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Protein

Isoaspartyl dipeptidase

Gene

iadA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the hydrolytic cleavage of a subset of L-isoaspartyl (L-beta-aspartyl) dipeptides. Used to degrade proteins damaged by L-isoaspartyl residues formation. The best substrate for the enzyme reported thus far is iso-Asp-Leu.4 Publications

Cofactori

Zn2+3 Publications, Co2+3 PublicationsNote: Binds 2 Zn2+ ions per subunit. Has highest activity with Zn2+ ions, but is also active with Co2+ ions.3 Publications

Enzyme regulationi

P-hydroxymercuribenzoate causes a slight inhibition (8 to 17 %). Iodoacetamide, o-iodosobenzoate and ammonium persulfate do not inhibit the enzyme activity.1 Publication

Kineticsi

  1. KM=0.81 mM for beta-aspartylleucine (at pH 8.0)1 Publication

    pH dependencei

    Optimum pH is 7.5. Active over a wide pH range.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi68Zinc 1; via tele nitrogen; catalytic4 Publications1
    Metal bindingi70Zinc 1; via tele nitrogen; catalytic4 Publications1
    Binding sitei106Substrate3 Publications1
    Binding sitei137Substrate3 Publications1
    Metal bindingi162Zinc 1; via carbamate group; catalytic4 Publications1
    Metal bindingi162Zinc 2; via carbamate group; catalytic4 Publications1
    Binding sitei169Substrate3 Publications1
    Metal bindingi201Zinc 2; via pros nitrogen; catalytic4 Publications1
    Metal bindingi230Zinc 2; via tele nitrogen; catalytic4 Publications1
    Binding sitei233Substrate3 Publications1
    Active sitei285Proton acceptor1 Publication1
    Metal bindingi285Zinc 1; catalytic4 Publications1
    Binding sitei289Substrate; via amide nitrogen and carbonyl oxygen3 Publications1

    GO - Molecular functioni

    • beta-aspartyl-peptidase activity Source: UniProtKB
    • hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Source: InterPro
    • metallopeptidase activity Source: UniProtKB-KW
    • zinc ion binding Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Metalloprotease, Protease

    Keywords - Ligandi

    Cobalt, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:G7925-MONOMER.
    ECOL316407:JW4291-MONOMER.
    MetaCyc:G7925-MONOMER.
    BRENDAi3.4.19.5. 2026.
    SABIO-RKP39377.

    Protein family/group databases

    MEROPSiM38.001.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Isoaspartyl dipeptidase (EC:3.4.19.-)
    Gene namesi
    Name:iadA
    Synonyms:yjiF
    Ordered Locus Names:b4328, JW4291
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12567. iadA.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: UniProtKB
    • cytosol Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    No observable phenotype. Does not result in reduced stationary phase or heat shock survival. Approximately 31% of the enzyme activity present.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi77E → D or Q: Reduces activity 100000-fold. 2 Publications1
    Mutagenesisi137Y → A or F: Reduces activity 1000-fold. 2 Publications1
    Mutagenesisi169R → K: Reduces activity 1000-fold. 1 Publication1
    Mutagenesisi169R → M: Loss of activity. 1 Publication1
    Mutagenesisi233R → K: Reduces activity 1000-fold. 1 Publication1
    Mutagenesisi233R → M: Loss of activity. 1 Publication1
    Mutagenesisi285D → A: Reduces activity 100000-fold. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000791781 – 390Isoaspartyl dipeptidaseAdd BLAST390

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei162N6-carboxylysine4 Publications1

    Post-translational modificationi

    Carbamylation allows a single lysine to coordinate two zinc ions (PubMed:12718528, PubMed:12946361, PubMed:15882050, PubMed:16289685).4 Publications

    Proteomic databases

    PaxDbiP39377.
    PRIDEiP39377.

    Interactioni

    Protein-protein interaction databases

    BioGridi4261005. 9 interactors.
    DIPiDIP-10001N.
    IntActiP39377. 4 interactors.
    STRINGi511145.b4328.

    Structurei

    Secondary structure

    1390
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi5 – 7Combined sources3
    Beta strandi10 – 14Combined sources5
    Beta strandi16 – 25Combined sources10
    Beta strandi27 – 31Combined sources5
    Beta strandi34 – 39Combined sources6
    Beta strandi46 – 49Combined sources4
    Beta strandi51 – 54Combined sources4
    Beta strandi59 – 62Combined sources4
    Beta strandi64 – 69Combined sources6
    Helixi80 – 82Combined sources3
    Helixi89 – 94Combined sources6
    Beta strandi97 – 102Combined sources6
    Helixi113 – 126Combined sources14
    Beta strandi128 – 135Combined sources8
    Beta strandi137 – 140Combined sources4
    Beta strandi144 – 146Combined sources3
    Helixi148 – 154Combined sources7
    Beta strandi158 – 167Combined sources10
    Helixi175 – 192Combined sources18
    Beta strandi197 – 202Combined sources6
    Turni206 – 209Combined sources4
    Helixi210 – 217Combined sources8
    Helixi223 – 225Combined sources3
    Beta strandi226 – 229Combined sources4
    Helixi231 – 233Combined sources3
    Helixi235 – 246Combined sources12
    Beta strandi251 – 254Combined sources4
    Beta strandi259 – 261Combined sources3
    Helixi263 – 272Combined sources10
    Helixi277 – 279Combined sources3
    Beta strandi280 – 283Combined sources4
    Beta strandi289 – 293Combined sources5
    Beta strandi295 – 297Combined sources3
    Beta strandi299 – 304Combined sources6
    Helixi309 – 321Combined sources13
    Helixi325 – 329Combined sources5
    Helixi330 – 332Combined sources3
    Helixi334 – 339Combined sources6
    Beta strandi356 – 359Combined sources4
    Beta strandi365 – 370Combined sources6
    Beta strandi373 – 377Combined sources5
    Beta strandi380 – 383Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1ONWX-ray1.65A/B1-390[»]
    1ONXX-ray2.10A/B1-390[»]
    1PO9X-ray2.00A/B1-390[»]
    1POJX-ray3.30A/B1-390[»]
    1POKX-ray2.70A/B1-390[»]
    1YBQX-ray2.00A/B1-390[»]
    2AQOX-ray1.95A/B1-390[»]
    2AQVX-ray1.95A/B1-390[»]
    ProteinModelPortaliP39377.
    SMRiP39377.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39377.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni75 – 77Substrate binding3

    Sequence similaritiesi

    Belongs to the peptidase M38 family.Curated

    Phylogenomic databases

    eggNOGiENOG4105DYB. Bacteria.
    ENOG410XNTK. LUCA.
    HOGENOMiHOG000275891.
    InParanoidiP39377.
    KOiK01305.
    OMAiPTHINRN.
    PhylomeDBiP39377.

    Family and domain databases

    CDDicd01308. Isoaspartyl-dipeptidase. 1 hit.
    Gene3Di2.30.40.10. 1 hit.
    InterProiIPR006680. Amidohydro-rel.
    IPR033826. Isoaspartyl-dipeptidase.
    IPR011059. Metal-dep_hydrolase_composite.
    IPR032466. Metal_Hydrolase.
    IPR010229. Pept_M38_dipep.
    [Graphical view]
    PfamiPF01979. Amidohydro_1. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001238. IadA. 1 hit.
    SUPFAMiSSF51338. SSF51338. 2 hits.
    SSF51556. SSF51556. 1 hit.
    TIGRFAMsiTIGR01975. isoAsp_dipep. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P39377-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MIDYTAAGFT LLQGAHLYAP EDRGICDVLV ANGKIIAVAS NIPSDIVPNC
    60 70 80 90 100
    TVVDLSGQIL CPGFIDQHVH LIGGGGEAGP TTRTPEVALS RLTEAGVTSV
    110 120 130 140 150
    VGLLGTDSIS RHPESLLAKT RALNEEGISA WMLTGAYHVP SRTITGSVEK
    160 170 180 190 200
    DVAIIDRVIG VKCAISDHRS AAPDVYHLAN MAAESRVGGL LGGKPGVTVF
    210 220 230 240 250
    HMGDSKKALQ PIYDLLENCD VPISKLLPTH VNRNVPLFEQ ALEFARKGGT
    260 270 280 290 300
    IDITSSIDEP VAPAEGIARA VQAGIPLARV TLSSDGNGSQ PFFDDEGNLT
    310 320 330 340 350
    HIGVAGFETL LETVQVLVKD YDFSISDALR PLTSSVAGFL NLTGKGEILP
    360 370 380 390
    GNDADLLVMT PELRIEQVYA RGKLMVKDGK ACVKGTFETA
    Length:390
    Mass (Da):41,084
    Last modified:February 1, 1995 - v1
    Checksum:i9CEEC838381545B5
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U15029 Genomic DNA. Translation: AAC43299.1.
    U14003 Genomic DNA. Translation: AAA97224.1.
    U00096 Genomic DNA. Translation: AAC77284.1.
    AP009048 Genomic DNA. Translation: BAE78321.1.
    PIRiB55889.
    RefSeqiNP_418748.1. NC_000913.3.
    WP_000568432.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77284; AAC77284; b4328.
    BAE78321; BAE78321; BAE78321.
    GeneIDi948853.
    KEGGiecj:JW4291.
    eco:b4328.
    PATRICi32124258. VBIEscCol129921_4472.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U15029 Genomic DNA. Translation: AAC43299.1.
    U14003 Genomic DNA. Translation: AAA97224.1.
    U00096 Genomic DNA. Translation: AAC77284.1.
    AP009048 Genomic DNA. Translation: BAE78321.1.
    PIRiB55889.
    RefSeqiNP_418748.1. NC_000913.3.
    WP_000568432.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1ONWX-ray1.65A/B1-390[»]
    1ONXX-ray2.10A/B1-390[»]
    1PO9X-ray2.00A/B1-390[»]
    1POJX-ray3.30A/B1-390[»]
    1POKX-ray2.70A/B1-390[»]
    1YBQX-ray2.00A/B1-390[»]
    2AQOX-ray1.95A/B1-390[»]
    2AQVX-ray1.95A/B1-390[»]
    ProteinModelPortaliP39377.
    SMRiP39377.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4261005. 9 interactors.
    DIPiDIP-10001N.
    IntActiP39377. 4 interactors.
    STRINGi511145.b4328.

    Protein family/group databases

    MEROPSiM38.001.

    Proteomic databases

    PaxDbiP39377.
    PRIDEiP39377.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77284; AAC77284; b4328.
    BAE78321; BAE78321; BAE78321.
    GeneIDi948853.
    KEGGiecj:JW4291.
    eco:b4328.
    PATRICi32124258. VBIEscCol129921_4472.

    Organism-specific databases

    EchoBASEiEB2455.
    EcoGeneiEG12567. iadA.

    Phylogenomic databases

    eggNOGiENOG4105DYB. Bacteria.
    ENOG410XNTK. LUCA.
    HOGENOMiHOG000275891.
    InParanoidiP39377.
    KOiK01305.
    OMAiPTHINRN.
    PhylomeDBiP39377.

    Enzyme and pathway databases

    BioCyciEcoCyc:G7925-MONOMER.
    ECOL316407:JW4291-MONOMER.
    MetaCyc:G7925-MONOMER.
    BRENDAi3.4.19.5. 2026.
    SABIO-RKP39377.

    Miscellaneous databases

    EvolutionaryTraceiP39377.
    PROiP39377.

    Family and domain databases

    CDDicd01308. Isoaspartyl-dipeptidase. 1 hit.
    Gene3Di2.30.40.10. 1 hit.
    InterProiIPR006680. Amidohydro-rel.
    IPR033826. Isoaspartyl-dipeptidase.
    IPR011059. Metal-dep_hydrolase_composite.
    IPR032466. Metal_Hydrolase.
    IPR010229. Pept_M38_dipep.
    [Graphical view]
    PfamiPF01979. Amidohydro_1. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001238. IadA. 1 hit.
    SUPFAMiSSF51338. SSF51338. 2 hits.
    SSF51556. SSF51556. 1 hit.
    TIGRFAMsiTIGR01975. isoAsp_dipep. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiIADA_ECOLI
    AccessioniPrimary (citable) accession number: P39377
    Secondary accession number(s): Q2M5Y5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: November 30, 2016
    This is version 144 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. Peptidase families
      Classification of peptidase families and list of entries
    4. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.