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Protein

L-Ala-D/L-Glu epimerase

Gene

TM_0006

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
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 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 a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.1 Publication

Catalytic activityi

L-alanyl-D-glutamate = L-alanyl-L-glutamate.2 Publications

Cofactori

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

Kineticsi

  1. KM=2.8 mM for L-Ala-L-Glu (at pH 7.5 and 28 degrees Celsius)1 Publication
  2. KM=1.3 mM for L-Ala-L-Phe (at pH 7.5 and 28 degrees Celsius)1 Publication
  3. KM=0.71 mM for L-Ala-L-Tyr (at pH 7.5 and 28 degrees Celsius)1 Publication
  4. KM=5.3 mM for L-Ala-L-His (at pH 7.5 and 28 degrees Celsius)1 Publication
  5. KM=2.9 mM for L-Ala-L-Leu (at pH 7.5 and 28 degrees Celsius)1 Publication
  6. KM=4.7 mM for L-Ile-L-Phe (at pH 7.5 and 28 degrees Celsius)1 Publication
  7. KM=3.9 mM for L-Lys-L-Phe (at pH 7.5 and 28 degrees Celsius)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 sitei134 – 1341Substrate
    Binding sitei159 – 1591Substrate
    Active sitei161 – 1611Proton acceptor; specific for (R)-substrate epimerizationBy similarity
    Metal bindingi188 – 1881Magnesium
    Binding sitei190 – 1901Substrate
    Metal bindingi216 – 2161Magnesium
    Metal bindingi241 – 2411Magnesium
    Active sitei265 – 2651Proton acceptor; specific for (S)-substrate epimerizationBy similarity
    Binding sitei292 – 2921Substrate; via carbonyl oxygen
    Binding sitei317 – 3171Substrate
    Binding sitei319 – 3191Substrate

    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

    SABIO-RKQ9WXM1.
    UniPathwayiUPA00549.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    L-Ala-D/L-Glu epimerase (EC:5.1.1.202 Publications)
    Short name:
    AE epimerase
    Short name:
    AEE
    Gene namesi
    Ordered Locus Names:TM_0006
    OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
    Taxonomic identifieri243274 [NCBI]
    Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
    Proteomesi
    • UP000008183 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 345345L-Ala-D/L-Glu epimerasePRO_0000388972Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi243274.TM0006.

    Structurei

    Secondary structure

    1
    345
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 2220Combined sources
    Beta strandi25 – 3915Combined sources
    Beta strandi44 – 496Combined sources
    Helixi53 – 564Combined sources
    Helixi60 – 656Combined sources
    Helixi67 – 748Combined sources
    Helixi79 – 813Combined sources
    Helixi82 – 898Combined sources
    Helixi96 – 11419Combined sources
    Helixi118 – 1214Combined sources
    Beta strandi127 – 1315Combined sources
    Beta strandi133 – 1353Combined sources
    Helixi140 – 15213Combined sources
    Beta strandi156 – 1616Combined sources
    Helixi166 – 17914Combined sources
    Beta strandi184 – 1885Combined sources
    Helixi195 – 20713Combined sources
    Beta strandi213 – 2164Combined sources
    Helixi224 – 23310Combined sources
    Beta strandi234 – 2363Combined sources
    Beta strandi238 – 2414Combined sources
    Helixi247 – 25610Combined sources
    Beta strandi260 – 2645Combined sources
    Helixi266 – 28217Combined sources
    Turni283 – 2853Combined sources
    Beta strandi287 – 2904Combined sources
    Helixi297 – 31014Combined sources
    Beta strandi314 – 3163Combined sources
    Helixi320 – 3234Combined sources
    Beta strandi324 – 3263Combined sources
    Beta strandi332 – 3365Combined sources
    Beta strandi339 – 3413Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ZADX-ray1.60A/B/C/D1-345[»]
    3DEQX-ray2.10A/B/C/D1-345[»]
    3DERX-ray1.90A/B/C/D1-345[»]
    3DESX-ray2.30A/B/C/D1-345[»]
    3DFYX-ray2.10A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-345[»]
    ProteinModelPortaliQ9WXM1.
    SMRiQ9WXM1. Positions 2-345.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9WXM1.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105DTQ. Bacteria.
    COG4948. LUCA.
    InParanoidiQ9WXM1.
    OMAiDFDAPLM.
    OrthoDBiEOG6S52NQ.

    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.

    Q9WXM1-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSRIVNVKLS LKRYEYEKPF HITGSVSSES RNVEVEIVLE SGVKGYGEAS
    60 70 80 90 100
    PSFRVNGERV EALLAIENAV REMITGIDVR NYARIFEITD RLFGFPSLKA
    110 120 130 140 150
    AVQFATLDAL SQELGTQVCY LLGGKRDEIE TDKTVGIDTV ENRVKEAKKI
    160 170 180 190 200
    FEEGFRVIKI KVGENLKEDI EAVEEIAKVT RGAKYIVDAN MGYTQKEAVE
    210 220 230 240 250
    FARAVYQKGI DIAVYEQPVR REDIEGLKFV RFHSPFPVAA DESARTKFDV
    260 270 280 290 300
    MRLVKEEAVD YVNIKLMKSG ISDALAIVEI AESSGLKLMI GCMGESSLGI
    310 320 330 340
    NQSVHFALGT GAFEFHDLDS HLMLKEEVFR GKFIQDGPRM RVKDQ
    Length:345
    Mass (Da):38,664
    Last modified:November 1, 1999 - v1
    Checksum:i587BDE71BB1E777B
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000512 Genomic DNA. Translation: AAD35100.1.
    PIRiH72429.
    RefSeqiNP_227822.1. NC_000853.1.
    WP_004082436.1. NZ_CP011107.1.

    Genome annotation databases

    EnsemblBacteriaiAAD35100; AAD35100; TM_0006.
    GeneIDi896814.
    KEGGitma:TM0006.
    PATRICi23934852. VBITheMar51294_0004.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000512 Genomic DNA. Translation: AAD35100.1.
    PIRiH72429.
    RefSeqiNP_227822.1. NC_000853.1.
    WP_004082436.1. NZ_CP011107.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ZADX-ray1.60A/B/C/D1-345[»]
    3DEQX-ray2.10A/B/C/D1-345[»]
    3DERX-ray1.90A/B/C/D1-345[»]
    3DESX-ray2.30A/B/C/D1-345[»]
    3DFYX-ray2.10A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-345[»]
    ProteinModelPortaliQ9WXM1.
    SMRiQ9WXM1. Positions 2-345.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi243274.TM0006.

    Protocols and materials databases

    DNASUi896814.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAD35100; AAD35100; TM_0006.
    GeneIDi896814.
    KEGGitma:TM0006.
    PATRICi23934852. VBITheMar51294_0004.

    Phylogenomic databases

    eggNOGiENOG4105DTQ. Bacteria.
    COG4948. LUCA.
    InParanoidiQ9WXM1.
    OMAiDFDAPLM.
    OrthoDBiEOG6S52NQ.

    Enzyme and pathway databases

    UniPathwayiUPA00549.
    SABIO-RKQ9WXM1.

    Miscellaneous databases

    EvolutionaryTraceiQ9WXM1.

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
    2. "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: CATALYTIC ACTIVITY.
    3. "Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening."
      Kalyanaraman C., Imker H.J., Fedorov A.A., Fedorov E.V., Glasner M.E., Babbitt P.C., Almo S.C., Gerlt J.A., Jacobson M.P.
      Structure 16:1668-1677(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH SUBSTRATE AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
    4. "Crystal structure of muconate cycloisomerase from Thermotoga maritima MSB8."
      RIKEN structural genomics initiative (RSGI)
      Submitted (FEB-2009) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.

    Entry informationi

    Entry nameiAEEP_THEMA
    AccessioniPrimary (citable) accession number: Q9WXM1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 24, 2009
    Last sequence update: November 1, 1999
    Last modified: April 13, 2016
    This is version 88 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. 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

    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.