IADA_ECOLI
ID IADA_ECOLI Reviewed; 390 AA.
AC P39377; Q2M5Y5;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 174.
DE RecName: Full=Isoaspartyl dipeptidase;
DE EC=3.4.19.-;
GN Name=iadA; Synonyms=yjiF; OrderedLocusNames=b4328, JW4291;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-24; 35-39; 84-91;
RP 112-118; 122-147; 170-185; 187-204; 226-238; 247-264 AND 365-371, FUNCTION,
RP CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=7876157; DOI=10.1074/jbc.270.8.4076;
RA Gary J.D., Clarke S.;
RT "Purification and characterization of an isoaspartyl dipeptidase from
RT Escherichia coli.";
RL J. Biol. Chem. 270:4076-4087(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=4880759; DOI=10.1016/s0021-9258(18)91928-9;
RA Haley E.E.;
RT "Purification and properties of a beta-aspartyl peptidase from Escherichia
RT coli.";
RL J. Biol. Chem. 243:5748-5752(1968).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 13-389 IN COMPLEX WITH ASPARTATE
RP AND ZINC IONS, FUNCTION, COFACTOR, AND CARBOXYLATION AT LYS-162.
RX PubMed=12718528; DOI=10.1021/bi034233p;
RA Thoden J.B., Marti-Arbona R., Raushel F.M., Holden H.M.;
RT "High-resolution X-ray structure of isoaspartyl dipeptidase from
RT Escherichia coli.";
RL Biochemistry 42:4874-4882(2003).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH INHIBITOR;
RP ASPARAGINE AND ZINC IONS, COFACTOR, ACTIVE SITE, AND CARBOXYLATION AT
RP LYS-162.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=12946361; DOI=10.1016/s0022-2836(03)00845-3;
RA Jozic D., Kaiser J.T., Huber R., Bode W., Maskos K.;
RT "X-ray structure of isoaspartyl dipeptidase from E.coli: a dinuclear zinc
RT peptidase evolved from amidohydrolases.";
RL J. Mol. Biol. 332:243-256(2003).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND
RP ZINC IONS, CATALYTIC ACTIVITY, FUNCTION, COFACTOR, CARBOXYLATION AT
RP LYS-162, AND MUTAGENESIS OF GLU-77; TYR-137; ARG-169; ARG-233 AND ASP-285.
RX PubMed=15882050; DOI=10.1021/bi050008r;
RA Marti-Arbona R., Fresquet V., Thoden J.B., Davis M.L., Holden H.M.,
RA Raushel F.M.;
RT "Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from
RT Escherichia coli.";
RL Biochemistry 44:7115-7124(2005).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF MUTANTS GLN-77 AND PHE-137 IN
RP COMPLEX WITH ZINC IONS, CARBOXYLATION AT LYS-162, AND MUTAGENESIS OF GLU-77
RP AND TYR-137.
RX PubMed=16289685; DOI=10.1016/j.bioorg.2005.10.002;
RA Marti-Arbona R., Thoden J.B., Holden H.M., Raushel F.M.;
RT "Functional significance of Glu-77 and Tyr-137 within the active site of
RT isoaspartyl dipeptidase.";
RL Bioorg. Chem. 33:448-458(2005).
CC -!- FUNCTION: Catalyzes the hydrolytic cleavage of a subset of L-
CC isoaspartyl (L-beta-aspartyl) dipeptides. Used to degrade proteins
CC damaged by L-isoaspartyl residues formation. The best substrate for the
CC enzyme reported thus far is iso-Asp-Leu. {ECO:0000269|PubMed:12718528,
CC ECO:0000269|PubMed:15882050, ECO:0000269|PubMed:4880759,
CC ECO:0000269|PubMed:7876157}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:12718528, ECO:0000269|PubMed:12946361,
CC ECO:0000269|PubMed:15882050};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:12718528, ECO:0000269|PubMed:12946361,
CC ECO:0000269|PubMed:15882050};
CC Note=Binds 2 Zn(2+) ions per subunit. Has highest activity with Zn(2+)
CC ions, but is also active with Co(2+) ions.
CC {ECO:0000269|PubMed:12718528, ECO:0000269|PubMed:12946361,
CC ECO:0000269|PubMed:15882050};
CC -!- ACTIVITY REGULATION: P-hydroxymercuribenzoate causes a slight
CC inhibition (8 to 17 %). Iodoacetamide, o-iodosobenzoate and ammonium
CC persulfate do not inhibit the enzyme activity.
CC {ECO:0000269|PubMed:4880759}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.81 mM for beta-aspartylleucine (at pH 8.0)
CC {ECO:0000269|PubMed:4880759};
CC pH dependence:
CC Optimum pH is 7.5. Active over a wide pH range.
CC {ECO:0000269|PubMed:4880759};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:7876157}.
CC -!- PTM: Carboxylation allows a single lysine to coordinate two zinc ions
CC (PubMed:12718528, PubMed:12946361, PubMed:15882050, PubMed:16289685).
CC {ECO:0000269|PubMed:12718528, ECO:0000269|PubMed:12946361,
CC ECO:0000269|PubMed:15882050, ECO:0000269|PubMed:16289685}.
CC -!- DISRUPTION PHENOTYPE: No observable phenotype. Does not result in
CC reduced stationary phase or heat shock survival. Approximately 31% of
CC the enzyme activity present. {ECO:0000269|PubMed:7876157}.
CC -!- SIMILARITY: Belongs to the peptidase M38 family. {ECO:0000305}.
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DR EMBL; U15029; AAC43299.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97224.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77284.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78321.1; -; Genomic_DNA.
DR PIR; B55889; B55889.
DR RefSeq; NP_418748.1; NC_000913.3.
DR RefSeq; WP_000568432.1; NZ_STEB01000025.1.
DR PDB; 1ONW; X-ray; 1.65 A; A/B=1-390.
DR PDB; 1ONX; X-ray; 2.10 A; A/B=1-390.
DR PDB; 1PO9; X-ray; 2.00 A; A/B=1-390.
DR PDB; 1POJ; X-ray; 3.30 A; A/B=1-390.
DR PDB; 1POK; X-ray; 2.70 A; A/B=1-390.
DR PDB; 1YBQ; X-ray; 2.00 A; A/B=1-390.
DR PDB; 2AQO; X-ray; 1.95 A; A/B=1-390.
DR PDB; 2AQV; X-ray; 1.95 A; A/B=1-390.
DR PDB; 5LP3; EM; 10.50 A; A/B/C/D/E/F/G/H/I/J/K/L=1-390.
DR PDBsum; 1ONW; -.
DR PDBsum; 1ONX; -.
DR PDBsum; 1PO9; -.
DR PDBsum; 1POJ; -.
DR PDBsum; 1POK; -.
DR PDBsum; 1YBQ; -.
DR PDBsum; 2AQO; -.
DR PDBsum; 2AQV; -.
DR PDBsum; 5LP3; -.
DR AlphaFoldDB; P39377; -.
DR SMR; P39377; -.
DR BioGRID; 4261005; 12.
DR DIP; DIP-10001N; -.
DR IntAct; P39377; 4.
DR STRING; 511145.b4328; -.
DR DrugBank; DB02437; (5r)-5-Amino-6-Hydroxyhexylcarbamic Acid.
DR DrugBank; DB03801; Lysine Nz-Carboxylic Acid.
DR MEROPS; M38.001; -.
DR jPOST; P39377; -.
DR PaxDb; P39377; -.
DR PRIDE; P39377; -.
DR EnsemblBacteria; AAC77284; AAC77284; b4328.
DR EnsemblBacteria; BAE78321; BAE78321; BAE78321.
DR GeneID; 948853; -.
DR KEGG; ecj:JW4291; -.
DR KEGG; eco:b4328; -.
DR PATRIC; fig|1411691.4.peg.2361; -.
DR EchoBASE; EB2455; -.
DR eggNOG; COG1820; Bacteria.
DR HOGENOM; CLU_058216_0_0_6; -.
DR InParanoid; P39377; -.
DR OMA; HVHICGG; -.
DR PhylomeDB; P39377; -.
DR BioCyc; EcoCyc:G7925-MON; -.
DR BioCyc; MetaCyc:G7925-MON; -.
DR BRENDA; 3.4.19.5; 2026.
DR SABIO-RK; P39377; -.
DR EvolutionaryTrace; P39377; -.
DR PRO; PR:P39377; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0008798; F:beta-aspartyl-peptidase activity; IDA:UniProtKB.
DR GO; GO:0016810; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds; IEA:InterPro.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0008237; F:metallopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR CDD; cd01308; Isoaspartyl-dipeptidase; 1.
DR Gene3D; 2.30.40.10; -; 1.
DR InterPro; IPR006680; Amidohydro-rel.
DR InterPro; IPR033826; Isoaspartyl-dipeptidase.
DR InterPro; IPR011059; Metal-dep_hydrolase_composite.
DR InterPro; IPR032466; Metal_Hydrolase.
DR InterPro; IPR010229; Pept_M38_dipep.
DR Pfam; PF01979; Amidohydro_1; 1.
DR PIRSF; PIRSF001238; IadA; 1.
DR SUPFAM; SSF51338; SSF51338; 2.
DR SUPFAM; SSF51556; SSF51556; 1.
DR TIGRFAMs; TIGR01975; isoAsp_dipep; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalt; Cytoplasm; Direct protein sequencing; Hydrolase;
KW Metal-binding; Metalloprotease; Protease; Reference proteome; Zinc.
FT CHAIN 1..390
FT /note="Isoaspartyl dipeptidase"
FT /id="PRO_0000079178"
FT ACT_SITE 285
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:12946361"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:12718528,
FT ECO:0000269|PubMed:12946361, ECO:0000269|PubMed:15882050,
FT ECO:0000269|PubMed:16289685"
FT BINDING 70
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:12718528,
FT ECO:0000269|PubMed:12946361, ECO:0000269|PubMed:15882050,
FT ECO:0000269|PubMed:16289685"
FT BINDING 75..77
FT /ligand="substrate"
FT BINDING 106
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12718528,
FT ECO:0000305|PubMed:12946361, ECO:0000305|PubMed:15882050"
FT BINDING 137
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12718528,
FT ECO:0000305|PubMed:12946361, ECO:0000305|PubMed:15882050"
FT BINDING 162
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /note="via carbamate group"
FT /evidence="ECO:0000269|PubMed:12718528,
FT ECO:0000269|PubMed:12946361, ECO:0000269|PubMed:15882050,
FT ECO:0000269|PubMed:16289685"
FT BINDING 162
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /note="via carbamate group"
FT /evidence="ECO:0000269|PubMed:12718528,
FT ECO:0000269|PubMed:12946361, ECO:0000269|PubMed:15882050,
FT ECO:0000269|PubMed:16289685"
FT BINDING 169
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12718528,
FT ECO:0000305|PubMed:12946361, ECO:0000305|PubMed:15882050"
FT BINDING 201
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:12718528,
FT ECO:0000269|PubMed:12946361, ECO:0000269|PubMed:15882050,
FT ECO:0000269|PubMed:16289685"
FT BINDING 230
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:12718528,
FT ECO:0000269|PubMed:12946361, ECO:0000269|PubMed:15882050,
FT ECO:0000269|PubMed:16289685"
FT BINDING 233
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12718528,
FT ECO:0000305|PubMed:12946361, ECO:0000305|PubMed:15882050"
FT BINDING 285
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:12718528,
FT ECO:0000269|PubMed:12946361, ECO:0000269|PubMed:15882050,
FT ECO:0000269|PubMed:16289685"
FT BINDING 289
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12718528,
FT ECO:0000305|PubMed:12946361, ECO:0000305|PubMed:15882050"
FT MOD_RES 162
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000269|PubMed:12718528,
FT ECO:0000269|PubMed:12946361, ECO:0000269|PubMed:15882050,
FT ECO:0000269|PubMed:16289685"
FT MUTAGEN 77
FT /note="E->D,Q: Reduces activity 100000-fold."
FT /evidence="ECO:0000269|PubMed:15882050,
FT ECO:0000269|PubMed:16289685"
FT MUTAGEN 137
FT /note="Y->A,F: Reduces activity 1000-fold."
FT /evidence="ECO:0000269|PubMed:15882050,
FT ECO:0000269|PubMed:16289685"
FT MUTAGEN 169
FT /note="R->K: Reduces activity 1000-fold."
FT /evidence="ECO:0000269|PubMed:15882050"
FT MUTAGEN 169
FT /note="R->M: Loss of activity."
FT /evidence="ECO:0000269|PubMed:15882050"
FT MUTAGEN 233
FT /note="R->K: Reduces activity 1000-fold."
FT /evidence="ECO:0000269|PubMed:15882050"
FT MUTAGEN 233
FT /note="R->M: Loss of activity."
FT /evidence="ECO:0000269|PubMed:15882050"
FT MUTAGEN 285
FT /note="D->A: Reduces activity 100000-fold."
FT /evidence="ECO:0000269|PubMed:15882050"
FT HELIX 5..7
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 10..14
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 16..25
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 27..31
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 34..39
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 46..49
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 51..54
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 59..62
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 64..69
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 80..82
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 89..94
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 97..102
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 113..126
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 128..135
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 137..140
FT /evidence="ECO:0007829|PDB:1PO9"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 148..154
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 158..167
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 175..192
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 197..202
FT /evidence="ECO:0007829|PDB:1ONW"
FT TURN 206..209
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 210..217
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 226..229
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 231..233
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 235..246
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 251..254
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 259..261
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 263..272
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 277..279
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 280..283
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 289..293
FT /evidence="ECO:0007829|PDB:1YBQ"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:1ONX"
FT STRAND 299..304
FT /evidence="ECO:0007829|PDB:1YBQ"
FT HELIX 309..321
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 325..329
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 330..332
FT /evidence="ECO:0007829|PDB:1ONW"
FT HELIX 334..339
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 356..359
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 365..370
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 373..377
FT /evidence="ECO:0007829|PDB:1ONW"
FT STRAND 380..383
FT /evidence="ECO:0007829|PDB:1ONW"
SQ SEQUENCE 390 AA; 41084 MW; 9CEEC838381545B5 CRC64;
MIDYTAAGFT LLQGAHLYAP EDRGICDVLV ANGKIIAVAS NIPSDIVPNC TVVDLSGQIL
CPGFIDQHVH LIGGGGEAGP TTRTPEVALS RLTEAGVTSV VGLLGTDSIS RHPESLLAKT
RALNEEGISA WMLTGAYHVP SRTITGSVEK DVAIIDRVIG VKCAISDHRS AAPDVYHLAN
MAAESRVGGL LGGKPGVTVF HMGDSKKALQ PIYDLLENCD VPISKLLPTH VNRNVPLFEQ
ALEFARKGGT IDITSSIDEP VAPAEGIARA VQAGIPLARV TLSSDGNGSQ PFFDDEGNLT
HIGVAGFETL LETVQVLVKD YDFSISDALR PLTSSVAGFL NLTGKGEILP GNDADLLVMT
PELRIEQVYA RGKLMVKDGK ACVKGTFETA
