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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei24 – 241Substrate1 Publication
    Binding sitei135 – 1351Substrate1 Publication
    Binding sitei160 – 1601Substrate1 Publication
    Active sitei162 – 1621Proton acceptor; specific for (R)-substrate epimerization1 Publication
    Metal bindingi191 – 1911Magnesium2 Publications
    Metal bindingi219 – 2191Magnesium2 Publications
    Metal bindingi244 – 2441Magnesium2 Publications
    Active sitei268 – 2681Proton acceptor; specific for (S)-substrate epimerization1 Publication
    Binding sitei296 – 2961Substrate; via carbonyl oxygen1 Publication
    Binding sitei298 – 2981Substrate; via amide nitrogen1 Publication
    Binding sitei321 – 3211Substrate1 Publication
    Binding sitei323 – 3231Substrate1 Publication

    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)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 366366L-Ala-D/L-Glu epimerasePRO_0000388970Add
    BLAST

    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

    1
    366
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 2019Combined sources
    Beta strandi25 – 3814Combined sources
    Beta strandi43 – 486Combined sources
    Turni52 – 554Combined sources
    Helixi59 – 6810Combined sources
    Helixi70 – 745Combined sources
    Helixi79 – 813Combined sources
    Helixi82 – 9110Combined sources
    Beta strandi92 – 954Combined sources
    Helixi97 – 11418Combined sources
    Helixi119 – 1235Combined sources
    Beta strandi128 – 1325Combined sources
    Beta strandi134 – 1363Combined sources
    Helixi141 – 15414Combined sources
    Beta strandi158 – 1625Combined sources
    Beta strandi164 – 1663Combined sources
    Helixi168 – 18215Combined sources
    Beta strandi184 – 1918Combined sources
    Helixi198 – 21013Combined sources
    Beta strandi215 – 2195Combined sources
    Helixi227 – 23610Combined sources
    Beta strandi241 – 2433Combined sources
    Helixi250 – 25910Combined sources
    Beta strandi263 – 2675Combined sources
    Helixi269 – 2724Combined sources
    Helixi275 – 28713Combined sources
    Beta strandi291 – 2944Combined sources
    Helixi301 – 31313Combined sources
    Beta strandi317 – 3204Combined sources
    Helixi324 – 3274Combined sources
    Beta strandi328 – 3303Combined sources
    Beta strandi333 – 3364Combined sources
    Beta strandi338 – 3403Combined sources
    Beta strandi343 – 3453Combined sources
    Beta strandi349 – 3513Combined sources
    Beta strandi354 – 3574Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JPMX-ray2.25A/B/C/D1-366[»]
    1TKKX-ray2.10A/B/C/D/E/F/G/H1-366[»]
    ProteinModelPortaliO34508.
    SMRiO34508. Positions 1-359.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO34508.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105DTQ. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000185903.
    InParanoidiO34508.
    KOiK19802.
    OMAiDFDAPLM.
    OrthoDBiEOG6S52NQ.
    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JPMX-ray2.25A/B/C/D1-366[»]
    1TKKX-ray2.10A/B/C/D/E/F/G/H1-366[»]
    ProteinModelPortaliO34508.
    SMRiO34508. Positions 1-359.
    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.
    OMAiDFDAPLM.
    OrthoDBiEOG6S52NQ.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Sequence of the Bacillus subtilis genome between xlyA and ykoR."
      Devine K.M.
      Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    3. "Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases."
      Schmidt D.M.Z., Hubbard B.K., Gerlt J.A.
      Biochemistry 40:15707-15715(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, PROBABLE ROLE IN MUREIN PEPTIDE METABOLISM.
      Strain: 168.
    4. "Identification of AbrB-regulated genes involved in biofilm formation by Bacillus subtilis."
      Hamon M.A., Stanley N.R., Britton R.A., Grossman A.D., Lazazzera B.A.
      Mol. Microbiol. 52:847-860(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    5. "How bacteria consume their own exoskeletons (turnover and recycling of cell wall peptidoglycan)."
      Park J.T., Uehara T.
      Microbiol. Mol. Biol. Rev. 72:211-227(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROBABLE FUNCTION IN PEPTIDOGLYCAN DEGRADATION, REVIEW.
    6. "Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis."
      Gulick A.M., Schmidt D.M.Z., Gerlt J.A., Rayment I.
      Biochemistry 40:15716-15724(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, COFACTOR, SUBUNIT.
      Strain: 168.
    7. "Evolution of enzymatic activities in the enolase superfamily: structure of a substrate-liganded complex of the L-Ala-D/L-Glu epimerase from Bacillus subtilis."
      Klenchin V.A., Schmidt D.M.Z., Gerlt J.A., Rayment I.
      Biochemistry 43:10370-10378(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND MAGNESIUM, COFACTOR, ACTIVE SITES, REACTION MECHANISM.
      Strain: 168.

    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: April 13, 2016
    This is version 95 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.