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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-Experimental evidence at protein leveli

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

Catalytic activityi

L-alanyl-D-glutamate = L-alanyl-L-glutamate.1 Publication

Cofactori

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

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

    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
    Binding sitei24Substrate1 Publication1
    Binding sitei135Substrate1 Publication1
    Binding sitei160Substrate1 Publication1
    Active sitei162Proton acceptor; specific for (R)-substrate epimerization1 Publication1
    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

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Cell wall biogenesis/degradation

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciBSUB:BSU12980-MONOMER.
    SABIO-RKO34508.
    UniPathwayiUPA00549.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    L-Ala-D/L-Glu epimerase (EC:5.1.1.201 Publication)
    Short name:
    AE epimerase
    Short name:
    AEE
    Gene namesi
    Name:ykfB
    Ordered Locus Names:BSU12980
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00003889701 – 366L-Ala-D/L-Glu epimeraseAdd BLAST366

    Proteomic databases

    PaxDbiO34508.

    Expressioni

    Inductioni

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

    Interactioni

    Subunit structurei

    Homooctamer; tetramer of dimers.2 Publications

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100007196.

    Structurei

    Secondary structure

    1366
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 20Combined sources19
    Beta strandi25 – 38Combined sources14
    Beta strandi43 – 48Combined sources6
    Turni52 – 55Combined sources4
    Helixi59 – 68Combined sources10
    Helixi70 – 74Combined sources5
    Helixi79 – 81Combined sources3
    Helixi82 – 91Combined sources10
    Beta strandi92 – 95Combined sources4
    Helixi97 – 114Combined sources18
    Helixi119 – 123Combined sources5
    Beta strandi128 – 132Combined sources5
    Beta strandi134 – 136Combined sources3
    Helixi141 – 154Combined sources14
    Beta strandi158 – 162Combined sources5
    Beta strandi164 – 166Combined sources3
    Helixi168 – 182Combined sources15
    Beta strandi184 – 191Combined sources8
    Helixi198 – 210Combined sources13
    Beta strandi215 – 219Combined sources5
    Helixi227 – 236Combined sources10
    Beta strandi241 – 243Combined sources3
    Helixi250 – 259Combined sources10
    Beta strandi263 – 267Combined sources5
    Helixi269 – 272Combined sources4
    Helixi275 – 287Combined sources13
    Beta strandi291 – 294Combined sources4
    Helixi301 – 313Combined sources13
    Beta strandi317 – 320Combined sources4
    Helixi324 – 327Combined sources4
    Beta strandi328 – 330Combined sources3
    Beta strandi333 – 336Combined sources4
    Beta strandi338 – 340Combined sources3
    Beta strandi343 – 345Combined sources3
    Beta strandi349 – 351Combined sources3
    Beta strandi354 – 357Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    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[»]
    ProteinModelPortaliO34508.
    SMRiO34508.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO34508.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105DTQ. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000185903.
    InParanoidiO34508.
    KOiK19802.
    OMAiCMVGSMI.
    PhylomeDBiO34508.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF13378. MR_MLE_C. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.

    Sequencei

    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
    Checksum:i8E33E7955435CE8B
    GO

    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.

    Genome annotation databases

    EnsemblBacteriaiCAB13155; CAB13155; BSU12980.
    GeneIDi939862.
    KEGGibsu:BSU12980.
    PATRICi18974353. VBIBacSub10457_1369.

    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:
    PDBei
    RCSB PDBi
    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[»]
    ProteinModelPortaliO34508.
    SMRiO34508.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100007196.

    Proteomic databases

    PaxDbiO34508.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB13155; CAB13155; BSU12980.
    GeneIDi939862.
    KEGGibsu:BSU12980.
    PATRICi18974353. VBIBacSub10457_1369.

    Phylogenomic databases

    eggNOGiENOG4105DTQ. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000185903.
    InParanoidiO34508.
    KOiK19802.
    OMAiCMVGSMI.
    PhylomeDBiO34508.

    Enzyme and pathway databases

    UniPathwayiUPA00549.
    BioCyciBSUB:BSU12980-MONOMER.
    SABIO-RKO34508.

    Miscellaneous databases

    EvolutionaryTraceiO34508.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF13378. MR_MLE_C. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiAEEP_BACSU
    AccessioniPrimary (citable) accession number: O34508
    Secondary accession number(s): Q796M5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 24, 2009
    Last sequence update: January 1, 1998
    Last modified: November 2, 2016
    This is version 98 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. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    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.