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P11444

- MANR_PSEPU

UniProt

P11444 - MANR_PSEPU

Protein

Mandelate racemase

Gene

mdlA

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 95 (01 Oct 2014)
      Sequence version 1 (01 Oct 1989)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    (S)-mandelate = (R)-mandelate.

    Cofactori

    Divalent metal ions. Magnesium seems to be the preferred ion.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei166 – 1661Proton acceptor; specific for S-mandelate
    Metal bindingi195 – 1951Magnesium
    Metal bindingi221 – 2211Magnesium
    Metal bindingi247 – 2471Magnesium
    Active sitei297 – 2971Proton acceptor; specific for R-mandelate
    Binding sitei317 – 3171Substrate1 Publication

    GO - Molecular functioni

    1. mandelate racemase activity Source: UniProtKB-EC
    2. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. cellular amino acid catabolic process Source: InterPro
    2. mandelate catabolic process Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Mandelate pathway

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-2421.
    UniPathwayiUPA00873; UER00852.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Mandelate racemase (EC:5.1.2.2)
    Short name:
    MR
    Gene namesi
    Name:mdlA
    OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
    Taxonomic identifieri303 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi166 – 1661K → A, M or Q: Loss of activity. 1 Publication
    Mutagenesisi297 – 2971H → N: Loss of activity. 1 Publication
    Mutagenesisi317 – 3171E → Q: Reduces activity 10000-fold.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 359359Mandelate racemasePRO_0000171247Add
    BLAST

    Interactioni

    Subunit structurei

    Homooctamer.1 Publication

    Structurei

    Secondary structure

    1
    359
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 1612
    Beta strandi22 – 243
    Beta strandi27 – 293
    Beta strandi31 – 4111
    Beta strandi46 – 527
    Helixi56 – 583
    Helixi59 – 7315
    Beta strandi76 – 783
    Helixi80 – 9011
    Turni91 – 944
    Helixi98 – 11821
    Helixi123 – 1264
    Beta strandi134 – 1396
    Helixi144 – 15714
    Beta strandi161 – 1666
    Helixi172 – 18615
    Beta strandi188 – 1958
    Helixi202 – 21413
    Beta strandi218 – 2214
    Helixi229 – 2368
    Beta strandi243 – 2453
    Helixi252 – 2609
    Beta strandi265 – 2673
    Turni271 – 2755
    Helixi276 – 29015
    Helixi300 – 3089
    Beta strandi316 – 3183
    Turni321 – 3255
    Beta strandi330 – 3334
    Beta strandi336 – 3383
    Beta strandi341 – 3444
    Helixi351 – 3577

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DTNX-ray2.10A1-359[»]
    1MDLX-ray1.85A1-359[»]
    1MDRX-ray2.10A1-359[»]
    1MNSX-ray2.00A3-359[»]
    1MRAX-ray2.10A1-359[»]
    2MNRX-ray1.90A3-359[»]
    3UXKX-ray2.20A/B/C/D1-359[»]
    3UXLX-ray2.20A/B/C/D1-359[»]
    4FP1X-ray1.68A/B1-359[»]
    4HNCX-ray1.89A/B1-359[»]
    4M6UX-ray1.80A/B1-359[»]
    ProteinModelPortaliP11444.
    SMRiP11444. Positions 3-359.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP11444.

    Family & Domainsi

    Sequence similaritiesi

    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.
    IPR001354. MR_MLE.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF01188. MR_MLE. 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.

    P11444-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSEVLITGLR TRAVNVPLAY PVHTAVGTVG TAPLVLIDLA TSAGVVGHSY    50
    LFAYTPVALK SLKQLLDDMA AMIVNEPLAP VSLEAMLAKR FCLAGYTGLI 100
    RMAAAGIDMA AWDALGKVHE TPLVKLLGAN ARPVQAYDSH SLDGVKLATE 150
    RAVTAAELGF RAVKTKIGYP ALDQDLAVVR SIRQAVGDDF GIMVDYNQSL 200
    DVPAAIKRSQ ALQQEGVTWI EEPTLQHDYE GHQRIQSKLN VPVQMGENWL 250
    GPEEMFKALS IGACRLAMPD AMKIGGVTGW IRASALAQQF GIPMSSHLFQ 300
    EISAHLLAAT PTAHWLERLD LAGSVIEPTL TFEGGNAVIP DLPGVGIIWR 350
    EKEIGKYLV 359
    Length:359
    Mass (Da):38,565
    Last modified:October 1, 1989 - v1
    Checksum:i1C105BCA021F4028
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M19043 Genomic DNA. Translation: AAA25887.1.
    AY143338 Genomic DNA. Translation: AAC15504.1.
    PIRiA28700.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M19043 Genomic DNA. Translation: AAA25887.1 .
    AY143338 Genomic DNA. Translation: AAC15504.1 .
    PIRi A28700.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1DTN X-ray 2.10 A 1-359 [» ]
    1MDL X-ray 1.85 A 1-359 [» ]
    1MDR X-ray 2.10 A 1-359 [» ]
    1MNS X-ray 2.00 A 3-359 [» ]
    1MRA X-ray 2.10 A 1-359 [» ]
    2MNR X-ray 1.90 A 3-359 [» ]
    3UXK X-ray 2.20 A/B/C/D 1-359 [» ]
    3UXL X-ray 2.20 A/B/C/D 1-359 [» ]
    4FP1 X-ray 1.68 A/B 1-359 [» ]
    4HNC X-ray 1.89 A/B 1-359 [» ]
    4M6U X-ray 1.80 A/B 1-359 [» ]
    ProteinModelPortali P11444.
    SMRi P11444. Positions 3-359.
    ModBasei Search...
    MobiDBi Search...

    Chemistry

    BindingDBi P11444.
    ChEMBLi CHEMBL4739.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00873 ; UER00852 .
    BioCyci MetaCyc:MONOMER-2421.

    Miscellaneous databases

    EvolutionaryTracei P11444.

    Family and domain databases

    Gene3Di 3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProi IPR029065. Enolase_C-like.
    IPR029017. Enolase_N_like.
    IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N.
    IPR001354. MR_MLE.
    [Graphical view ]
    PANTHERi PTHR13794. PTHR13794. 1 hit.
    Pfami PF01188. MR_MLE. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view ]
    SMARTi SM00922. MR_MLE. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    PROSITEi PS00908. MR_MLE_1. 1 hit.
    PS00909. MR_MLE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning, DNA sequence analysis, and expression in Escherichia coli of the gene for mandelate racemase from Pseudomonas putida."
      Ransom S.C., Gerlt J.A., Powers V.M., Kenyon G.L.
      Biochemistry 27:540-545(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 12633 / DSM 291 / JCM 13063 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90.
    2. "Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli."
      Tsou A.Y., Ransom S.C., Gerlt J.A., Buechter D.D., Babbitt P.C., Kenyon G.L.
      Biochemistry 29:9856-9862(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 12633 / DSM 291 / JCM 13063 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90.
    3. "Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous."
      Neidhart D.J., Kenyon G.L., Gerlt J.A., Petsko G.A.
      Nature 347:692-694(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: SIMILARITY TO MLE.
    4. "Mechanism of the reaction catalyzed by mandelate racemase. 3. Asymmetry in reactions catalyzed by the H297N mutant."
      Landro J.A., Kallarakal A.T., Ransom S.C., Gerlt J.A., Kozarich J.W., Neidhart D.J., Kenyon G.L.
      Biochemistry 30:9274-9281(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF HIS-297.
    5. "Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-A resolution: identification of the active site and possible catalytic residues."
      Neidhart D.J., Howell P.L., Petsko G.A., Powers V.M., Li R.S., Kenyon G.L., Gerlt J.A.
      Biochemistry 30:9264-9273(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
    6. "Mechanism of the reaction catalyzed by mandelate racemase: importance of electrophilic catalysis by glutamic acid 317."
      Mitra B., Kallarakal A.T., Kozarich J.W., Gerlt J.A., Clifton J.G., Petsko G.A., Kenyon G.L.
      Biochemistry 34:2777-2787(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF MUTANT GLN-317.
    7. "Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the K166R mutant."
      Kallarakal A.T., Mitra B., Kozarich J.W., Gerlt J.A., Clifton J.G., Petsko G.A., Kenyon G.L.
      Biochemistry 34:2788-2797(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF MUTANT ARG-166 IN COMPLEX WITH SUBSTRATE, MUTAGENESIS OF LYS-166.

    Entry informationi

    Entry nameiMANR_PSEPU
    AccessioniPrimary (citable) accession number: P11444
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: October 1, 1989
    Last modified: October 1, 2014
    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

    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

    External Data

    Dasty 3