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Protein

Aminopeptidase YpdF

Gene

ypdF

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Hydrolyzes the N-terminal methionine when the next amino acid is alanine, proline or serine. The substrate preference for methionyl aminopeptidase activity is Pro > Ala > Ser. Also able to hydrolyze the Xaa-Pro peptide bond when the first amino acid is alanine, asparagine or methionine.1 Publication

Cofactori

Co2+, Mn2+, Ni2+Note: Co2+, Mn2+ or Ni2+.

GO - Molecular functioni

  • aminopeptidase activity Source: EcoCyc

GO - Biological processi

  • proteolysis Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Aminopeptidase, Hydrolase, Protease

Enzyme and pathway databases

BioCyciEcoCyc:G7248-MONOMER.
ECOL316407:JW2382-MONOMER.
MetaCyc:G7248-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Aminopeptidase YpdF (EC:3.4.11.-)
Gene namesi
Name:ypdF
Ordered Locus Names:b2385, JW2382
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14153. ypdF.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001851051 – 361Aminopeptidase YpdFAdd BLAST361

Proteomic databases

PaxDbiP76524.
PRIDEiP76524.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
groLP0A6F52EBI-1128711,EBI-543750

Protein-protein interaction databases

BioGridi4259189. 12 interactors.
DIPiDIP-48229N.
IntActiP76524. 1 interactor.
STRINGi511145.b2385.

Structurei

Secondary structure

1361
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi2 – 14Combined sources13
Beta strandi17 – 21Combined sources5
Helixi24 – 31Combined sources8
Beta strandi39 – 45Combined sources7
Beta strandi47 – 52Combined sources6
Turni53 – 55Combined sources3
Helixi56 – 62Combined sources7
Beta strandi66 – 75Combined sources10
Helixi77 – 87Combined sources11
Beta strandi92 – 95Combined sources4
Turni97 – 99Combined sources3
Helixi102 – 111Combined sources10
Beta strandi112 – 118Combined sources7
Helixi121 – 125Combined sources5
Helixi130 – 153Combined sources24
Helixi160 – 173Combined sources14
Beta strandi177 – 181Combined sources5
Beta strandi184 – 187Combined sources4
Helixi188 – 192Combined sources5
Beta strandi208 – 213Combined sources6
Beta strandi215 – 217Combined sources3
Beta strandi224 – 229Combined sources6
Turni237 – 239Combined sources3
Helixi243 – 258Combined sources16
Helixi266 – 279Combined sources14
Helixi283 – 285Combined sources3
Beta strandi290 – 293Combined sources4
Beta strandi295 – 305Combined sources11
Beta strandi317 – 320Combined sources4
Beta strandi323 – 326Combined sources4
Turni327 – 329Combined sources3
Beta strandi330 – 333Combined sources4
Beta strandi335 – 340Combined sources6
Beta strandi342 – 347Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5CNXX-ray2.60A/B/C1-361[»]
ProteinModelPortaliP76524.
SMRiP76524.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase M24 family.Curated

Phylogenomic databases

eggNOGiENOG4105DC7. Bacteria.
COG0006. LUCA.
HOGENOMiHOG000008760.
InParanoidiP76524.
KOiK08326.
OMAiTWCLALF.
PhylomeDBiP76524.

Family and domain databases

Gene3Di3.40.350.10. 1 hit.
3.90.230.10. 1 hit.
InterProiIPR029149. Creatin/AminoP/Spt16_NTD.
IPR028980. Creatinase/Aminopeptidase_P_N.
IPR000587. Creatinase_N.
IPR000994. Pept_M24.
IPR001714. Pept_M24_MAP.
[Graphical view]
PfamiPF01321. Creatinase_N. 1 hit.
PF00557. Peptidase_M24. 1 hit.
[Graphical view]
PRINTSiPR00599. MAPEPTIDASE.
SUPFAMiSSF53092. SSF53092. 1 hit.
SSF55920. SSF55920. 1 hit.

Sequencei

Sequence statusi: Complete.

P76524-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTLLASLRDW LKAQQLDAVL LSSRQNKQPH LGISTGSGYV VISRESAHIL
60 70 80 90 100
VDSRYYVEVE ARAQGYQLHL LDATNTLTTI VNQIIADEQL QTLGFEGQQV
110 120 130 140 150
SWETAHRWQS ELNAKLVSAT PDVLRQIKTP EEVEKIRLAC GIADRGAEHI
160 170 180 190 200
RRFIQAGMSE REIAAELEWF MRQQGAEKAS FDTIVASGWR GALPHGKASD
210 220 230 240 250
KIVAAGEFVT LDFGALYQGY CSDMTRTLLV NGEGVSAESH LLFNVYQIVL
260 270 280 290 300
QAQLAAISAI RPGVRCQQVD DAARRVITEA GYGDYFGHNT GHAIGIEVHE
310 320 330 340 350
DPRFSPRDTT TLQPGMLLTV EPGIYLPGQG GVRIEDVVLV TPQGAEVLYA
360
MPKTVLLTGE A
Length:361
Mass (Da):39,624
Last modified:February 1, 1997 - v1
Checksum:i34E97443005EB8D3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75444.1.
AP009048 Genomic DNA. Translation: BAA16255.2.
PIRiF65012.
RefSeqiNP_416886.1. NC_000913.3.
WP_000173288.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75444; AAC75444; b2385.
BAA16255; BAA16255; BAA16255.
GeneIDi946853.
KEGGiecj:JW2382.
eco:b2385.
PATRICi32120149. VBIEscCol129921_2483.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75444.1.
AP009048 Genomic DNA. Translation: BAA16255.2.
PIRiF65012.
RefSeqiNP_416886.1. NC_000913.3.
WP_000173288.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5CNXX-ray2.60A/B/C1-361[»]
ProteinModelPortaliP76524.
SMRiP76524.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259189. 12 interactors.
DIPiDIP-48229N.
IntActiP76524. 1 interactor.
STRINGi511145.b2385.

Proteomic databases

PaxDbiP76524.
PRIDEiP76524.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75444; AAC75444; b2385.
BAA16255; BAA16255; BAA16255.
GeneIDi946853.
KEGGiecj:JW2382.
eco:b2385.
PATRICi32120149. VBIEscCol129921_2483.

Organism-specific databases

EchoBASEiEB3905.
EcoGeneiEG14153. ypdF.

Phylogenomic databases

eggNOGiENOG4105DC7. Bacteria.
COG0006. LUCA.
HOGENOMiHOG000008760.
InParanoidiP76524.
KOiK08326.
OMAiTWCLALF.
PhylomeDBiP76524.

Enzyme and pathway databases

BioCyciEcoCyc:G7248-MONOMER.
ECOL316407:JW2382-MONOMER.
MetaCyc:G7248-MONOMER.

Miscellaneous databases

PROiP76524.

Family and domain databases

Gene3Di3.40.350.10. 1 hit.
3.90.230.10. 1 hit.
InterProiIPR029149. Creatin/AminoP/Spt16_NTD.
IPR028980. Creatinase/Aminopeptidase_P_N.
IPR000587. Creatinase_N.
IPR000994. Pept_M24.
IPR001714. Pept_M24_MAP.
[Graphical view]
PfamiPF01321. Creatinase_N. 1 hit.
PF00557. Peptidase_M24. 1 hit.
[Graphical view]
PRINTSiPR00599. MAPEPTIDASE.
SUPFAMiSSF53092. SSF53092. 1 hit.
SSF55920. SSF55920. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiYPDF_ECOLI
AccessioniPrimary (citable) accession number: P76524
Secondary accession number(s): P76951
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: February 1, 1997
Last modified: November 30, 2016
This is version 115 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, 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.