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MetaCyc Enzyme: aminopeptidase B

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

Synonyms: yfhI

Species: Escherichia coli K-12 substr. MG1655

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 [Suzuki01a]. 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, Suzuki01b]. 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 [Suzuki01b]. Reports disagree on whether [Suzuki01b] 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]

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

Gene-Reaction Schematic: ?

Instance reaction of [a dipeptide + H2O → 2 a standard α amino acid] (3.4.13.18):
i1: L-glutamyl-L-glutamate + H2O → 2 L-glutamate (3.4.13.7)

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

Credits:
Created in EcoCyc 04-Jun-2014 by Keseler I , SRI International
Imported from EcoCyc 16-Sep-2014 by Paley S , 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.

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

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 [Suzuki01b ]

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Activators (Unknown Mechanism): Mn2+ [Suzuki01b] , Ni2+ [Suzuki01b]

Inhibitors (Unknown Mechanism): EDTA [Suzuki01b]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-leucyl-glycine
13500.0
110.5
[Suzuki01b]
L-cysteinyl-glycine
7800.0
178.33
[Suzuki01b]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 41
[Kawula94, UniProt10]
Alternate sequence: P; UniProt: (in Ref. 5; U01827);
Sequence-Conflict 155
[Suzuki96, UniProt10]
Alternate sequence: 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: TRRRASCRTLLRTISKAGCISTARRLTVKRRLNSGLRALRDLVCAR; UniProt: (in Ref. 1; BAA12689);

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

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

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

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

Suzuki01a: 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

Suzuki01b: 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."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Wed Nov 26, 2014, BIOCYC13B.