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Escherichia coli K-12 substr. MG1655 Enzyme: aminopeptidase B



Gene: pepB Accession Numbers: EG12310 (EcoCyc), b2523, ECK2520

Synonyms: yfhI

Regulation Summary Diagram: ?

Subunit composition of aminopeptidase B = [PepB]6
         aminopeptidase B = PepB

Summary:
Aminopeptidase B (PepB) belongs to the M17 family of metallopeptidases. PepB is one of four cysteinylglycinases in E. coli, along with aminopeptidase A, aminopeptidase N, and peptidase D [Suzuki01]. PepA, PepB or PepN can process the heptapeptide-nucleotide Microcin C after removal of the formyl group from fMet, thereby releasing the nonhydrolyzable aspartyl-adenylate that inhibits aspartyl-tRNA synthetase [Kazakov08].

Aminopeptidase B cleaves Cys-Gly, Leu-Gly, and Leu-Gly-Gly in vitro [Miller78a, Hermsdorf79, Suzuki01a]. A panel of 11 aminopeptidase substrates has been tested; the cleavage profile of PepB is Lys/Leu/Met/Gly > Pro/Tyr > Thr/Gln/Trp [Bhosale10].

Divalent cations, including some that are not effective stimulators of activity, stabilize aminopeptidase B against heat inactivation [Suzuki01a]. Reports disagree on whether [Suzuki01a] or not [Bhosale10] EDTA inhibits enzyme activity.

Overexpression of pepB partially rescues the growth defect of a pepN mutant in minimal media [Bhosale10].

Locations: cytosol

Map Position: [2,653,097 <- 2,654,380] (57.18 centisomes)
Length: 1284 bp / 427 aa

Molecular Weight of Polypeptide: 46.18 kD (from nucleotide sequence)

Molecular Weight of Multimer: 275.0 kD (experimental) [Bhosale10]

Unification Links: ASAP:ABE-0008305 , DIP:DIP-10455N , EchoBASE:EB2216 , EcoGene:EG12310 , EcoliWiki:b2523 , Mint:MINT-1236207 , ModBase:P37095 , OU-Microarray:b2523 , PortEco:pepB , PR:PRO_000023508 , Pride:P37095 , Protein Model Portal:P37095 , RefSeq:NP_417018 , RegulonDB:EG12310 , SMR:P37095 , String:511145.b2523 , UniProt:P37095

Relationship Links: InterPro:IN-FAMILY:IPR000819 , InterPro:IN-FAMILY:IPR008330 , InterPro:IN-FAMILY:IPR011356 , Panther:IN-FAMILY:PTHR11963:SF3 , Pfam:IN-FAMILY:PF00883 , Pfam:IN-FAMILY:PF12404 , Prints:IN-FAMILY:PR00481 , Prosite:IN-FAMILY:PS00631

In Paralogous Gene Group: 427 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006508 - proteolysis Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Bhosale10]
GO:0043171 - peptide catabolic process Inferred from experiment [Miller78a]
GO:0019538 - protein metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0004177 - aminopeptidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Bhosale10]
GO:0042802 - identical protein binding Inferred from experiment [Bhosale10]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11]
GO:0008235 - metalloexopeptidase activity Inferred by computational analysis [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:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Lasserre06]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]

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

Essentiality data for pepB 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:
Curated 15-Dec-2006 by Shearer A , SRI International
Revised 04-Jun-2014 by Keseler I , SRI International
Last-Curated ? 04-Jun-2014 by Keseler I , SRI International


Enzymatic reaction of: aminopeptidase

EC Number: 3.4.11.23

a protein + H2O <=> a standard α amino acid + a peptide

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.

Inhibitors (Unknown Mechanism): o-phenanthroline [Bhosale10]


Enzymatic reaction of: cysteinylglycine dipeptidase (aminopeptidase B)

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.

Alternative Substrates for L-cysteinyl-glycine: L-leucyl-glycine [Suzuki01a ]

Activators (Unknown Mechanism): Mn2+ [Suzuki01a] , Ni2+ [Suzuki01a]

Inhibitors (Unknown Mechanism): EDTA [Suzuki01a]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-leucyl-glycine
13500.0
110.5
[Suzuki01a]
L-cysteinyl-glycine
7800.0
178.33
[Suzuki01a]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 41
[Kawula94, UniProt10]
Alternate sequence: L → P; UniProt: (in Ref. 5; U01827);
Sequence-Conflict 155
[Suzuki96, UniProt10]
Alternate sequence: Q → P; UniProt: (in Ref. 1; BAA12689);
Metal-Binding-Site 195
[UniProt10a]
UniProt: Manganese 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 200
[UniProt10a]
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity;
Active-Site 207
[UniProt10a]
UniProt: Non-Experimental Qualifier: potential;
Metal-Binding-Site 218
[UniProt10a]
UniProt: Manganese 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 277
[UniProt10a]
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 279
[UniProt10a]
UniProt: Manganese 1; Non-Experimental Qualifier: by similarity;
Active-Site 281
[UniProt10a]
UniProt: Non-Experimental Qualifier: potential;
Sequence-Conflict 375 -> 427
[Suzuki96, UniProt10]
Alternate sequence: STAAGFLSHFVENYQQGWLHIDCSATYRKAPVEQWSAGATGLGVRTIANLLTA → TRRRASCRTLLRTISKAGCISTARRLTVKRRLNSGLRALRDLVCAR; UniProt: (in Ref. 1; BAA12689);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b2523 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12310; 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

Bhosale10: Bhosale M, Pande S, Kumar A, Kairamkonda S, Nandi D (2010). "Characterization of two M17 family members in Escherichia coli, Peptidase A and Peptidase B." Biochem Biophys Res Commun 395(1);76-81. PMID: 20350528

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

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."

Hermsdorf79: Hermsdorf CL, Simmonds S, Saunders A (1979). "Soluble di- and aminopeptidases in Escherichia K-12. Dispensible enzymes." Int J Pept Protein Res 13(2);146-51. PMID: 372108

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

Kawula94: Kawula TH, Lelivelt MJ (1994). "Mutations in a gene encoding a new Hsp70 suppress rapid DNA inversion and bgl activation, but not proU derepression, in hns-1 mutant Escherichia coli." J Bacteriol 176(3);610-9. PMID: 8300516

Kazakov08: Kazakov T, Vondenhoff GH, Datsenko KA, Novikova M, Metlitskaya A, Wanner BL, Severinov K (2008). "Escherichia coli peptidase A, B, or N can process translation inhibitor microcin C." J Bacteriol 190(7);2607-10. PMID: 18223070

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

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

Miller78a: Miller CG, Schwartz G (1978). "Peptidase-deficient mutants of Escherichia coli." J Bacteriol 135(2);603-11. PMID: 355237

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

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

Suzuki01a: Suzuki H, Kamatani S, Kumagai H (2001). "Purification and characterization of aminopeptidase B from Escherichia coli K-12." Biosci Biotechnol Biochem 65(7);1549-58. PMID: 11515538

Suzuki96: Suzuki H., Kim E., Yamamoto N., Hashimoto W., Yamamoto K., Kumagai H. (1996). "Mapping, cloning, and DNA sequencing of pepB gene which encodes peptidase B of Escherichia coli K-12." J. Ferment. Bioeng., Volume 82, page(s) 392-397.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."


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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 Sun Dec 21, 2014, biocyc14.