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Protein

Aminopeptidase YpdE

Gene

ypdE

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Has a broad aminopeptidase activity on non-blocked peptides by progressively cleaving amino acids off the peptide substrate. Aminopeptidase activity stops at the residue before the first proline in the peptide. Cannot cleave when proline is the first N-terminal residue.1 Publication

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Co2+Curated1 Publication, Ni2+Curated1 Publication, Mn2+Curated1 Publication, Cu2+Curated1 PublicationNote: Binds 2 divalent metal cations per subunit. Can use cobalt, and to a lesser extent, nickel, manganese or copper.Curated1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi62Divalent metal cation 1By similarity1
Metal bindingi166Divalent metal cation 1By similarity1
Metal bindingi166Divalent metal cation 2By similarity1
<p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei198Proton acceptorBy similarity1
Metal bindingi199Divalent metal cation 2By similarity1
Metal bindingi221Divalent metal cation 1By similarity1
Metal bindingi308Divalent metal cation 2By similarity1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

  • aminopeptidase activity Source: EcoliWiki
  • metal ion binding Source: UniProtKB-KW
  • metallopeptidase activity Source: EcoliWiki

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionAminopeptidase, Hydrolase, Metalloprotease, Protease
LigandCobalt, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

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BioCyci
EcoCyc:G7247-MONOMER
MetaCyc:G7247-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Aminopeptidase YpdE (EC:3.4.11.-)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:ypdE
Ordered Locus Names:b2384, JW2381
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

Escherichia coli strain K12 genome database

More...
EcoGenei
EG14152 ypdE

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000716591 – 345Aminopeptidase YpdEAdd BLAST345

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

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jPOSTi
P77585

PaxDb, a database of protein abundance averages across all three domains of life

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PaxDbi
P77585

PRoteomics IDEntifications database

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PRIDEi
P77585

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

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BioGridi
4260561, 10 interactors

Database of interacting proteins

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DIPi
DIP-48263N

Protein interaction database and analysis system

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IntActi
P77585, 8 interactors

STRING: functional protein association networks

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STRINGi
316385.ECDH10B_2549

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
P77585

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P77585

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the peptidase M42 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
ENOG4105CN9 Bacteria
COG1363 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000291973

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
P77585

Database for complete collections of gene phylogenies

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PhylomeDBi
P77585

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.40.30.40, 1 hit

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR008007 Peptidase_M42
IPR023367 Peptidase_M42_dom2

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF05343 Peptidase_M42, 1 hit

PIRSF; a whole-protein classification database

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PIRSFi
PIRSF001123 PepA_GA, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P77585-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDLSLLKALS EADAIASSEQ EVRQILLEEA DRLQKEVRFD GLGSVLIRLN
60 70 80 90 100
ESTGPKVMIC AHMDEVGFMV RSISREGAID VLPVGNVRMA ARQLQPVRIT
110 120 130 140 150
TREECKIPGL LDGDRQGNDV SAMRVDIGAR SYDEVMQAGI RPGDRVTFDT
160 170 180 190 200
TFQVLPHQRV MGKAFDDRLG CYLLVTLLRE LHDAELPAEV WLVASSSEEV
210 220 230 240 250
GLRGGQTATR AVSPDVAIVL DTACWAKNFD YGAANHRQIG NGPMLVLSDK
260 270 280 290 300
SLIAPPKLTA WVETVAAEIG VPLQADMFSN GGTDGGAVHL TGTGVPTVVM
310 320 330 340
GPATRHGHCA ASIADCRDIL QMQQLLSALI QRLTRETVVQ LTDFR
Length:345
Mass (Da):37,409
Last modified:February 1, 1997 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iFB2D88A5C11590A1
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

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DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC75443.1
AP009048 Genomic DNA Translation: BAA16254.1

Protein sequence database of the Protein Information Resource

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PIRi
E65012

NCBI Reference Sequences

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RefSeqi
NP_416885.1, NC_000913.3
WP_000366028.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

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EnsemblBacteriai
AAC75443; AAC75443; b2384
BAA16254; BAA16254; BAA16254

Database of genes from NCBI RefSeq genomes

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GeneIDi
946848

KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGGi
ecj:JW2381
eco:b2384

Pathosystems Resource Integration Center (PATRIC)

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PATRICi
fig|1411691.4.peg.4344

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC75443.1
AP009048 Genomic DNA Translation: BAA16254.1
PIRiE65012
RefSeqiNP_416885.1, NC_000913.3
WP_000366028.1, NZ_LN832404.1

3D structure databases

ProteinModelPortaliP77585
SMRiP77585
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260561, 10 interactors
DIPiDIP-48263N
IntActiP77585, 8 interactors
STRINGi316385.ECDH10B_2549

Proteomic databases

jPOSTiP77585
PaxDbiP77585
PRIDEiP77585

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75443; AAC75443; b2384
BAA16254; BAA16254; BAA16254
GeneIDi946848
KEGGiecj:JW2381
eco:b2384
PATRICifig|1411691.4.peg.4344

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB3904
EcoGeneiEG14152 ypdE

Phylogenomic databases

eggNOGiENOG4105CN9 Bacteria
COG1363 LUCA
HOGENOMiHOG000291973
InParanoidiP77585
PhylomeDBiP77585

Enzyme and pathway databases

BioCyciEcoCyc:G7247-MONOMER
MetaCyc:G7247-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P77585

Family and domain databases

Gene3Di2.40.30.40, 1 hit
InterProiView protein in InterPro
IPR008007 Peptidase_M42
IPR023367 Peptidase_M42_dom2
PfamiView protein in Pfam
PF05343 Peptidase_M42, 1 hit
PIRSFiPIRSF001123 PepA_GA, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiYPDE_ECOLI
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P77585
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: February 1, 1997
Last modified: January 16, 2019
This is version 118 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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