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Protein

L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))

Gene

mdh

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible oxidation of (S)-malate and (S)-sulfolactate to oxaloacetate and sulfopyruvate, respectively. Can use both NADH and NADPH, although activity is higher with NADPH. Oxidation of (S)-sulfolactate is observed only in the presence of NADP+. Can also oxidize tartrate. Cannot reduce pyruvate, nor alpha-ketoglutarate.3 Publications

Catalytic activityi

A (2S)-2-hydroxycarboxylate + NAD(P)+ = a 2-oxocarboxylate + NAD(P)H.3 Publications

Kineticsi

kcat is 0.33 sec(-1) for NAD-dependent malate oxidation. kcat is 0.069 sec(-1) for NADP-dependent malate oxidation.1 Publication

Manual assertion based on experiment ini

  1. KM=0.15 mM for (S)-malate (in the presence of NAD+)1 Publication
  2. KM=0.41 mM for (S)-malate (in the presence of NAD+)1 Publication
  3. KM=0.025 mM for (S)-malate (in the presence of NADP+)1 Publication
  4. KM=0.084 mM for (S)-malate (in the presence of NADP+)1 Publication
  5. KM=4.6 mM for (S)-sulfolactate (in the presence of NADP+)1 Publication
  6. KM=11 mM for (2S,3S)-tartrate (in the presence of NAD+)1 Publication
  7. KM=5.1 mM for (2S,3S)-tartrate (in the presence of NADP+)1 Publication
  8. KM=0.25 mM for oxaloacetate (in the presence of NADH)1 Publication
  9. KM=0.30 mM for oxaloacetate (in the presence of NADPH)1 Publication
  10. KM=1.3 mM for sulfopyruvate (in the presence of NADH)1 Publication
  11. KM=0.19 mM for sulfopyruvate (in the presence of NADPH)1 Publication
  12. KM=0.14 mM for NADH1 Publication
  13. KM=0.02 mM for NADPH1 Publication
  1. Vmax=0.6 µmol/min/mg enzyme toward (S)-malate (in the presence of NAD+)1 Publication
  2. Vmax=3 µmol/min/mg enzyme toward (S)-malate (in the presence of NADP+)1 Publication
  3. Vmax=3 µmol/min/mg enzyme toward (S)-sulfolactate (in the presence of NADP+)1 Publication
  4. Vmax=29 µmol/min/mg enzyme toward oxaloacetate (in the presence of NADH)1 Publication
  5. Vmax=49 µmol/min/mg enzyme toward oxaloacetate (in the presence of NADPH)1 Publication
  6. Vmax=43 µmol/min/mg enzyme toward sulfopyruvate (in the presence of NADH)1 Publication
  7. Vmax=69 µmol/min/mg enzyme toward sulfopyruvate (in the presence of NADPH)1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei86SubstrateBy similarity1
Binding sitei92SubstrateBy similarity1
Binding sitei99NADP1 Publication1
Binding sitei123SubstrateBy similarity1
Binding sitei154SubstrateBy similarity1
Active sitei178Proton acceptorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi7 – 13NADP1 Publication7
Nucleotide bindingi34 – 37NADP1 Publication4
Nucleotide bindingi121 – 123NADP1 Publication3

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Tricarboxylic acid cycle

Keywords - Ligandi

NAD, NADP

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-18778.
BRENDAi1.1.1.B46. 3260.
SABIO-RKQ60176.

Names & Taxonomyi

Protein namesi
Recommended name:
L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))Curated (EC:1.1.1.3753 Publications)
Alternative name(s):
MdhII1 Publication
Gene namesi
Name:mdh
Synonyms:mdhB
Ordered Locus Names:MJ0490
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001134851 – 313L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))Add BLAST313

Interactioni

Subunit structurei

Homotetramer.3 Publications

Protein-protein interaction databases

STRINGi243232.MJ_0490.

Structurei

Secondary structure

1313
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 6Combined sources5
Turni7 – 9Combined sources3
Helixi11 – 21Combined sources11
Beta strandi28 – 33Combined sources6
Helixi35 – 37Combined sources3
Helixi38 – 52Combined sources15
Beta strandi60 – 65Combined sources6
Helixi69 – 72Combined sources4
Beta strandi76 – 80Combined sources5
Helixi92 – 113Combined sources22
Beta strandi117 – 120Combined sources4
Beta strandi122 – 124Combined sources3
Helixi125 – 136Combined sources12
Beta strandi142 – 145Combined sources4
Helixi149 – 163Combined sources15
Helixi167 – 169Combined sources3
Beta strandi174 – 176Combined sources3
Beta strandi182 – 184Combined sources3
Helixi186 – 188Combined sources3
Helixi196 – 198Combined sources3
Helixi200 – 204Combined sources5
Helixi207 – 217Combined sources11
Helixi219 – 222Combined sources4
Beta strandi225 – 227Combined sources3
Helixi232 – 244Combined sources13
Beta strandi249 – 263Combined sources15
Beta strandi265 – 276Combined sources12
Beta strandi279 – 283Combined sources5
Helixi290 – 310Combined sources21

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HYEX-ray1.90A1-313[»]
1HYGX-ray2.80A/B1-313[»]
ProteinModelPortaliQ60176.
SMRiQ60176.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ60176.

Family & Domainsi

Sequence similaritiesi

Belongs to the LDH/MDH superfamily.Curated

Phylogenomic databases

eggNOGiarCOG00246. Archaea.
COG0039. LUCA.
InParanoidiQ60176.
KOiK00024.
OMAiSARCRYE.
PhylomeDBiQ60176.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
InterProiIPR001557. L-lactate/malate_DH.
IPR018177. L-lactate_DH_AS.
IPR022383. Lactate/malate_DH_C.
IPR001236. Lactate/malate_DH_N.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR11540. PTHR11540. 1 hit.
PfamiPF02866. Ldh_1_C. 1 hit.
PF00056. Ldh_1_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000102. Lac_mal_DH. 1 hit.
PRINTSiPR00086. LLDHDRGNASE.
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF56327. SSF56327. 1 hit.

Sequencei

Sequence statusi: Complete.

Q60176-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVTIIGASG RVGSATALLL AKEPFMKDLV LIGREHSINK LEGLREDIYD
60 70 80 90 100
ALAGTRSDAN IYVESDENLR IIDESDVVII TSGVPRKEGM SRMDLAKTNA
110 120 130 140 150
KIVGKYAKKI AEICDTKIFV ITNPVDVMTY KALVDSKFER NQVFGLGTHL
160 170 180 190 200
DSLRFKVAIA KFFGVHIDEV RTRIIGEHGD SMVPLLSATS IGGIPIQKFE
210 220 230 240 250
RFKELPIDEI IEDVKTKGEQ IIRLKGGSEF GPAAAILNVV RCIVNNEKRL
260 270 280 290 300
LTLSAYVDGE FDGIRDVCIG VPVKIGRDGI EEVVSIELDK DEIIAFRKSA
310
EIIKKYCEEV KNL
Length:313
Mass (Da):34,609
Last modified:November 1, 1997 - v1
Checksum:iA7C0DB67C50151CC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98481.1.
PIRiB64361.
RefSeqiWP_010869991.1. NC_000909.1.

Genome annotation databases

EnsemblBacteriaiAAB98481; AAB98481; MJ_0490.
GeneIDi1451352.
KEGGimja:MJ_0490.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98481.1.
PIRiB64361.
RefSeqiWP_010869991.1. NC_000909.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HYEX-ray1.90A1-313[»]
1HYGX-ray2.80A/B1-313[»]
ProteinModelPortaliQ60176.
SMRiQ60176.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_0490.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB98481; AAB98481; MJ_0490.
GeneIDi1451352.
KEGGimja:MJ_0490.

Phylogenomic databases

eggNOGiarCOG00246. Archaea.
COG0039. LUCA.
InParanoidiQ60176.
KOiK00024.
OMAiSARCRYE.
PhylomeDBiQ60176.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-18778.
BRENDAi1.1.1.B46. 3260.
SABIO-RKQ60176.

Miscellaneous databases

EvolutionaryTraceiQ60176.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
InterProiIPR001557. L-lactate/malate_DH.
IPR018177. L-lactate_DH_AS.
IPR022383. Lactate/malate_DH_C.
IPR001236. Lactate/malate_DH_N.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR11540. PTHR11540. 1 hit.
PfamiPF02866. Ldh_1_C. 1 hit.
PF00056. Ldh_1_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000102. Lac_mal_DH. 1 hit.
PRINTSiPR00086. LLDHDRGNASE.
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF56327. SSF56327. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiMDH_METJA
AccessioniPrimary (citable) accession number: Q60176
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: November 2, 2016
This is version 135 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. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  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.