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P26297

- LDHD_LACDA

UniProt

P26297 - LDHD_LACDA

Protein

D-lactate dehydrogenase

Gene

ldhA

Organism
Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 111 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    (R)-lactate + NAD+ = pyruvate + NADH.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei236 – 2361
    Binding sitei260 – 2601NADBy similarity
    Active sitei265 – 2651
    Active sitei297 – 2971Proton donor

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi153 – 17927NADH1 PublicationAdd
    BLAST
    Nucleotide bindingi156 – 1572NADBy similarity
    Nucleotide bindingi234 – 2363NADBy similarity
    Nucleotide bindingi297 – 3004NADBy similarity

    GO - Molecular functioni

    1. D-lactate dehydrogenase activity Source: UniProtKB-EC
    2. NAD binding Source: InterPro

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciLDEL390333:GIXG-99-MONOMER.
    SABIO-RKP26297.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-lactate dehydrogenase (EC:1.1.1.28)
    Short name:
    D-LDH
    Alternative name(s):
    D-specific 2-hydroxyacid dehydrogenase
    Gene namesi
    Name:ldhA
    Ordered Locus Names:Ldb0101
    OrganismiLactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081)
    Taxonomic identifieri390333 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaeLactobacillus
    ProteomesiUP000001259: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi206 – 2061H → Q: Increase of activity. 1 Publication
    Mutagenesisi236 – 2361R → K: Decrease of activity. 1 Publication
    Mutagenesisi260 – 2601D → N: Decrease of activity. 1 Publication
    Mutagenesisi265 – 2651E → Q: Decrease of activity. 1 Publication
    Mutagenesisi297 – 2971H → Q: 90% loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed
    Chaini2 – 333332D-lactate dehydrogenasePRO_0000075953Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi390333.Ldb0101.

    Structurei

    Secondary structure

    1
    333
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 64
    Helixi11 – 133
    Helixi14 – 229
    Beta strandi27 – 315
    Turni38 – 403
    Helixi41 – 444
    Beta strandi48 – 525
    Helixi60 – 689
    Beta strandi73 – 797
    Helixi86 – 916
    Beta strandi95 – 973
    Helixi104 – 12017
    Helixi122 – 1309
    Helixi144 – 1463
    Beta strandi147 – 1526
    Helixi156 – 16712
    Beta strandi171 – 1755
    Helixi181 – 1855
    Helixi193 – 1997
    Beta strandi201 – 2055
    Helixi211 – 2133
    Helixi219 – 2246
    Beta strandi229 – 2335
    Helixi237 – 2393
    Helixi242 – 2509
    Beta strandi253 – 2608
    Turni266 – 2705
    Helixi281 – 2888
    Beta strandi292 – 2943
    Helixi303 – 32119
    Beta strandi327 – 3293

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DLDmodel-A1-333[»]
    1J49X-ray2.20A/B1-333[»]
    1J4AX-ray1.90A/B/C/D1-333[»]
    ProteinModelPortaliP26297.
    SMRiP26297. Positions 1-332.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP26297.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1052.
    HOGENOMiHOG000136695.
    KOiK03778.
    OMAiGHIGQVF.
    OrthoDBiEOG61VZ8G.

    Family and domain databases

    Gene3Di3.40.50.720. 2 hits.
    InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR006140. D-isomer_DH_NAD-bd.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    [Graphical view]
    PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
    PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P26297-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTKIFAYAIR EDEKPFLKEW EDAHKDVEVE YTDKLLTPET VALAKGADGV    50
    VVYQQLDYTA ETLQALADNG ITKMSLRNVG VDNIDMAKAK ELGFQITNVP 100
    VYSPNAIAEH AAIQAARILR QDKAMDEKVA RHDLRWAPTI GREVRDQVVG 150
    VIGTGHIGQV FMQIMEGFGA KVIAYDIFRN PELEKKGYYV DSLDDLYKQA 200
    DVISLHVPDV PANVHMINDE SIAKMKQDVV IVNVSRGPLV DTDAVIRGLD 250
    SGKIFGYAMD VYEGEVGIFN EDWEGKEFPD ARLADLIARP NVLVTPHTAF 300
    YTTHAVRNMV VKAFDNNLEL VEGKEAETPV KVG 333
    Length:333
    Mass (Da):37,049
    Last modified:January 23, 2007 - v3
    Checksum:i16E8B68D54B9D9D4
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti41 – 411V → A in AAA25246. (PubMed:1569100)Curated
    Sequence conflicti117 – 1171R → A in CAA42781. (PubMed:1915894)Curated
    Sequence conflicti122 – 1221D → A in AAA25246. (PubMed:1569100)Curated
    Sequence conflicti152 – 1521I → V in AAA25246. (PubMed:1569100)Curated
    Sequence conflicti174 – 1741A → T in CAA42781. (PubMed:1915894)Curated
    Sequence conflicti220 – 2201E → K in AAA25246. (PubMed:1569100)Curated
    Sequence conflicti254 – 2541I → V in AAA25246. (PubMed:1569100)Curated
    Sequence conflicti268 – 2681I → V in AAA25246. (PubMed:1569100)Curated
    Sequence conflicti273 – 2731W → R in AAA25246. (PubMed:1569100)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X60220 Genomic DNA. Translation: CAA42781.1.
    M85224 Genomic DNA. Translation: AAA25246.1.
    CR954253 Genomic DNA. Translation: CAI96942.1.
    PIRiA38094.
    RefSeqiYP_618304.1. NC_008054.1.

    Genome annotation databases

    EnsemblBacteriaiCAI96942; CAI96942; Ldb0101.
    GeneIDi4085369.
    KEGGildb:Ldb0101.
    PATRICi22215856. VBILacDel123523_0087.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X60220 Genomic DNA. Translation: CAA42781.1 .
    M85224 Genomic DNA. Translation: AAA25246.1 .
    CR954253 Genomic DNA. Translation: CAI96942.1 .
    PIRi A38094.
    RefSeqi YP_618304.1. NC_008054.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1DLD model - A 1-333 [» ]
    1J49 X-ray 2.20 A/B 1-333 [» ]
    1J4A X-ray 1.90 A/B/C/D 1-333 [» ]
    ProteinModelPortali P26297.
    SMRi P26297. Positions 1-332.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 390333.Ldb0101.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAI96942 ; CAI96942 ; Ldb0101 .
    GeneIDi 4085369.
    KEGGi ldb:Ldb0101.
    PATRICi 22215856. VBILacDel123523_0087.

    Phylogenomic databases

    eggNOGi COG1052.
    HOGENOMi HOG000136695.
    KOi K03778.
    OMAi GHIGQVF.
    OrthoDBi EOG61VZ8G.

    Enzyme and pathway databases

    BioCyci LDEL390333:GIXG-99-MONOMER.
    SABIO-RK P26297.

    Miscellaneous databases

    EvolutionaryTracei P26297.

    Family and domain databases

    Gene3Di 3.40.50.720. 2 hits.
    InterProi IPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR006140. D-isomer_DH_NAD-bd.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view ]
    Pfami PF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    [Graphical view ]
    PROSITEi PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
    PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning of the D-lactate dehydrogenase gene from Lactobacillus delbrueckii subsp. bulgaricus by complementation in Escherichia coli."
      Bernard N., Ferain T., Garmyn D., Hols P., Delcour J.
      FEBS Lett. 290:61-64(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Primary structure, physicochemical properties, and chemical modification of NAD(+)-dependent D-lactate dehydrogenase. Evidence for the presence of Arg-235, His-303, Tyr-101, and Trp-19 at or near the active site."
      Kochhar S., Hunziker P., Leong-Morgenthaler P.M., Hottinger H.
      J. Biol. Chem. 267:8499-8513(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
    3. "Cloning and overexpression of the Lactobacillus bulgaricus NAD(+)-dependent D-lactate dehydrogenase gene in Escherichia coli: purification and characterization of the recombinant enzyme."
      Kochhar S., Chuard N., Hottinger H.
      Biochem. Biophys. Res. Commun. 185:705-712(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 11842 / DSM 20081.
    5. "Evolutionary relationship of NAD(+)-dependent D-lactate dehydrogenase: comparison of primary structure of 2-hydroxy acid dehydrogenases."
      Kochhar S., Hunziker P., Leong-Morgenthaler P.M., Hottinger H.
      Biochem. Biophys. Res. Commun. 184:60-66(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: SIMILARITY TO OTHER ENZYMES OF THIS FAMILY.
    6. "D-2-hydroxy-4-methylvalerate dehydrogenase from Lactobacillus delbrueckii subsp. bulgaricus. II. Mutagenic analysis of catalytically important residues."
      Bernard N., Johnsen K., Gelpi J.L., Alvarez J.A., Ferain T., Garmyn D., Hols P., Cortes A., Clarke A.R., Holbrook J.J., Delcour J.
      Eur. J. Biochem. 244:213-219(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF HIS-206; ARG-236; ASP-260; GLU-265 AND HIS-297.
    7. "Prediction of structurally conserved regions of D-specific hydroxy acid dehydrogenases by multiple alignment with formate dehydrogenase."
      Vinals C., Depiereux E., Feytmans E.
      Biochem. Biophys. Res. Commun. 192:182-188(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: 3D-STRUCTURE MODELING.
    8. "Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus."
      Razeto A., Kochhar S., Hottinger H., Dauter M., Wilson K.S., Lamzin V.S.
      J. Mol. Biol. 318:109-119(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH NADH, SUBUNIT.

    Entry informationi

    Entry nameiLDHD_LACDA
    AccessioniPrimary (citable) accession number: P26297
    Secondary accession number(s): Q1G7V7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1992
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 111 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3