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

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

Synonyms: yjiF

Regulation Summary Diagram: ?

Regulation summary diagram for iadA

Subunit composition of isoaspartyl dipeptidase = [IadA]8

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, 354°)
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: ?

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 [GOA01a, 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 [GOA01a]
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]

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.

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:

Km (μM)
β-aspartyl dipeptide

pH(opt): 6-9 [MartiArbona05]

Sequence Features

Protein sequence of IadA with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 68
UniProt: Zinc 1; via tele nitrogen; catalytic.
Metal-Binding-Site 70
UniProt: Zinc 1; via tele nitrogen; catalytic.
Protein-Segment 75 -> 77
UniProt: Substrate binding; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 77
[MartiArbona05a, MartiArbona05, UniProt11a]
E → D or Q: Reduces activity 100000-fold.
Amino-Acid-Sites-That-Bind 106
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 137
UniProt: Substrate.
Mutagenesis-Variant 137
[MartiArbona05a, MartiArbona05, UniProt11a]
Y → A or F: Reduces activity 1000-fold.
N6-carboxylysine-Modification 162
[MartiArbona05a, MartiArbona05, Jozic03, Thoden03, UniProt15]
UniProt: N6-carboxylysine.
Metal-Binding-Site 162
UniProt: Zinc 1; via carbamate group; catalytic.
Amino-Acid-Sites-That-Bind 169
UniProt: Substrate.
Mutagenesis-Variant 169
[MartiArbona05, UniProt11a]
[MartiArbona05, UniProt11a]
R → M: Loss of activity.
R → K: Reduces activity 1000-fold.
Metal-Binding-Site 201
UniProt: Zinc 2; via pros nitrogen; catalytic.
Metal-Binding-Site 230
UniProt: Zinc 2; via tele nitrogen; catalytic.
Amino-Acid-Sites-That-Bind 233
UniProt: Substrate.
Mutagenesis-Variant 233
[MartiArbona05, UniProt11a]
[MartiArbona05, UniProt11a]
R → M: Loss of activity.
R → K: Reduces activity 1000-fold.
Metal-Binding-Site 285
UniProt: Zinc 1; catalytic.
Active-Site 285
[Jozic03, UniProt14a]
UniProt: Proton acceptor.
Mutagenesis-Variant 285
[MartiArbona05, UniProt11a]
UniProt: Reduces activity 100000-fold.
Amino-Acid-Sites-That-Bind 289
UniProt: Substrate; via amide nitrogen and carbonyl oxygen.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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


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

GOA01a: 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

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

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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."

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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 19.0 on Fri Oct 9, 2015, biocyc14.