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Escherichia coli K-12 substr. MG1655 Enzyme: N-acetyl-anhydromuramyl-L-alanine-amidase



Gene: ampD Accession Numbers: EG10041 (EcoCyc), b0110, ECK0109

Regulation Summary Diagram: ?

Summary:
ampD is a member of the ampDE operon. AmpD is a cytosolic N-acetylmuramyl-L-alanine amidase responsible for breakdown of anhMurNAc-tri-, tetra-, and pentapeptides to release the peptides for recycling [Holtje94, Jacobs94].

ampC encodes β-lactamase, though Escherichia coli lacks the ampR gene encoding the regulator for ampC expression. In Enterobacter cloacae the signal molecule for AmpR dependent induction of ampC expression was identified as anhMurNAc-pentapeptide [Dietz97]. Deletion from Escherichia coli of ampD resulted in overproduction of cephalosporinase when ampC and ampR were provided from Enterobacter cloacae due to the build-up of anhMurNAc-pentapeptide in the cytoplasm [Honore89, Dietz97]. Deletion from E. coli of ampD and ampE resulted in overexpression of AmpC β-lactamase when ampC and ampR were provided from Citrobacter freundii [Lindquist89].

In an ampD mutant, N-acetylmuramyl-L-alanyl-D-glutamylmesodiaminopimelic acid accumulates in the periplasm [Dietz96].

Reviews: [Bennett93, Park08]

Locations: cytosol

Map Position: [118,733 -> 119,284] (2.56 centisomes)
Length: 552 bp / 183 aa

Molecular Weight of Polypeptide: 20.536 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000380 , CGSC:30478 , EchoBASE:EB0039 , EcoGene:EG10041 , EcoliWiki:b0110 , ModBase:P13016 , OU-Microarray:b0110 , PortEco:ampD , PR:PRO_000022096 , Pride:P13016 , Protein Model Portal:P13016 , RefSeq:NP_414652 , RegulonDB:EG10041 , SMR:P13016 , String:511145.b0110 , Swiss-Model:P13016 , UniProt:P13016

Relationship Links: InterPro:IN-FAMILY:IPR002502 , Pfam:IN-FAMILY:PF01510 , Smart:IN-FAMILY:SM00644

In Paralogous Gene Group: 218 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009254 - peptidoglycan turnover Inferred from experiment [Jacobs94]
GO:0009253 - peptidoglycan catabolic process Inferred by computational analysis [GOA01a]
GO:0071555 - cell wall organization Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008745 - N-acetylmuramoyl-L-alanine amidase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Holtje94]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell structure murein
metabolism central intermediary metabolism murein turnover, recycling
regulation type of regulation unknown

Essentiality data for ampD 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 ? 16-Mar-2006 by Shearer A , SRI International


Enzymatic reaction of: N-acetylmuramyl-L-alanine amidase (N-acetyl-anhydromuramyl-L-alanine-amidase)

EC Number: 3.5.1.28

GlcNAc-1,6-anhMurNAc-L-Ala-γ-D-Glu-DAP-D-Ala + H2O <=> N-acetyl-β-D-glucosamine(anhydrous)-N-acetylmuramate + L-Ala-γ-D-Glu-meso-DAP-D-Ala

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: anhydromuropeptides recycling


Enzymatic reaction of: N-acetylmuramyl-L-alanine amidase (N-acetyl-anhydromuramyl-L-alanine-amidase)

EC Number: 3.5.1.28

a peptidoglycan + H2O <=> N-acetylmuramate + a peptide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

This reaction is reversible.


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 34
[UniProt10a]
UniProt: Zinc; catalytic; Non-Experimental Qualifier: by similarity;
Active-Site 116
[UniProt11]
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 154
[UniProt10a]
UniProt: Zinc; catalytic; Non-Experimental Qualifier: by similarity;
Amino-Acid-Site 162
[UniProt11]
UniProt: Transition state stabilizer; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 164
[UniProt10a]
UniProt: Zinc; catalytic; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0110 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10041; 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

Bennett93: Bennett PM, Chopra I (1993). "Molecular basis of beta-lactamase induction in bacteria." Antimicrob Agents Chemother 37(2);153-8. PMID: 8452343

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

Dietz96: Dietz H, Pfeifle D, Wiedemann B (1996). "Location of N-acetylmuramyl-L-alanyl-D-glutamylmesodiaminopimelic acid, presumed signal molecule for beta-lactamase induction, in the bacterial cell." Antimicrob Agents Chemother 40(9);2173-7. PMID: 8878601

Dietz97: Dietz H, Pfeifle D, Wiedemann B (1997). "The signal molecule for beta-lactamase induction in Enterobacter cloacae is the anhydromuramyl-pentapeptide." Antimicrob Agents Chemother 41(10);2113-20. PMID: 9333034

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."

Holtje94: Holtje JV, Kopp U, Ursinus A, Wiedemann B (1994). "The negative regulator of beta-lactamase induction AmpD is a N-acetyl-anhydromuramyl-L-alanine amidase." FEMS Microbiol Lett 122(1-2);159-64. PMID: 7958768

Honore89: Honore N, Nicolas MH, Cole ST (1989). "Regulation of enterobacterial cephalosporinase production: the role of a membrane-bound sensory transducer." Mol Microbiol 1989;3(8);1121-30. PMID: 2607970

Jacobs94: Jacobs C, Huang LJ, Bartowsky E, Normark S, Park JT (1994). "Bacterial cell wall recycling provides cytosolic muropeptides as effectors for beta-lactamase induction." EMBO J 1994;13(19);4684-94. PMID: 7925310

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

Lindquist89: Lindquist S, Galleni M, Lindberg F, Normark S (1989). "Signalling proteins in enterobacterial AmpC beta-lactamase regulation." Mol Microbiol 3(8);1091-102. PMID: 2691840

Park08: Park JT, Uehara T (2008). "How bacteria consume their own exoskeletons (turnover and recycling of cell wall peptidoglycan)." Microbiol Mol Biol Rev 72(2);211-27, table of contents. PMID: 18535144

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 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."

Other References Related to Gene Regulation

Raghavan11a: Raghavan R, Sage A, Ochman H (2011). "Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli." J Bacteriol 193(11);2871-4. PMID: 21460078


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 Fri Nov 28, 2014, biocyc12.