhibit GalR-mediated DNA looping repression." Nucleic Acids Res 40(20);10064-72. PMID: 22941635

El08: El Qaidi S, Allemand F, Oberto J, Plumbridge J (2008). "Repression of galP, the galactose transporter in Escherichia coli, requires the specific regulator of N-acetylglucosamine metabolism." Mol Microbiol. PMID: 19007420

Geanacopoulos01: Geanacopoulos M, Vasmatzis G, Zhurkin VB, Adhya S (2001). "Gal repressosome contains an antiparallel DNA loop." Nat Struct Biol 8(5);432-6. PMID: 11323719

Geanacopoulos97: Geanacopoulos M, Adhya S (1997). "Functional characterization of roles of GalR and GalS as regulators of the gal regulon." J Bacteriol 1997;179(1);228-34. PMID: 8982002

GuidiRontani84: Guidi-Rontani C, Danchin A, Ullmann A (1984). "Transcriptional control of polarity in Escherichia coli by cAMP." Mol Gen Genet 195(1-2);96-100. PMID: 6092868

Horvath10a: Horvath P, Hunziker A, Erdossy J, Krishna S, Semsey S (2010). "Timing of gene transcription in the galactose utilization system of Escherichia coli." J Biol Chem 285(49);38062-8. PMID: 20923764

Irani89: Irani M, Musso R, Adhya S (1989). "Cyclic-AMP-dependent switch in initiation of transcription from the two promoters of the Escherichia coli gal operon: identification and assay of 5'-triphosphate ends of mRNA by GTP:RNA guanyltransferase." J Bacteriol 1989;171(3);1623-30. PMID: 2537823

Ji11: Ji SC, Wang X, Yun SH, Jeon HJ, Lee HJ, Kim H, Lim HM (2011). "In vivo transcription dynamics of the galactose operon: a study on the promoter transition from P1 to P2 at onset of stationary phase." PLoS One 6(3);e17646. PMID: 21445255

Kar01: Kar S, Adhya S (2001). "Recruitment of HU by piggyback: a special role of GalR in repressosome assembly." Genes Dev 15(17);2273-81. PMID: 11544184

Lee08b: Lee HJ, Jeon HJ, Ji SC, Yun SH, Lim HM (2008). "Establishment of an mRNA gradient depends on the promoter: an investigation of polarity in gene expression." J Mol Biol 378(2);318-27. PMID: 18374359

Lewis99a: Lewis DE, Geanacopoulos M, Adhya S (1999). "Role of HU and DNA supercoiling in transcription repression: specialized nucleoprotein repression complex at gal promoters in Escherichia coli." Mol Microbiol 31(2);451-61. PMID: 10027963

Lia03: Lia G, Bensimon D, Croquette V, Allemand JF, Dunlap D, Lewis DE, Adhya S, Finzi L (2003). "Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping." Proc Natl Acad Sci U S A 100(20);11373-7. PMID: 14500788

Lyubchenko97: Lyubchenko YL, Shlyakhtenko LS, Aki T, Adhya S (1997). "Atomic force microscopic demonstration of DNA looping by GalR and HU." Nucleic Acids Res 25(4);873-6. PMID: 9016640

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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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