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Escherichia coli K-12 substr. MG1655 Enzyme: AMP nucleosidase



Gene: amn Accession Numbers: EG10039 (EcoCyc), b1982, ECK1977

Regulation Summary Diagram: ?

Subunit composition of AMP nucleosidase = [Amn]6

Summary:
AMP nucleosidase is the primary intracellular mechanism for AMP degradation in E. coli. The adenine which is produced in the nucleosidase reaction can be reincorporated into the purine pool [Leung80, Leung89]. The enzyme catalyzes the hydrolysis of the N-glycosidic bond of AMP producing produce adenine and D-ribose 5-phosphate.

An amp mutant carrying a small deletion has been used to analyze structure-function relationships [KvalnesKrick93a]. The reaction mechanism has been studied by analysis of kinetic isotope effects [Parkin84, Parkin87, Parkin91]. Amn is a member of the nucleoside phosphorylase (nucleosidase) family I which includes, for example, E. coli DeoD and Udp [Mushegian94, Zhang04i].

Expression of amp is induced under limiting phosphate conditions [Leung89]. Expression of amn is activated by PhoB [Baek06].

Crystal structures of AMP nucleosidase in the unliganded form and in complex with formycin 5'-monophosphate or inorganic phosphate have been determined [Giranda89, Zhang04i]. The enzyme is a homohexamer [Giranda89, Zhang04i], and each monomer consists of a catalytic and a proposed regulatory domain. The catalytic domain resembles nucleoside phosphorylases [Zhang04i, Mushegian94]. The enzyme appears to be found only in prokaryotes and is of interest as an antimicrobial drug target [Zhang04i].

In E. coli knockout of amn by mutation caused an over 30% increase in ATP levels across its viable temperature range and the mutants also had significantly higher viability at low temperatures than wild-type cells [Morrison08]. These data, along with pathway engineering studies [Parry11], suggest that Amn may be important in the regulation of intracellular pools of adenine nucleotides.

Gene Citations: [Leung84]

Locations: cytosol

Map Position: [2,053,085 -> 2,054,539] (44.25 centisomes)
Length: 1455 bp / 484 aa

Molecular Weight of Polypeptide: 53.995 kD (from nucleotide sequence), 52.0 kD (experimental) [Leung80 ]

Molecular Weight of Multimer: 280 kD (experimental) [Leung80]

pI: 6.56

Unification Links: ASAP:ABE-0006579 , CGSC:17764 , EchoBASE:EB0037 , EcoGene:EG10039 , EcoliWiki:b1982 , ModBase:P0AE12 , OU-Microarray:b1982 , PortEco:amn , PR:PRO_000022094 , Pride:P0AE12 , Protein Model Portal:P0AE12 , RefSeq:NP_416489 , RegulonDB:EG10039 , SMR:P0AE12 , String:511145.b1982 , Swiss-Model:P0AE12 , UniProt:P0AE12

Relationship Links: InterPro:IN-FAMILY:IPR000845 , InterPro:IN-FAMILY:IPR011271 , InterPro:IN-FAMILY:IPR018017 , InterPro:IN-FAMILY:IPR018953 , Panther:IN-FAMILY:PTHR21234 , PDB:Structure:1T8R , PDB:Structure:1T8S , PDB:Structure:1T8W , PDB:Structure:1T8Y , Pfam:IN-FAMILY:PF01048 , Pfam:IN-FAMILY:PF10423

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0009116 - nucleoside metabolic process Inferred by computational analysis [GOA01a]
GO:0044209 - AMP salvage Inferred by computational analysis [UniProtGOA12, GOA01a]
Molecular Function: GO:0008714 - AMP nucleosidase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Leung80]
GO:0042802 - identical protein binding Inferred from experiment [Leung80, Zhang04i]
GO:0003824 - catalytic activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for amn 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 ? 08-Dec-2011 by Fulcher C , SRI International


Enzymatic reaction of: AMP nucleosidase

Synonyms: AMP phosphoribohydrolase, adenosine monophosphate nucleosidase

EC Number: 3.2.2.4

AMP + H2O <=> D-ribofuranose 5-phosphate + 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. [Parkin87]

In Pathways: adenosine nucleotides degradation III

Activators (Allosteric): MgATP2- [Schramm78, Leung80]

Inhibitors (Allosteric): phosphate [Comment 5]

Inhibitors (Competitive): formycin 5'-PO4 [Comment 6]

Kinetic Parameters:

Substrate
Km (μM)
Citations
AMP
120.0
[Schramm78, BRENDA14]
AMP
15000.0
[Parkin84, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 300 -> 302
[Leung89, UniProt10a]
Alternate sequence: WLM → CY; UniProt: (in Ref. 1; AAA23433);
Sequence-Conflict 311 -> 316
[Leung89, UniProt10a]
Alternate sequence: ESQAIG → KVRPLA; UniProt: (in Ref. 1; AAA23433);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1982 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10039; 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

Baek06: Baek JH, Lee SY (2006). "Novel gene members in the Pho regulon of Escherichia coli." FEMS Microbiol Lett 264(1);104-9. PMID: 17020555

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

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

Giranda89: Giranda VL, Berman HM, Schramm VL (1989). "Crystallographic quaternary structural analysis of AMP nucleosidases from Escherichia coli and Azotobacter vinelandii." J Biol Chem 264(26);15674-80. PMID: 2670945

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."

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

KvalnesKrick93a: Kvalnes-Krick K, Labdon JE, Ma X, Nieves E, Schramm VL (1993). "Mutagenic analysis of AMP nucleosidase from Escherichia coli. Deletion of a region similar to AMP deaminase and peptide characterization by mass spectrometry." J Biol Chem 268(12);8717-26. PMID: 8473316

Leung80: Leung HB, Schramm VL (1980). "Adenylate degradation in Escherichia coli. The role of AMP nucleosidase and properties of the purified enzyme." J Biol Chem 1980;255(22);10867-74. PMID: 7000783

Leung84: Leung HB, Schramm VL (1984). "The structural gene for AMP nucleosidase. Mapping, cloning, and overproduction of the enzyme." J Biol Chem 259(11);6972-8. PMID: 6327703

Leung89: Leung HB, Kvalnes-Krick KL, Meyer SL, deRiel JK, Schramm VL (1989). "Structure and regulation of the AMP nucleosidase gene (amn) from Escherichia coli." Biochemistry 1989;28(22);8726-33. PMID: 2690948

Morrison08: Morrison BA, Shain DH (2008). "An AMP nucleosidase gene knockout in Escherichia coli elevates intracellular ATP levels and increases cold tolerance." Biol Lett 4(1);53-6. PMID: 18029299

Mushegian94: Mushegian AR, Koonin EV (1994). "Unexpected sequence similarity between nucleosidases and phosphoribosyltransferases of different specificity." Protein Sci 3(7);1081-8. PMID: 7920254

Parkin84: Parkin DW, Schramm VL (1984). "Effects of allosteric activation on the primary and secondary kinetic isotope effects for three AMP nucleosidases." J Biol Chem 259(15);9418-25. PMID: 6378909

Parkin87: Parkin DW, Schramm VL (1987). "Catalytic and allosteric mechanism of AMP nucleosidase from primary, beta-secondary, and multiple heavy atom kinetic isotope effects." Biochemistry 26(3);913-20. PMID: 3552037

Parkin91: Parkin DW, Mentch F, Banks GA, Horenstein BA, Schramm VL (1991). "Transition-state analysis of a Vmax mutant of AMP nucleosidase by the application of heavy-atom kinetic isotope effects." Biochemistry 30(18);4586-94. PMID: 2021651

Parry11: Parry BR, Shain DH (2011). "Manipulations of AMP metabolic genes increase growth rate and cold tolerance in Escherichia coli: implications for psychrophilic evolution." Mol Biol Evol 28(7);2139-45. PMID: 21300985

Schramm78: Schramm VL, Leung HB (1978). "Adenosine monophosphate nucleosidase from Azotobacter vinelandii and Escherichia coli." Methods Enzymol 1978;51;263-70. PMID: 357895

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

Zhang04i: Zhang Y, Cottet SE, Ealick SE (2004). "Structure of Escherichia coli AMP nucleosidase reveals similarity to nucleoside phosphorylases." Structure (Camb) 12(8);1383-94. PMID: 15296732


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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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