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P26297

- LDHD_LACDA

UniProt

P26297 - LDHD_LACDA

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Protein
D-lactate dehydrogenase
Gene
ldhA, Ldb0101
Organism
Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Sites

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi153 – 17927NADH
Add
BLAST
Nucleotide bindingi156 – 1572NAD By similarity
Nucleotide bindingi234 – 2363NAD By similarity
Nucleotide bindingi297 – 3004NAD By similarity

GO - Molecular functioni

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

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 dehydrogenase
PRO_0000075953Add
BLAST

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi390333.Ldb0101.

Structurei

Secondary structure

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.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti41 – 411V → A in AAA25246. 1 Publication
Sequence conflicti117 – 1171R → A in CAA42781. 1 Publication
Sequence conflicti122 – 1221D → A in AAA25246. 1 Publication
Sequence conflicti152 – 1521I → V in AAA25246. 1 Publication
Sequence conflicti174 – 1741A → T in CAA42781. 1 Publication
Sequence conflicti220 – 2201E → K in AAA25246. 1 Publication
Sequence conflicti254 – 2541I → V in AAA25246. 1 Publication
Sequence conflicti268 – 2681I → V in AAA25246. 1 Publication
Sequence conflicti273 – 2731W → R in AAA25246. 1 Publication

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 110 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

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

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