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Escherichia coli K-12 substr. MG1655 Enzyme: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase



Gene: mtn Accession Numbers: EG11090 (EcoCyc), b0159, ECK0158

Synonyms: pfs, yadA

Regulation Summary Diagram: ?

Subunit composition of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase = [Mtn]2
         5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase monomer = Mtn

Summary:
The mtn gene encodes 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase [Cornell98]. The enzyme catalyzes glycosidic bond cleavage in S-adenosylhomocysteine and 5'-methylthioadenosine substrates, with a higher Vmax toward 5'-methylthioadenosine [Della85]. Although MTA was thought to be the preferred substrate [ChoiRhee05], it was later shown that 5'-methylthioadenosine, S-adenosylhomocysteine and 5'-deoxyadenosine are hydrolyzed with similar catalytic efficiency [Farrar10]. The E. coli B enzyme has been characterized in detail [Ferro76, Della85, Allart98].

An mtn mutant is auxotrophic for biotin due to the accumulation of 5'-deoxyadenosine, which inhibits biotin synthase activity [ChoiRhee05].

Crystal structures of the enzyme bound to adenine (1.9 Å resolution) [Lee01b], formycin A (2.2 Å resolution) [Lee03], and 5'-methylthiotubercidin (2.0 Å resolution) [Lee03] are presented, and the implications of the structures with respect to catalysis are discussed [Lee01b, Lee03]. Additional crystal structures of the wild-type and mutant enzymes have been determined, allowing analysis of the conformational motions occuring during the catalytic cycle [Lee05b, Lee05c, Lee05d]. Conformational flexibility of the active site appears to be important for substrate specificity of the enzyme [Siu11]. Transition state analogue inhibitors of the enzyme have been designed and tested [Singh05, Singh05a, Longshaw10, Wang12b, Clinch12, Motley13].

Mtn has potential as a drug target [Cornell96, Gutierrez09].

Expression of mtn increases at the end of log phase growth and can be increased by salt stress [Kim06c].

Citations: [Schauder01, Shen10]

Locations: cytosol

Map Position: [178,455 <- 179,153] (3.85 centisomes)
Length: 699 bp / 232 aa

Molecular Weight of Polypeptide: 24.354 kD (from nucleotide sequence), 26.0 kD (experimental) [Cornell98 ]

Molecular Weight of Multimer: 52.0 kD (experimental) [Wang12b]

Unification Links: ASAP:ABE-0000545 , EchoBASE:EB1082 , EcoGene:EG11090 , EcoliWiki:b0159 , ModBase:P0AF12 , OU-Microarray:b0159 , PortEco:mtn , PR:PRO_000023306 , Pride:P0AF12 , Protein Model Portal:P0AF12 , RefSeq:NP_414701 , RegulonDB:EG11090 , SMR:P0AF12 , String:511145.b0159 , Swiss-Model:P0AF12 , UniProt:P0AF12

Relationship Links: InterPro:IN-FAMILY:IPR000845 , InterPro:IN-FAMILY:IPR010049 , InterPro:IN-FAMILY:IPR018017 , Panther:IN-FAMILY:PTHR21234 , Panther:IN-FAMILY:PTHR21234:SF6 , PDB:Structure:1JYS , PDB:Structure:1NC1 , PDB:Structure:1NC3 , PDB:Structure:1Y6Q , PDB:Structure:1Y6R , PDB:Structure:1Z5N , PDB:Structure:1Z5O , PDB:Structure:1Z5P , PDB:Structure:3O4V , Pfam:IN-FAMILY:PF01048

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0019284 - L-methionine biosynthetic process from S-adenosylmethionine Inferred from experiment Inferred by computational analysis [GOA06, Cornell98]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0009086 - methionine biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0009116 - nucleoside metabolic process Inferred by computational analysis [GOA01a]
GO:0009164 - nucleoside catabolic process Inferred by computational analysis [GOA01a]
GO:0019509 - L-methionine biosynthetic process from methylthioadenosine Inferred by computational analysis [UniProtGOA12, GOA01a]
GO:0033353 - S-adenosylmethionine cycle
Molecular Function: GO:0008782 - adenosylhomocysteine nucleosidase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Cornell98]
GO:0008930 - methylthioadenosine nucleosidase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Cornell98]
GO:0042803 - protein homodimerization activity Inferred from experiment [Wang12b]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for mtn 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]
Yes [Feist07, Comment 3]

Credits:
Last-Curated ? 23-Dec-2013 by Keseler I , SRI International


Enzymatic reaction of: S-adenosylhomocysteine nucleosidase

Synonyms: MTA/SAH nucleosidase, MTA/AdoHcy nucleosidase

EC Number: 3.2.2.9

S-ribosyl-L-homocysteine + adenine <=> S-adenosyl-L-homocysteine + H2O

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.

Alternative Products for S-adenosyl-L-homocysteine: 5'-ethylthioadenosine [Ferro76 ] , 5'-n-propylthioadenosine [Ferro76 ]

In Pathways: autoinducer AI-2 biosynthesis I , S-adenosyl-L-methionine cycle I

Summary:
Purification of the enzyme reported in [Della85, Allart98] was from E. coli B.

Inhibitors (Competitive): 5'-ethylthioadenosine [Ferro76] , 5'-n-propylthioadenosine [Ferro76]

Inhibitors (Unknown Mechanism): formycin A [Lee03] , S-tubercidinylhomocysteine [Della85] , 5'-methylthiotubercidin [Lee03, Della85] , S-formycinylhomocysteine [Della85] , 5'-chloroformycin [Della85] , 5'-methylthioformycin [Della85]

Kinetic Parameters:

Substrate
Km (μM)
Citations
S-adenosyl-L-homocysteine
4.3
[Della85]


Enzymatic reaction of: 5'-methylthioadenosine nucleosidase (5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase)

Synonyms: MTAN

EC Number: 3.2.2.16

S-methyl-5'-thioadenosine + H2O <=> S-methyl-5-thio-D-ribose + adenine

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: S-methyl-5'-thioadenosine degradation IV

Summary:
A range of inhibitors of the enzyme was tested in [Cornell96].

Purification of the enzyme reported in [Della85, Allart98] was from E. coli B.

Inhibitors (Competitive): 5'-(p-nitrophenyl)thioadenosine [Cornell96]

Inhibitors (Unknown Mechanism): 5'-n-propylthioadenosine [Cornell96] , S-adenosyl-L-homocysteine [Cornell98]

Kinetic Parameters:

Substrate
Km (μM)
Citations
S-methyl-5'-thioadenosine
0.45
[Cornell98]

T(opt): 37-45 °C [Cornell96]


Enzymatic reaction of: 5'-deoxyadenosine nucleosidase (5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase)

5'-deoxyadenosine + H2O <=> 5-deoxy-D-ribose + adenine

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.

Kinetic Parameters:

Substrate
Km (μM)
Citations
5'-deoxyadenosine
4.6
[Farrar10]


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 12
[Lee05d, UniProt11]
Alternate sequence: E → Q; UniProt: Loss of nucleosidase activity.
Active-Site 12
[UniProt10]
UniProt: Proton acceptor; Non-Experimental Qualifier: probable;
Amino-Acid-Sites-That-Bind 78
[UniProt10a]
UniProt: Substrate; via amide nitrogen;
Amino-Acid-Sites-That-Bind 152
[UniProt10a]
UniProt: Substrate; via amide nitrogen and carbonyl oxygen;
Protein-Segment 173 -> 174
[UniProt10]
UniProt: Substrate binding; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 197
[Lee05d, UniProt11]
Alternate sequence: D → N; UniProt: Alters the hydrogen bond network in the active site.
Amino-Acid-Sites-That-Bind 197
[UniProt10a]
UniProt: Substrate;
Sequence-Conflict 212 -> 232
[Wurgler90, UniProt10a]
Alternate sequence: AVAAKQSSLMVESLVQKLAHG → LLPLNSPA; UniProt: (in Ref. 1; AAA23678/AAA24322);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0159 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11090; confirmed by SwissProt match.


References

Allart98: Allart B, Gatel M, Guillerm D, Guillerm G (1998). "The catalytic mechanism of adenosylhomocysteine/methylthioadenosine nucleosidase from Escherichia coli--chemical evidence for a transition state with a substantial oxocarbenium character." Eur J Biochem 256(1);155-62. PMID: 9746359

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

Challand09: Challand MR, Ziegert T, Douglas P, Wood RJ, Kriek M, Shaw NM, Roach PL (2009). "Product inhibition in the radical S-adenosylmethionine family." FEBS Lett 583(8);1358-62. PMID: 19328201

ChoiRhee05: Choi-Rhee E, Cronan JE (2005). "A nucleosidase required for in vivo function of the S-adenosyl-L-methionine radical enzyme, biotin synthase." Chem Biol 12(5);589-93. PMID: 15911379

Clinch12: Clinch K, Evans GB, Frohlich RF, Gulab SA, Gutierrez JA, Mason JM, Schramm VL, Tyler PC, Woolhouse AD (2012). "Transition state analogue inhibitors of human methylthioadenosine phosphorylase and bacterial methylthioadenosine/S-adenosylhomocysteine nucleosidase incorporating acyclic ribooxacarbenium ion mimics." Bioorg Med Chem 20(17);5181-7. PMID: 22854195

Cornell96: Cornell KA, Swarts WE, Barry RD, Riscoe MK (1996). "Characterization of recombinant Eschericha coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase: analysis of enzymatic activity and substrate specificity." Biochem Biophys Res Commun 228(3);724-32. PMID: 8941345

Cornell98: Cornell KA, Riscoe MK (1998). "Cloning and expression of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase: identification of the pfs gene product." Biochim Biophys Acta 1396(1);8-14. PMID: 9524204

Della85: Della Ragione F, Porcelli M, Carteni-Farina M, Zappia V, Pegg AE (1985). "Escherichia coli S-adenosylhomocysteine/5'-methylthioadenosine nucleosidase. Purification, substrate specificity and mechanism of action." Biochem J 232(2);335-41. PMID: 3911944

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

Farrar10: Farrar CE, Siu KK, Howell PL, Jarrett JT (2010). "Biotin synthase exhibits burst kinetics and multiple turnovers in the absence of inhibition by products and product-related biomolecules." Biochemistry 49(46);9985-96. PMID: 20961145

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

Ferro76: Ferro AJ, Barrett A, Shapiro SK (1976). "Kinetic properties and the effect of substrate analogues on 5'-methylthioadenosine nucleosidase from Escherichia coli." Biochim Biophys Acta 438(2);487-94. PMID: 782530

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."

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

Gutierrez09: Gutierrez JA, Crowder T, Rinaldo-Matthis A, Ho MC, Almo SC, Schramm VL (2009). "Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing." Nat Chem Biol 5(4):251-7. PMID: 19270684

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

Kim06c: Kim Y, Lew CM, Gralla JD (2006). "Escherichia coli pfs transcription: regulation and proposed roles in autoinducer-2 synthesis and purine excretion." J Bacteriol 188(21);7457-63. PMID: 16950920

Lee01b: Lee JE, Cornell KA, Riscoe MK, Howell PL (2001). "Structure of E. coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase reveals similarity to the purine nucleoside phosphorylases." Structure (Camb) 9(10);941-53. PMID: 11591349

Lee03: Lee JE, Cornell KA, Riscoe MK, Howell PL (2003). "Structure of Escherichia coli 5'-methylthioadenosine/ S-adenosylhomocysteine nucleosidase inhibitor complexes provide insight into the conformational changes required for substrate binding and catalysis." J Biol Chem 278(10);8761-70. PMID: 12496243

Lee05b: Lee JE, Singh V, Evans GB, Tyler PC, Furneaux RH, Cornell KA, Riscoe MK, Schramm VL, Howell PL (2005). "Structural rationale for the affinity of pico- and femtomolar transition state analogues of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase." J Biol Chem 280(18);18274-82. PMID: 15746096

Lee05c: Lee JE, Luong W, Huang DJ, Cornell KA, Riscoe MK, Howell PL (2005). "Mutational analysis of a nucleosidase involved in quorum-sensing autoinducer-2 biosynthesis." Biochemistry 44(33);11049-57. PMID: 16101288

Lee05d: Lee JE, Smith GD, Horvatin C, Huang DJ, Cornell KA, Riscoe MK, Howell PL (2005). "Structural snapshots of MTA/AdoHcy nucleosidase along the reaction coordinate provide insights into enzyme and nucleoside flexibility during catalysis." J Mol Biol 352(3);559-74. PMID: 16109423

Longshaw10: Longshaw AI, Adanitsch F, Gutierrez JA, Evans GB, Tyler PC, Schramm VL (2010). "Design and synthesis of potent "sulfur-free" transition state analogue inhibitors of 5'-methylthioadenosine nucleosidase and 5'-methylthioadenosine phosphorylase." J Med Chem 53(18);6730-46. PMID: 20718423

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

Motley13: Motley MW, Schramm VL, Schwartz SD (2013). "Conformational freedom in tight binding enzymatic transition-state analogues." J Phys Chem B 117(33);9591-7. PMID: 23895500

Schauder01: Schauder S, Shokat K, Surette MG, Bassler BL (2001). "The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum-sensing signal molecule." Mol Microbiol 41(2);463-76. PMID: 11489131

Shen10: Shen Y, Liu J, Estiu G, Isin B, Ahn YY, Lee DS, Barabasi AL, Kapatral V, Wiest O, Oltvai ZN (2010). "Blueprint for antimicrobial hit discovery targeting metabolic networks." Proc Natl Acad Sci U S A 107(3);1082-7. PMID: 20080587

Singh05: Singh V, Evans GB, Lenz DH, Mason JM, Clinch K, Mee S, Painter GF, Tyler PC, Furneaux RH, Lee JE, Howell PL, Schramm VL (2005). "Femtomolar transition state analogue inhibitors of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Escherichia coli." J Biol Chem 280(18);18265-73. PMID: 15749708

Singh05a: Singh V, Lee JE, Nunez S, Howell PL, Schramm VL (2005). "Transition state structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Escherichia coli and its similarity to transition state analogues." Biochemistry 44(35);11647-59. PMID: 16128565

Siu11: Siu KK, Asmus K, Zhang AN, Horvatin C, Li S, Liu T, Moffatt B, Woods VL, Howell PL (2011). "Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases." J Struct Biol 173(1);86-98. PMID: 20554051

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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.

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."

Wang12b: Wang S, Lim J, Thomas K, Yan F, Angeletti RH, Schramm VL (2012). "A complex of methylthioadenosine/S-adenosylhomocysteine nucleosidase, transition state analogue, and nucleophilic water identified by mass spectrometry." J Am Chem Soc 134(3);1468-70. PMID: 22239413

Wurgler90: Wurgler SM, Richardson CC (1990). "Structure and regulation of the gene for dGTP triphosphohydrolase from Escherichia coli." Proc Natl Acad Sci U S A 87(7);2740-4. PMID: 2157212


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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 Fri Dec 19, 2014, BIOCYC14B.