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Escherichia coli K-12 substr. MG1655 Enzyme: isoaspartyl dipeptidase



Gene: iadA Accession Numbers: G7925 (EcoCyc), b4328, ECK4319

Synonyms: yjiF

Regulation Summary Diagram: ?

Subunit composition of isoaspartyl dipeptidase = [IadA]8

Summary:
Isoaspartyl dipeptidase is an enzyme that breaks down β linkages, the peptide bonds that can form spontaneously between the side chain of an aspartate residue and another amino acid [Haley68, Gary95].

Crystal structures of the enzyme have been solved [Thoden03, Jozic03, MartiArbona05, MartiArbona05a]. Isoaspartyl dipeptidase is a binuclear metalloenzyme that forms an octamer comprised of a tetramer of dimers. The reaction mechanism was investigated utilizing a number of site-directed mutants in the active site [MartiArbona05, MartiArbona05a].

An iadA mutant has no apparent growth defect; however, it still contains ~30% of wild type isoaspartyl dipeptidase activity [Gary95]. This may be due to a second enzyme, IaaA.

IadA: "isoaspartyl dipeptidase A" [Gary95]

Locations: cytosol

Map Position: [4,556,377 <- 4,557,549] (98.2 centisomes)
Length: 1173 bp / 390 aa

Molecular Weight of Polypeptide: 41.084 kD (from nucleotide sequence), 41.0 kD (experimental) [Gary95 ]

Molecular Weight of Multimer: 320.0 kD (experimental) [Thoden03]

Unification Links: ASAP:ABE-0014195 , DIP:DIP-10001N , EchoBASE:EB2455 , EcoGene:EG12567 , EcoliWiki:b4328 , ModBase:P39377 , OU-Microarray:b4328 , PortEco:iadA , PR:PRO_000022980 , Pride:P39377 , Protein Model Portal:P39377 , RefSeq:NP_418748 , RegulonDB:G7925 , SMR:P39377 , String:511145.b4328 , UniProt:P39377

Relationship Links: InterPro:IN-FAMILY:IPR010229 , InterPro:IN-FAMILY:IPR011059 , PDB:Structure:1ONW , PDB:Structure:1ONX , PDB:Structure:1PO9 , PDB:Structure:1POJ , PDB:Structure:1POK , PDB:Structure:1YBQ , PDB:Structure:2AQO , PDB:Structure:2AQV , Pfam:IN-FAMILY:PF01979

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment [Jozic03, Thoden03]
GO:0008798 - beta-aspartyl-peptidase activity Inferred from experiment Inferred by computational analysis [GOA01, Haley68, Gary95]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0008237 - metallopeptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, Gary95]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

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

Essentiality data for iadA 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]

Credits:
Revised 25-May-2011 by Brito D
Last-Curated ? 21-Oct-2011 by Keseler I , SRI International


Enzymatic reaction of: isoaspartyl dipeptidase

EC Number: 3.4.19.-

β-aspartyl dipeptide + H2O <=> L-aspartate + a standard α amino acid

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Summary:
Initial purification of the enzyme was reported from E. coli B [Haley68].

Substrate specificity has been investigated; the enzyme acts primarily on a subset of isoaspartyl dipeptides [Gary95, MartiArbona05].

Cofactors or Prosthetic Groups: Zn2+ [MartiArbona05, Thoden03]

Kinetic Parameters:

Substrate
Km (μM)
Citations
β-aspartyl dipeptide
230.0
[MartiArbona05]

pH(opt): 6-9 [MartiArbona05]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 68
[UniProt10a]
UniProt: Zinc 1;
Metal-Binding-Site 70
[UniProt10a]
UniProt: Zinc 1;
Protein-Segment 75 -> 77
[UniProt10]
UniProt: Substrate binding; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 77
[MartiArbona05a, MartiArbona05, UniProt11]
Alternate sequence: E → Q; UniProt: Reduces activity 100000-fold.
Alternate sequence: E → D; UniProt: Reduces activity 100000-fold.
Amino-Acid-Sites-That-Bind 106
[UniProt10a]
UniProt: Substrate;
Mutagenesis-Variant 137
[MartiArbona05a, MartiArbona05, UniProt11]
Alternate sequence: Y → F; UniProt: Reduces activity 1000-fold.
Alternate sequence: Y → A; UniProt: Reduces activity 1000-fold.
Amino-Acid-Sites-That-Bind 137
[UniProt10a]
UniProt: Substrate;
N6-carboxylysine-Modification 162
[UniProt11a]
UniProt: N6-carboxylysine.
Metal-Binding-Site 162
[UniProt10a]
UniProt: Zinc 1;
Mutagenesis-Variant 169
[MartiArbona05, UniProt11]
Alternate sequence: R → M; UniProt: Loss of activity.
Alternate sequence: R → K; UniProt: Reduces activity 1000-fold.
Amino-Acid-Sites-That-Bind 169
[UniProt10a]
UniProt: Substrate;
Metal-Binding-Site 201
[UniProt10a]
UniProt: Zinc 2;
Metal-Binding-Site 230
[UniProt10a]
UniProt: Zinc 2;
Mutagenesis-Variant 233
[MartiArbona05, UniProt11]
Alternate sequence: R → M; UniProt: Loss of activity.
Alternate sequence: R → K; UniProt: Reduces activity 1000-fold.
Amino-Acid-Sites-That-Bind 233
[UniProt10a]
UniProt: Substrate;
Active-Site 285
[Jozic03, UniProt14]
UniProt: Proton acceptor.
Mutagenesis-Variant 285
[MartiArbona05, UniProt11]
Alternate sequence: D → A; UniProt: Reduces activity 100000-fold.
Metal-Binding-Site 285
[UniProt10a]
UniProt: Zinc 1;
Amino-Acid-Sites-That-Bind 289
[UniProt10a]
UniProt: Substrate; via amide nitrogen and carbonyl oxygen;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

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

Gary95: Gary JD, Clarke S (1995). "Purification and characterization of an isoaspartyl dipeptidase from Escherichia coli." J Biol Chem 270(8);4076-87. PMID: 7876157

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."

Haley68: Haley EE (1968). "Purification and properties of a beta-aspartyl peptidase from Escherichia coli." J Biol Chem 243(21);5748-52. PMID: 4880759

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

Jozic03: Jozic D, Kaiser JT, Huber R, Bode W, Maskos K (2003). "X-ray structure of isoaspartyl dipeptidase from E.coli: a dinuclear zinc peptidase evolved from amidohydrolases." J Mol Biol 332(1);243-56. PMID: 12946361

MartiArbona05: Marti-Arbona R, Fresquet V, Thoden JB, Davis ML, Holden HM, Raushel FM (2005). "Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli." Biochemistry 44(19);7115-24. PMID: 15882050

MartiArbona05a: Marti-Arbona R, Thoden JB, Holden HM, Raushel FM (2005). "Functional significance of Glu-77 and Tyr-137 within the active site of isoaspartyl dipeptidase." Bioorg Chem 33(6);448-58. PMID: 16289685

Thoden03: Thoden JB, Marti-Arbona R, Raushel FM, Holden HM (2003). "High-resolution X-ray structure of isoaspartyl dipeptidase from Escherichia coli." Biochemistry 42(17);4874-82. PMID: 12718528

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 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."


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 Dec 19, 2014, biocyc12.