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Entry version 120 (02 Jun 2021)
Sequence version 1 (01 Jan 1998)
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Protein

L-Ala-D/L-Glu epimerase

Gene

ykfB

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:5 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

Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of the other Ala-X dipeptides L-Ala-L-Asp, L-Ala-L-Leu, L-Ala-L-Met, and L-Ala-L-Ser. Is not able to epimerize other L-Ala-X dipeptides. Is also active with L-Ser-L-Glu and, oddly, L-Pro-L-Glu, but not with L-Glu-L-Glu, L-Lys-L-Glu, L-Lys-L-Ala, or D-Ala-D-Ala.

1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<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

Mg2+2 PublicationsNote: Binds 1 Mg2+ ion per subunit.2 Publications

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

The catalytic efficiency is 25-fold higher with L-Ala-D-Glu than with L-Ala-D-Asp or L-Ala-D-Met as substrate.
  1. KM=320 µM for L-Ala-D-Glu (at pH 8.5)1 Publication
  2. KM=28 µM for L-Ala-D-Asp (at pH 8.5)1 Publication
  3. KM=510 µM for L-Ala-D-Met (at pH 8.5)1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: peptidoglycan degradation

This protein is involved in the pathway peptidoglycan degradation, which is part of Cell wall degradation.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan degradation and in Cell wall degradation.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei24Substrate1 Publication1
Binding sitei135Substrate1 Publication1
Binding sitei160Substrate1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> 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 sitei162Proton acceptor; specific for (R)-substrate epimerization1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> 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 bindingi191Magnesium2 Publications1
Metal bindingi219Magnesium2 Publications1
Metal bindingi244Magnesium2 Publications1
Active sitei268Proton acceptor; specific for (S)-substrate epimerization1 Publication1
Binding sitei296Substrate; via carbonyl oxygen1 Publication1
Binding sitei298Substrate; via amide nitrogen1 Publication1
Binding sitei321Substrate1 Publication1
Binding sitei323Substrate1 Publication1

<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

GO - Biological processi

<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 functionIsomerase
Biological processCell wall biogenesis/degradation
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

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BioCyci
BSUB:BSU12980-MONOMER

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
5.1.1.20, 658

SABIO-RK: Biochemical Reaction Kinetics Database

More...
SABIO-RKi
O34508

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00549

<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:
L-Ala-D/L-Glu epimerase (EC:5.1.1.201 Publication)
Short name:
AE epimerase
Short name:
AEE
<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:ykfB
Ordered Locus Names:BSU12980
<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>OrganismiBacillus subtilis (strain 168)
<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 identifieri224308 [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 lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
<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
  • UP000001570 <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

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003889701 – 366L-Ala-D/L-Glu epimeraseAdd BLAST366

Proteomic databases

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

More...
PaxDbi
O34508

PRoteomics IDEntifications database

More...
PRIDEi
O34508

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Repressed by AbrB, a transcription factor that negatively controls biofilm formation.1 Publication

<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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homooctamer; tetramer of dimers.

2 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
224308.BSU12980

<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

Secondary structure

1366
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

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SMRi
O34508

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
O34508

<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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG4948, Bacteria

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
O34508

Identification of Orthologs from Complete Genome Data

More...
OMAi
MFGCYSD

Database for complete collections of gene phylogenies

More...
PhylomeDBi
O34508

Family and domain databases

Conserved Domains Database

More...
CDDi
cd03319, L-Ala-DL-Glu_epimerase, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.20.20.120, 1 hit
3.30.390.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR034603, Dipeptide_epimerase
IPR036849, Enolase-like_C_sf
IPR029017, Enolase-like_N
IPR029065, Enolase_C-like
IPR013342, Mandelate_racemase_C
IPR013341, Mandelate_racemase_N_dom

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF13378, MR_MLE_C, 1 hit
PF02746, MR_MLE_N, 1 hit

Structure-Function Linkage Database

More...
SFLDi
SFLDF00010, dipeptide_epimerase, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00922, MR_MLE, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF51604, SSF51604, 1 hit
SSF54826, SSF54826, 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>. The information is filed in different subsections. The current subsections and their content are listed below:<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.

O34508-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKIIRIETSR IAVPLTKPFK TALRTVYTAE SVIVRITYDS GAVGWGEAPP
60 70 80 90 100
TLVITGDSMD SIESAIHHVL KPALLGKSLA GYEAILHDIQ HLLTGNMSAK
110 120 130 140 150
AAVEMALYDG WAQMCGLPLY QMLGGYRDTL ETDYTVSVNS PEEMAADAEN
160 170 180 190 200
YLKQGFQTLK IKVGKDDIAT DIARIQEIRK RVGSAVKLRL DANQGWRPKE
210 220 230 240 250
AVTAIRKMED AGLGIELVEQ PVHKDDLAGL KKVTDATDTP IMADESVFTP
260 270 280 290 300
RQAFEVLQTR SADLINIKLM KAGGISGAEK INAMAEACGV ECMVGSMIET
310 320 330 340 350
KLGITAAAHF AASKRNITRF DFDAPLMLKT DVFNGGITYS GSTISMPGKP
360
GLGIIGAALL KGEKEQ
Length:366
Mass (Da):39,473
Last modified:January 1, 1998 - 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:i8E33E7955435CE8B
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

More...
DDBJi
Links Updated
AJ002571 Genomic DNA Translation: CAA05578.1
AL009126 Genomic DNA Translation: CAB13155.1

Protein sequence database of the Protein Information Resource

More...
PIRi
H69855

NCBI Reference Sequences

More...
RefSeqi
NP_389181.1, NC_000964.3
WP_003244980.1, NZ_JNCM01000035.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB13155; CAB13155; BSU_12980

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
939862

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU12980

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.179.peg.1410

<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
AJ002571 Genomic DNA Translation: CAA05578.1
AL009126 Genomic DNA Translation: CAB13155.1
PIRiH69855
RefSeqiNP_389181.1, NC_000964.3
WP_003244980.1, NZ_JNCM01000035.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JPMX-ray2.25A/B/C/D1-366[»]
1TKKX-ray2.10A/B/C/D/E/F/G/H1-366[»]
SMRiO34508
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU12980

Proteomic databases

PaxDbiO34508
PRIDEiO34508

Genome annotation databases

EnsemblBacteriaiCAB13155; CAB13155; BSU_12980
GeneIDi939862
KEGGibsu:BSU12980
PATRICifig|224308.179.peg.1410

Phylogenomic databases

eggNOGiCOG4948, Bacteria
InParanoidiO34508
OMAiMFGCYSD
PhylomeDBiO34508

Enzyme and pathway databases

UniPathwayiUPA00549
BioCyciBSUB:BSU12980-MONOMER
BRENDAi5.1.1.20, 658
SABIO-RKiO34508

Miscellaneous databases

EvolutionaryTraceiO34508

Family and domain databases

CDDicd03319, L-Ala-DL-Glu_epimerase, 1 hit
Gene3Di3.20.20.120, 1 hit
3.30.390.10, 1 hit
InterProiView protein in InterPro
IPR034603, Dipeptide_epimerase
IPR036849, Enolase-like_C_sf
IPR029017, Enolase-like_N
IPR029065, Enolase_C-like
IPR013342, Mandelate_racemase_C
IPR013341, Mandelate_racemase_N_dom
PfamiView protein in Pfam
PF13378, MR_MLE_C, 1 hit
PF02746, MR_MLE_N, 1 hit
SFLDiSFLDF00010, dipeptide_epimerase, 1 hit
SMARTiView protein in SMART
SM00922, MR_MLE, 1 hit
SUPFAMiSSF51604, SSF51604, 1 hit
SSF54826, SSF54826, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
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 nameiAEEP_BACSU
<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: O34508
Secondary accession number(s): Q796M5
<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: November 24, 2009
Last sequence update: January 1, 1998
Last modified: June 2, 2021
This is version 120 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

3D-structure, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
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