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Protein

Cytosol non-specific dipeptidase

Gene

pepD

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

Functioni

Dipeptidase with broad substrate specificity. Requires dipeptide substrates with an unblocked N-terminus and the amino group in the alpha or beta position. Non-protein amino acids and proline are not accepted in the C-terminal position, whereas some dipeptide amides and formyl amino acids are hydrolyzed. Also shows cysteinylglycinase activity, which is sufficient for E.coli to utilize cysteinylglycine as a cysteine source.3 Publications

Catalytic activityi

Hydrolysis of dipeptides, preferentially hydrophobic dipeptides including prolyl amino acids.2 Publications

Cofactori

Zn2+1 Publication, Co2+1 PublicationNote: Binds 2 Zn(2+) ions per subunit. Can also use Co2+.1 Publication

Enzyme regulationi

Inhibited by metal chelators.1 Publication

pH dependencei

Optimum pH is 9.1 Publication

Temperature dependencei

Optimum temperature is 37 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi76 – 761Zinc 2By similarity
Active sitei78 – 781By similarity
Metal bindingi115 – 1151Zinc 1By similarity
Metal bindingi115 – 1151Zinc 2By similarity
Active sitei145 – 1451Proton acceptorBy similarity
Metal bindingi146 – 1461Zinc 1By similarity
Metal bindingi169 – 1691Zinc 2By similarity
Metal bindingi457 – 4571Zinc 1By similarity

GO - Molecular functioni

  1. dipeptidase activity Source: EcoCyc
  2. metallodipeptidase activity Source: EcoCyc
  3. zinc ion binding Source: EcoCyc

GO - Biological processi

  1. peptide catabolic process Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Dipeptidase, Hydrolase, Metalloprotease, Protease

Keywords - Ligandi

Cobalt, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10695-MONOMER.
ECOL316407:JW0227-MONOMER.
MetaCyc:EG10695-MONOMER.

Protein family/group databases

MEROPSiM20.007.

Names & Taxonomyi

Protein namesi
Recommended name:
Cytosol non-specific dipeptidase (EC:3.4.13.18)
Alternative name(s):
Aminoacyl-histidine dipeptidase
Beta-alanyl-histidine dipeptidase
Carnosinase
Cysteinylglycinase
Peptidase D
Xaa-His dipeptidase
Short name:
X-His dipeptidase
Gene namesi
Name:pepD
Synonyms:pepH
Ordered Locus Names:b0237, JW0227
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10695. pepD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 485484Cytosol non-specific dipeptidasePRO_0000185354Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei296 – 2961N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP15288.
PRIDEiP15288.

2D gel databases

SWISS-2DPAGEP15288.

Expressioni

Gene expression databases

GenevestigatoriP15288.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
hscBP0A6L91EBI-542419,EBI-561519
yggXP0A8P31EBI-542419,EBI-1123057

Protein-protein interaction databases

DIPiDIP-10456N.
IntActiP15288. 69 interactions.
MINTiMINT-1252343.
STRINGi511145.b0237.

Structurei

3D structure databases

ProteinModelPortaliP15288.
SMRiP15288. Positions 2-485.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase M20C family.Curated

Phylogenomic databases

eggNOGiCOG2195.
HOGENOMiHOG000282306.
InParanoidiP15288.
KOiK01270.
OMAiKGGYPGW.
OrthoDBiEOG6BCSRT.
PhylomeDBiP15288.

Family and domain databases

InterProiIPR002933. Peptidase_M20.
IPR011650. Peptidase_M20_dimer.
IPR001160. Peptidase_M20C.
[Graphical view]
PfamiPF07687. M20_dimer. 1 hit.
PF01546. Peptidase_M20. 1 hit.
[Graphical view]
PIRSFiPIRSF016599. Xaa-His_dipept. 1 hit.
PRINTSiPR00934. XHISDIPTASE.
TIGRFAMsiTIGR01893. aa-his-dipept. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P15288-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSELSQLSPQ PLWDIFAKIC SIPHPSYHEE QLAEYIVGWA KEKGFHVERD
60 70 80 90 100
QVGNILIRKP ATAGMENRKP VVLQAHLDMV PQKNNDTVHD FTKDPIQPYI
110 120 130 140 150
DGEWVKARGT TLGADNGIGM ASALAVLADE NVVHGPLEVL LTMTEEAGMD
160 170 180 190 200
GAFGLQGNWL QADILINTDS EEEGEIYMGC AGGIDFTSNL HLDREAVPAG
210 220 230 240 250
FETFKLTLKG LKGGHSGGEI HVGLGNANKL LVRFLAGHAE ELDLRLIDFN
260 270 280 290 300
GGTLRNAIPR EAFATIAVAA DKVDVLKSLV NTYQEILKNE LAEKEKNLAL
310 320 330 340 350
LLDSVANDKA ALIAKSRDTF IRLLNATPNG VIRNSDVAKG VVETSLNVGV
360 370 380 390 400
VTMTDNNVEI HCLIRSLIDS GKDYVVSMLD SLGKLAGAKT EAKGAYPGWQ
410 420 430 440 450
PDANSPVMHL VRETYQRLFN KTPNIQIIHA GLECGLFKKP YPEMDMVSIG
460 470 480
PTITGPHSPD EQVHIESVGH YWTLLTELLK EIPAK
Length:485
Mass (Da):52,915
Last modified:January 22, 2007 - v3
Checksum:iCD870032876460E1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M34034 Unassigned DNA. Translation: AAA16111.1.
U70214 Genomic DNA. Translation: AAB08657.1.
U00096 Genomic DNA. Translation: AAC73341.1.
AP009048 Genomic DNA. Translation: BAA77906.1.
X14790 Genomic DNA. Translation: CAA32892.1.
PIRiJU0300.
RefSeqiNP_414772.1. NC_000913.3.
YP_488532.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73341; AAC73341; b0237.
BAA77906; BAA77906; BAA77906.
GeneIDi12930771.
945013.
KEGGiecj:Y75_p0228.
eco:b0237.
PATRICi32115589. VBIEscCol129921_0239.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M34034 Unassigned DNA. Translation: AAA16111.1.
U70214 Genomic DNA. Translation: AAB08657.1.
U00096 Genomic DNA. Translation: AAC73341.1.
AP009048 Genomic DNA. Translation: BAA77906.1.
X14790 Genomic DNA. Translation: CAA32892.1.
PIRiJU0300.
RefSeqiNP_414772.1. NC_000913.3.
YP_488532.1. NC_007779.1.

3D structure databases

ProteinModelPortaliP15288.
SMRiP15288. Positions 2-485.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-10456N.
IntActiP15288. 69 interactions.
MINTiMINT-1252343.
STRINGi511145.b0237.

Protein family/group databases

MEROPSiM20.007.

2D gel databases

SWISS-2DPAGEP15288.

Proteomic databases

PaxDbiP15288.
PRIDEiP15288.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73341; AAC73341; b0237.
BAA77906; BAA77906; BAA77906.
GeneIDi12930771.
945013.
KEGGiecj:Y75_p0228.
eco:b0237.
PATRICi32115589. VBIEscCol129921_0239.

Organism-specific databases

EchoBASEiEB0689.
EcoGeneiEG10695. pepD.

Phylogenomic databases

eggNOGiCOG2195.
HOGENOMiHOG000282306.
InParanoidiP15288.
KOiK01270.
OMAiKGGYPGW.
OrthoDBiEOG6BCSRT.
PhylomeDBiP15288.

Enzyme and pathway databases

BioCyciEcoCyc:EG10695-MONOMER.
ECOL316407:JW0227-MONOMER.
MetaCyc:EG10695-MONOMER.

Miscellaneous databases

PROiP15288.

Gene expression databases

GenevestigatoriP15288.

Family and domain databases

InterProiIPR002933. Peptidase_M20.
IPR011650. Peptidase_M20_dimer.
IPR001160. Peptidase_M20C.
[Graphical view]
PfamiPF07687. M20_dimer. 1 hit.
PF01546. Peptidase_M20. 1 hit.
[Graphical view]
PIRSFiPIRSF016599. Xaa-His_dipept. 1 hit.
PRINTSiPR00934. XHISDIPTASE.
TIGRFAMsiTIGR01893. aa-his-dipept. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Peptidase D gene (pepD) of Escherichia coli K-12: nucleotide sequence, transcript mapping, and comparison with other peptidase genes."
    Henrich B., Monnerjahn U., Plapp R.
    J. Bacteriol. 172:4641-4651(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
    Strain: K12.
  2. "Systematic sequencing of the Escherichia coli genome: analysis of the 4.0 - 6.0 min (189,987 - 281,416bp) region."
    Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T., Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S., Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.
    Submitted (JAN-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Sequence of minutes 4-25 of Escherichia coli."
    Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
    Submitted (DEC-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "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(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Accurate mapping of the Escherichia coli pepD gene by sequence analysis of its 5' flanking region."
    Henrich B., Schroeder U., Frank R.W., Plapp R.
    Mol. Gen. Genet. 215:369-373(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-56, PROTEIN SEQUENCE OF 2-13.
    Strain: K12.
  7. "Peptidase-deficient mutants of Escherichia coli."
    Miller C.G., Schwartz G.
    J. Bacteriol. 135:603-611(1977) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  8. "Peptidase D of Escherichia coli K-12, a metallopeptidase of low substrate specificity."
    Schroeder U., Henrich B., Fink J., Plapp R.
    FEMS Microbiol. Lett. 123:153-159(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBSTRATE SPECIFICITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
  9. "Aminopeptidases A, B, and N and dipeptidase D are the four cysteinylglycinases of Escherichia coli K-12."
    Suzuki H., Kamatani S., Kim E.-S., Kumagai H.
    J. Bacteriol. 183:1489-1490(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
    Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
    Mol. Cell. Proteomics 8:215-225(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-296, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.

Entry informationi

Entry nameiPEPD_ECOLI
AccessioniPrimary (citable) accession number: P15288
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 31, 1990
Last sequence update: January 22, 2007
Last modified: January 6, 2015
This is version 133 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

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

External Data

Dasty 3

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 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.