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Protein

L-Ala-D/L-Glu epimerase

Gene

ycjG

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has a role in the recycling 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 all the L-Ala-X dipeptides, except L-Ala-L-Arg, L-Ala-L-Lys and L-Ala-L-Pro. Is also active with L-Gly-L-Glu, L-Phe-L-Glu, and L-Ser-L-Glu, but not with L-Glu-L-Glu, L-Lys-L-Glu, L-Pro-L-Glu, L-Lys-L-Ala, or D-Ala-D-Ala.2 Publications

Catalytic activityi

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

Cofactori

Mg2+By similarityNote: Binds 1 Mg2+ ion per subunit.By similarity

Kineticsi

  1. KM=0.13 mM for L-Ala-D-Glu (at pH 8.5)1 Publication
  2. KM=0.19 mM for L-Ala-D-Asp (at pH 8.5)1 Publication
  3. KM=0.69 mM for L-Ala-D-Met (at pH 8.5)1 Publication
  4. KM=1.8 mM for L-Ala-D-Gln (at pH 8.5)1 Publication

    Pathwayi: peptidoglycan recycling

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

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei124 – 1241SubstrateBy similarity
    Binding sitei149 – 1491SubstrateBy similarity
    Active sitei151 – 1511Proton acceptor; specific for (R)-substrate epimerizationBy similarity
    Metal bindingi176 – 1761MagnesiumBy similarity
    Metal bindingi202 – 2021MagnesiumBy similarity
    Metal bindingi225 – 2251MagnesiumBy similarity
    Active sitei247 – 2471Proton acceptor; specific for (S)-substrate epimerizationBy similarity
    Binding sitei275 – 2751Substrate; via carbonyl oxygenBy similarity
    Binding sitei297 – 2971SubstrateBy similarity
    Binding sitei299 – 2991SubstrateBy similarity

    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

    BioCyciEcoCyc:G6661-MONOMER.
    ECOL316407:JW1318-MONOMER.
    MetaCyc:G6661-MONOMER.
    RETL1328306-WGS:GSTH-2361-MONOMER.
    SABIO-RKP51981.
    UniPathwayiUPA00544.

    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:ycjG
    Synonyms:ycjH
    Ordered Locus Names:b1325, JW1318
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13228. ycjG.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 321321L-Ala-D/L-Glu epimerasePRO_0000171261Add
    BLAST

    Proteomic databases

    EPDiP51981.
    PaxDbiP51981.
    PRIDEiP51981.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    BioGridi4260152. 370 interactions.
    IntActiP51981. 1 interaction.
    STRINGi511145.b1325.

    Structurei

    Secondary structure

    1
    321
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 1412Combined sources
    Beta strandi25 – 3612Combined sources
    Beta strandi39 – 457Combined sources
    Helixi49 – 513Combined sources
    Helixi55 – 639Combined sources
    Helixi66 – 705Combined sources
    Helixi75 – 817Combined sources
    Helixi86 – 10116Combined sources
    Turni102 – 1043Combined sources
    Helixi107 – 1115Combined sources
    Beta strandi117 – 1215Combined sources
    Beta strandi123 – 1253Combined sources
    Helixi130 – 14213Combined sources
    Beta strandi146 – 1516Combined sources
    Helixi157 – 16711Combined sources
    Beta strandi171 – 1766Combined sources
    Helixi186 – 19510Combined sources
    Beta strandi200 – 2023Combined sources
    Helixi211 – 2144Combined sources
    Beta strandi222 – 2254Combined sources
    Helixi231 – 2333Combined sources
    Helixi234 – 2374Combined sources
    Beta strandi241 – 2466Combined sources
    Helixi248 – 2514Combined sources
    Helixi254 – 26613Combined sources
    Beta strandi270 – 2734Combined sources
    Helixi280 – 2867Combined sources
    Helixi287 – 2926Combined sources
    Beta strandi294 – 2963Combined sources
    Helixi300 – 3034Combined sources
    Beta strandi304 – 3063Combined sources
    Beta strandi313 – 3153Combined sources
    Beta strandi318 – 3203Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JPDX-ray2.60X1-321[»]
    ProteinModelPortaliP51981.
    SMRiP51981. Positions 1-321.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP51981.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4107S8C. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000185901.
    InParanoidiP51981.
    KOiK19802.
    OMAiRVYEEAW.
    OrthoDBiEOG68WR4X.
    PhylomeDBiP51981.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
    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.
    PROSITEiPS00908. MR_MLE_1. 1 hit.
    PS00909. MR_MLE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P51981-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MRTVKVFEEA WPLHTPFVIA RGSRSEARVV VVELEEEGIK GTGECTPYPR
    60 70 80 90 100
    YGESDASVMA QIMSVVPQLE KGLTREELQK ILPAGAARNA LDCALWDLAA
    110 120 130 140 150
    RRQQQSLADL IGITLPETVI TAQTVVIGTP DQMANSASTL WQAGAKLLKV
    160 170 180 190 200
    KLDNHLISER MVAIRTAVPD ATLIVDANES WRAEGLAARC QLLADLGVAM
    210 220 230 240 250
    LEQPLPAQDD AALENFIHPL PICADESCHT RSNLKALKGR YEMVNIKLDK
    260 270 280 290 300
    TGGLTEALAL ATEARAQGFS LMLGCMLCTS RAISAALPLV PQVSFADLDG
    310 320
    PTWLAVDVEP ALQFTTGELH L
    Length:321
    Mass (Da):34,674
    Last modified:November 1, 1997 - v2
    Checksum:iB0AA31DD4EC2E2CB
    GO

    Sequence cautioni

    The sequence U33213 differs from that shown. Reason: Frameshift at position 285. Curated
    The sequence U33213 differs from that shown. Reason: Erroneous termination at position 275. Translated as Cys.Curated

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti236 – 2361A → R in U33213 (PubMed:7499381).Curated
    Sequence conflicti244 – 2441V → I in U33213 (PubMed:7499381).Curated
    Sequence conflicti257 – 2571Missing in U33213 (PubMed:7499381).Curated
    Sequence conflicti259 – 2591A → G in U33213 (PubMed:7499381).Curated
    Sequence conflicti301 – 3011P → S in U33213 (PubMed:7499381).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U33213 Genomic DNA. No translation available.
    U00096 Genomic DNA. Translation: AAC74407.2.
    AP009048 Genomic DNA. Translation: BAA14907.1.
    PIRiH64881.
    RefSeqiNP_415841.4. NC_000913.3.
    WP_001261211.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74407; AAC74407; b1325.
    BAA14907; BAA14907; BAA14907.
    GeneIDi946013.
    KEGGiecj:JW1318.
    eco:b1325.
    PATRICi32117924. VBIEscCol129921_1382.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U33213 Genomic DNA. No translation available.
    U00096 Genomic DNA. Translation: AAC74407.2.
    AP009048 Genomic DNA. Translation: BAA14907.1.
    PIRiH64881.
    RefSeqiNP_415841.4. NC_000913.3.
    WP_001261211.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JPDX-ray2.60X1-321[»]
    ProteinModelPortaliP51981.
    SMRiP51981. Positions 1-321.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260152. 370 interactions.
    IntActiP51981. 1 interaction.
    STRINGi511145.b1325.

    Proteomic databases

    EPDiP51981.
    PaxDbiP51981.
    PRIDEiP51981.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74407; AAC74407; b1325.
    BAA14907; BAA14907; BAA14907.
    GeneIDi946013.
    KEGGiecj:JW1318.
    eco:b1325.
    PATRICi32117924. VBIEscCol129921_1382.

    Organism-specific databases

    EchoBASEiEB3018.
    EcoGeneiEG13228. ycjG.

    Phylogenomic databases

    eggNOGiENOG4107S8C. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000185901.
    InParanoidiP51981.
    KOiK19802.
    OMAiRVYEEAW.
    OrthoDBiEOG68WR4X.
    PhylomeDBiP51981.

    Enzyme and pathway databases

    UniPathwayiUPA00544.
    BioCyciEcoCyc:G6661-MONOMER.
    ECOL316407:JW1318-MONOMER.
    MetaCyc:G6661-MONOMER.
    RETL1328306-WGS:GSTH-2361-MONOMER.
    SABIO-RKP51981.

    Miscellaneous databases

    EvolutionaryTraceiP51981.
    PROiP51981.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
    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.
    PROSITEiPS00908. MR_MLE_1. 1 hit.
    PS00909. MR_MLE_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Thioredoxin-linked 'thiol peroxidase' from periplasmic space of Escherichia coli."
      Cha M.-K., Kim H.-K., Kim I.-H.
      J. Biol. Chem. 270:28635-28641(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. Rudd K.E.
      Unpublished observations (MAR-1996)
      Cited for: IDENTIFICATION.
    6. "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.
      Strain: K12 / MG1655 / ATCC 47076.
    7. "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: FUNCTION IN PEPTIDOGLYCAN RECYCLING, REVIEW.
    8. "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 (2.6 ANGSTROMS), SUBUNIT.
      Strain: K12 / MG1655 / ATCC 47076.

    Entry informationi

    Entry nameiAEEP_ECOLI
    AccessioniPrimary (citable) accession number: P51981
    Secondary accession number(s): P51982, P76048, P77345
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: November 1, 1997
    Last modified: April 13, 2016
    This is version 129 of the entry and version 2 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. 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.