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Escherichia coli K-12 substr. MG1655 Enzyme: aminopeptidase A/I and DNA-binding transcriptional repressor



Gene: pepA Accession Numbers: EG10694 (EcoCyc), b4260, ECK4253

Synonyms: carP, xerB, cytosol aminopeptidase, leucine aminopeptidase

Regulation Summary Diagram: ?

Subunit composition of aminopeptidase A/I and DNA-binding transcriptional repressor = [PepA]6
         aminopeptidase A/I = PepA

Summary:
Aminopeptidase A/I is a Peptidase that binds DNA and controls the transcription of the operon involved in the synthesis of carbamoyl phosphate, which is an intermediate related to the pyrimidine nucleotide pathway [Charlier95, Devroede04, Devroede06, Minh09]. This protein also is required for maintenance of plasmid monomers, which is critical for proper plasmid segregation [Miller78, Stirling89, Reijns05, Paul04, Minh09].

Aminopeptidase A/I is a part of the site-specific recombination system required to decatenate the plasmids ColE1 and pSC101, maintaining them as monomers [Flinn89, Stirling89, Colloms96]. Aminopeptidase A/I is responsible for coordinating DNA strands during recombination, pairing cer sites in ColE1 plasmids and allowing the formation of Holliday junctions [Gourlay04, Guhathakurta95, McCulloch94]. Aminopeptidase A/I, along with ArgR, may be involved in blocking trans-recombination, thus preventing the formation of new catenated plasmids during recombination [Guhathakurta96]. This overall role in site-specific recombination is independent of Aminopeptidase A/I's peptidase activity [McCulloch94a].

Aminopeptidase A/I binds specifically to several DNA regions, including the the regulatory region before the carAp promoter [Charlier95]. This regulatory region wraps around the aminopeptidase A/I hexamer, effectively cutting the distance between the upstream IHF binding site and the transcriptional start site by 235 base pairs, as well as presumably blocking the intervening transcription factor binding sites [Minh09].

If Aminopeptidase A/I is not present to bind to the carAB control region, pyrimidine regulation of that promoter is impaired [Charlier95a]. This transcriptional repression requires additional protein factors apart from Aminopeptidase A/I binding to DNA [Charlier00].

Aminopeptidase A/I comprises a hexamer of PepA monomers [Strater99].

Review: [Commichau08]

Locations: cytosol

Map Position: [4,482,463 <- 4,483,974] (96.61 centisomes)
Length: 1512 bp / 503 aa

Molecular Weight of Polypeptide: 54.88 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013953 , CGSC:30215 , DIP:DIP-47860N , EchoBASE:EB0688 , EcoGene:EG10694 , EcoliWiki:b4260 , ModBase:P68767 , OU-Microarray:b4260 , PortEco:pepA , Pride:P68767 , Protein Model Portal:P68767 , RefSeq:NP_418681 , RegulonDB:EG10694 , SMR:P68767 , String:511145.b4260 , UniProt:P68767

Relationship Links: InterPro:IN-FAMILY:IPR000819 , InterPro:IN-FAMILY:IPR008283 , InterPro:IN-FAMILY:IPR011356 , InterPro:IN-FAMILY:IPR023042 , Panther:IN-FAMILY:PTHR11963:SF3 , PDB:Structure:1GYT , Pfam:IN-FAMILY:PF00883 , Pfam:IN-FAMILY:PF02789 , Prints:IN-FAMILY:PR00481 , Prosite:IN-FAMILY:PS00631

In Paralogous Gene Group: 427 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006276 - plasmid maintenance Inferred from experiment [Stirling89]
GO:0006351 - transcription, DNA-templated Inferred from experiment [Stirling89, Gourlay04]
GO:0031564 - transcription antitermination Inferred from experiment [Charlier95]
GO:0042150 - plasmid recombination Inferred from experiment [Stirling89]
GO:0043171 - peptide catabolic process Inferred from experiment [Miller78]
GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0019538 - protein metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0001073 - DNA binding transcription antitermination factor activity Inferred from experiment [Charlier95]
GO:0003677 - DNA binding Inferred from experiment [Charlier95]
GO:0004177 - aminopeptidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Stirling89]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11]
GO:0008235 - metalloexopeptidase activity Inferred by computational analysis [GOA06, GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0030145 - manganese ion binding Inferred by computational analysis [GOA06, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005737 - cytoplasm Inferred by computational analysis [GOA06, GOA01]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer DNA related DNA recombination
information transfer protein related turnover, degradation
information transfer RNA related Transcription related
metabolism degradation of macromolecules proteins/peptides/glycopeptides

DNA binding site length: 27 base-pairs

Symmetry: Inverted Repeat

Regulated Transcription Units (2 total): ?

Notes:

Essentiality data for pepA 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]

Enzymatic reaction of: aminopeptidase

EC Number: 3.4.11.1

amino acids(n) + H2O <=> a standard α amino acid + amino acids(n-1)

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 physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: Zn2+ [Strater99a]

Activators (Unknown Mechanism): hydrogen carbonate [Strater99a]


Enzymatic reaction of: cysteinylglycine dipeptidase (aminopeptidase A/I and DNA-binding transcriptional repressor)

L-cysteinyl-glycine + H2O <=> L-cysteine + glycine

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.


Sequence Features

Feature Class Location Citations Comment
Acetylation-Modification 134
[Yu08]
 
Metal-Binding-Site 270
[UniProt10a]
UniProt: Manganese 2; Non-Experimental Qualifier: probable;
Metal-Binding-Site 275
[UniProt10a]
UniProt: Manganese 1; Non-Experimental Qualifier: probable;
Active-Site 282
[UniProt10a]
UniProt: Non-Experimental Qualifier: potential;
Metal-Binding-Site 293
[UniProt10a]
UniProt: Manganese 2; Non-Experimental Qualifier: probable;
Metal-Binding-Site 352
[UniProt10a]
UniProt: Manganese 1; Non-Experimental Qualifier: probable;
Mutagenesis-Variant 354
[McCulloch94a, UniProt11]
Alternate sequence: E → A; UniProt: Loss of activity.
Metal-Binding-Site 354
[UniProt10a]
UniProt: Manganese 1; Non-Experimental Qualifier: probable;
Active-Site 356
[UniProt10a]
UniProt: Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4260 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10694; 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

Charlier00: Charlier D, Kholti A, Huysveld N, Gigot D, Maes D, Thia-Toong TL, Glansdorff N (2000). "Mutational analysis of Escherichia coli PepA, a multifunctional DNA-binding aminopeptidase." J Mol Biol 302(2);411-26. PMID: 10970742

Charlier95: Charlier D, Hassanzadeh G, Kholti A, Gigot D, Pierard A, Glansdorff N (1995). "carP, involved in pyrimidine regulation of the Escherichia coli carbamoylphosphate synthetase operon encodes a sequence-specific DNA-binding protein identical to XerB and PepA, also required for resolution of ColEI multimers." J Mol Biol 1995;250(4);392-406. PMID: 7616564

Charlier95a: Charlier D, Gigot D, Huysveld N, Roovers M, Pierard A, Glansdorff N (1995). "Pyrimidine regulation of the Escherichia coli and Salmonella typhimurium carAB operons: CarP and integration host factor (IHF) modulate the methylation status of a GATC site present in the control region." J Mol Biol 1995;250(4);383-91. PMID: 7616563

Colloms96: Colloms SD, McCulloch R, Grant K, Neilson L, Sherratt DJ (1996). "Xer-mediated site-specific recombination in vitro." EMBO J 15(5);1172-81. PMID: 8605888

Commichau08: Commichau FM, Stulke J (2008). "Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression." Mol Microbiol 67(4);692-702. PMID: 18086213

Devroede04: Devroede N, Thia-Toong TL, Gigot D, Maes D, Charlier D (2004). "Purine and pyrimidine-specific repression of the Escherichia coli carAB operon are functionally and structurally coupled." J Mol Biol 336(1);25-42. PMID: 14741201

Devroede06: Devroede N, Huysveld N, Charlier D (2006). "Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase." J Bacteriol 188(9);3236-45. PMID: 16621816

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

Flinn89: Flinn H, Burke M, Stirling CJ, Sherratt DJ (1989). "Use of gene replacement to construct Escherichia coli strains carrying mutations in two genes required for stability of multicopy plasmids." J Bacteriol 171(4);2241-3. PMID: 2649493

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, 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."

Gourlay04: Gourlay SC, Colloms SD (2004). "Control of Cre recombination by regulatory elements from Xer recombination systems." Mol Microbiol 52(1);53-65. PMID: 15049810

Guhathakurta95: Guhathakurta A, Summers D (1995). "Involvement of ArgR and PepA in the pairing of ColE1 dimer resolution sites." Microbiology 141 ( Pt 5);1163-71. PMID: 7773410

Guhathakurta96: Guhathakurta A, Viney I, Summers D (1996). "Accessory proteins impose site selectivity during ColE1 dimer resolution." Mol Microbiol 20(3);613-20. PMID: 8736540

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

McCulloch94: McCulloch R, Coggins LW, Colloms SD, Sherratt DJ (1994). "Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo." EMBO J 13(8);1844-55. PMID: 8168483

McCulloch94a: McCulloch R, Burke ME, Sherratt DJ (1994). "Peptidase activity of Escherichia coli aminopeptidase A is not required for its role in Xer site-specific recombination." Mol Microbiol 12(2);241-51. PMID: 8057849

Miller78: Miller CG, Schwartz G (1978). "Peptidase-deficient mutants of Escherichia coli." J Bacteriol 135(2);603-11. PMID: 355237

Minh09: Minh PN, Devroede N, Massant J, Maes D, Charlier D (2009). "Insights into the architecture and stoichiometry of Escherichia coli PepA*DNA complexes involved in transcriptional control and site-specific DNA recombination by atomic force microscopy." Nucleic Acids Res 37(5):1463-76. PMID: 19136463

Paul04: Paul S, Summers D (2004). "ArgR and PepA, accessory proteins for XerCD-mediated resolution of ColE1 dimers, are also required for stable maintenance of the P1 prophage." Plasmid 52(1);63-8. PMID: 15212893

Reijns05: Reijns M, Lu Y, Leach S, Colloms SD (2005). "Mutagenesis of PepA suggests a new model for the Xer/cer synaptic complex." Mol Microbiol 57(4);927-41. PMID: 16091035

Stirling89: Stirling CJ, Colloms SD, Collins JF, Szatmari G, Sherratt DJ (1989). "xerB, an Escherichia coli gene required for plasmid ColE1 site-specific recombination, is identical to pepA, encoding aminopeptidase A, a protein with substantial similarity to bovine lens leucine aminopeptidase." EMBO J 8(5);1623-7. PMID: 2670557

Strater99: Strater N, Sherratt DJ, Colloms SD (1999). "X-ray structure of aminopeptidase A from Escherichia coli and a model for the nucleoprotein complex in Xer site-specific recombination." EMBO J 18(16);4513-22. PMID: 10449417

Strater99a: Strater N, Sun L, Kantrowitz ER, Lipscomb WN (1999). "A bicarbonate ion as a general base in the mechanism of peptide hydrolysis by dizinc leucine aminopeptidase." Proc Natl Acad Sci U S A 96(20);11151-5. PMID: 10500145

Suzuki01: Suzuki H, Kamatani S, Kim ES, Kumagai H (2001). "Aminopeptidases A, B, and N and dipeptidase D are the four cysteinylglycinases of Escherichia coli K-12." J Bacteriol 183(4);1489-90. PMID: 11157967

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.

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

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508


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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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