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P39377 (IADA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 127. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Isoaspartyl dipeptidase

EC=3.4.19.-
Gene names
Name:iadA
Synonyms:yjiF
Ordered Locus Names:b4328, JW4291
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length390 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.5 Ref.6 Ref.8

Cofactor

Binds 2 zinc ions per subunit. Has highest activity with zinc ions, but is also active with cobalt ions. Ref.6 Ref.7 Ref.8

Enzyme regulation

P-hydroxymercuribenzoate causes a slight inhibition (8 to 17 %). Iodoacetamide, o-iodosobenzoate and ammonium persulfate do not inhibit the enzyme activity. Ref.5

Subcellular location

Cytoplasm Ref.1.

Post-translational modification

Carbamylation allows a single lysine to coordinate two zinc ions (Ref.6, Ref.7, Ref.8, Ref.9).

Disruption phenotype

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

Sequence similarities

Belongs to the peptidase M38 family.

Biophysicochemical properties

Kinetic parameters:

KM=0.81 mM for beta-aspartylleucine (at pH 8.0) Ref.5

pH dependence:

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 390390Isoaspartyl dipeptidase
PRO_0000079178

Regions

Region75 – 773Substrate binding

Sites

Active site2851Proton acceptor Ref.7
Metal binding681Zinc 1; via tele nitrogen; catalytic
Metal binding701Zinc 1; via tele nitrogen; catalytic
Metal binding1621Zinc 1; via carbamate group; catalytic
Metal binding1621Zinc 2; via carbamate group; catalytic
Metal binding2011Zinc 2; via pros nitrogen; catalytic
Metal binding2301Zinc 2; via tele nitrogen; catalytic
Metal binding2851Zinc 1; catalytic
Binding site1061Substrate
Binding site1371Substrate
Binding site1691Substrate
Binding site2331Substrate
Binding site2891Substrate; via amide nitrogen and carbonyl oxygen

Amino acid modifications

Modified residue1621N6-carboxylysine

Experimental info

Mutagenesis771E → D or Q: Reduces activity 100000-fold. Ref.8 Ref.9
Mutagenesis1371Y → A or F: Reduces activity 1000-fold. Ref.8 Ref.9
Mutagenesis1691R → K: Reduces activity 1000-fold. Ref.8
Mutagenesis1691R → M: Loss of activity. Ref.8
Mutagenesis2331R → K: Reduces activity 1000-fold. Ref.8
Mutagenesis2331R → M: Loss of activity. Ref.8
Mutagenesis2851D → A: Reduces activity 100000-fold. Ref.8

Secondary structure

................................................................................. 390
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P39377 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: 9CEEC838381545B5

FASTA39041,084
        10         20         30         40         50         60 
MIDYTAAGFT LLQGAHLYAP EDRGICDVLV ANGKIIAVAS NIPSDIVPNC TVVDLSGQIL 

        70         80         90        100        110        120 
CPGFIDQHVH LIGGGGEAGP TTRTPEVALS RLTEAGVTSV VGLLGTDSIS RHPESLLAKT 

       130        140        150        160        170        180 
RALNEEGISA WMLTGAYHVP SRTITGSVEK DVAIIDRVIG VKCAISDHRS AAPDVYHLAN 

       190        200        210        220        230        240 
MAAESRVGGL LGGKPGVTVF HMGDSKKALQ PIYDLLENCD VPISKLLPTH VNRNVPLFEQ 

       250        260        270        280        290        300 
ALEFARKGGT IDITSSIDEP VAPAEGIARA VQAGIPLARV TLSSDGNGSQ PFFDDEGNLT 

       310        320        330        340        350        360 
HIGVAGFETL LETVQVLVKD YDFSISDALR PLTSSVAGFL NLTGKGEILP GNDADLLVMT 

       370        380        390 
PELRIEQVYA RGKLMVKDGK ACVKGTFETA 

« Hide

References

« Hide 'large scale' references
[1]"Purification and characterization of an isoaspartyl dipeptidase from Escherichia coli."
Gary J.D., Clarke S.
J. Biol. Chem. 270:4076-4087(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-24; 35-39; 84-91; 112-118; 122-147; 170-185; 187-204; 226-238; 247-264 AND 365-371, FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]"Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[4]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"Purification and properties of a beta-aspartyl peptidase from Escherichia coli."
Haley E.E.
J. Biol. Chem. 243:5748-5752(1968) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
[6]"High-resolution X-ray structure of isoaspartyl dipeptidase from Escherichia coli."
Thoden J.B., Marti-Arbona R., Raushel F.M., Holden H.M.
Biochemistry 42:4874-4882(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 13-389 IN COMPLEX WITH ASPARTATE AND ZINC IONS, FUNCTION, COFACTOR, CARBAMYLATION AT LYS-162.
[7]"X-ray structure of isoaspartyl dipeptidase from E.coli: a dinuclear zinc peptidase evolved from amidohydrolases."
Jozic D., Kaiser J.T., Huber R., Bode W., Maskos K.
J. Mol. Biol. 332:243-256(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH INHIBITOR; ASPARAGINE AND ZINC IONS, COFACTOR, ACTIVE SITE, CARBAMYLATION AT LYS-162.
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]"Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli."
Marti-Arbona R., Fresquet V., Thoden J.B., Davis M.L., Holden H.M., Raushel F.M.
Biochemistry 44:7115-7124(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND ZINC IONS, CATALYTIC ACTIVITY, FUNCTION, COFACTOR, CARBAMYLATION AT LYS-162, MUTAGENESIS OF GLU-77; TYR-137; ARG-169; ARG-233 AND ASP-285.
[9]"Functional significance of Glu-77 and Tyr-137 within the active site of isoaspartyl dipeptidase."
Marti-Arbona R., Thoden J.B., Holden H.M., Raushel F.M.
Bioorg. Chem. 33:448-458(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF MUTANTS GLN-77 AND PHE-137 IN COMPLEX WITH ZINC IONS, CARBAMYLATION AT LYS-162, MUTAGENESIS OF GLU-77 AND TYR-137.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U15029 Genomic DNA. Translation: AAC43299.1.
U14003 Genomic DNA. Translation: AAA97224.1.
U00096 Genomic DNA. Translation: AAC77284.1.
AP009048 Genomic DNA. Translation: BAE78321.1.
PIRB55889.
RefSeqNP_418748.1. NC_000913.3.
YP_492462.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalP39377.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10001N.
IntActP39377. 4 interactions.
STRING511145.b4328.

Protein family/group databases

MEROPSM38.001.

Proteomic databases

PaxDbP39377.
PRIDEP39377.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC77284; AAC77284; b4328.
BAE78321; BAE78321; BAE78321.
GeneID12932011.
948853.
KEGGecj:Y75_p4214.
eco:b4328.
PATRIC32124258. VBIEscCol129921_4472.

Organism-specific databases

EchoBASEEB2455.
EcoGeneEG12567. iadA.

Phylogenomic databases

eggNOGNOG04347.
HOGENOMHOG000275891.
KOK01305.
OMAIADHRSS.
OrthoDBEOG625JTQ.
PhylomeDBP39377.

Enzyme and pathway databases

BioCycEcoCyc:G7925-MONOMER.
ECOL316407:JW4291-MONOMER.
MetaCyc:G7925-MONOMER.
SABIO-RKP39377.

Gene expression databases

GenevestigatorP39377.

Family and domain databases

Gene3D2.30.40.10. 1 hit.
InterProIPR011059. Metal-dep_hydrolase_composite.
IPR010229. Pept_M38_dipep.
[Graphical view]
PIRSFPIRSF001238. IadA. 1 hit.
SUPFAMSSF51338. SSF51338. 2 hits.
TIGRFAMsTIGR01975. isoAsp_dipep. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP39377.
PROP39377.

Entry information

Entry nameIADA_ECOLI
AccessionPrimary (citable) accession number: P39377
Secondary accession number(s): Q2M5Y5
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: July 9, 2014
This is version 127 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene