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Protein

Malate dehydrogenase 1, mitochondrial

Gene

At1g53240

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes a reversible NAD-dependent dehydrogenase reaction involved in central metabolism and redox homeostasis between organelle compartments (Probable). Required for carbon dioxide and energy partitioning in leaves. May limit photorespiration during the dark phase (PubMed:20876337, PubMed:27208265). Its activity is essential to shuttle reductants out from the mitochondria to support the photorespiratory flux (PubMed:26889011). Can convert 2-oxoglutarate to (S)-2-hydroxyglutarate in vitro (PubMed:26203119).1 Publication4 Publications

Catalytic activityi

(S)-malate + NAD+ = oxaloacetate + NADH.1 Publication

Enzyme regulationi

Negatively regulated by ATP. Not redox-regulated. The formation of intramolecular disulfide bonds does not alter enzymatic activity.1 Publication

Kineticsi

  1. KM=0.8 mM for malate (at pH 7.5)1 Publication
  2. KM=0.11 mM for oxaloacetate (at pH 7.5)1 Publication
  3. KM=0.27 mM for oxaloacetate (at pH 7.4)1 Publication
  4. KM=0.6 mM for NAD+ (at pH 7.5)1 Publication
  5. KM=0.23 mM for NADH (at pH 7.5)1 Publication
  6. KM=41 mM for 2-ketoglutarate (at pH 7.4)1 Publication
  1. Vmax=0.087 mmol/min/mg enzyme toward malate (at pH 7.5)1 Publication
  2. Vmax=0.03 mmol/min/mg enzyme toward malate (at pH 7.4)1 Publication
  3. Vmax=1.2 mmol/min/mg enzyme toward oxaloacetate (at pH 7.5)1 Publication
  4. Vmax=2.39 mmol/min/mg enzyme toward oxaloacetate (at pH 7.4)1 Publication
  5. Vmax=79 µmol/min/mg enzyme toward NAD+ (at pH 7.5)1 Publication
  6. Vmax=2732 µmol/min/mg enzyme toward NADH (at pH 7.5)1 Publication
  7. Vmax=0.38 mmol/min/mg enzyme toward 2-ketoglutarate (at pH 7.4)1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei62NADBy similarity1
Binding sitei109SubstrateBy similarity1
Binding sitei115SubstrateBy similarity1
Binding sitei122NADBy similarity1
Binding sitei147SubstrateBy similarity1
Binding sitei181SubstrateBy similarity1
Active sitei205Proton acceptorBy similarity1
Binding sitei256NADBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi36 – 42NADBy similarity7
Nucleotide bindingi145 – 147NADBy similarity3

GO - Molecular functioni

  • copper ion binding Source: TAIR
  • L-malate dehydrogenase activity Source: TAIR

GO - Biological processi

  • carbohydrate metabolic process Source: InterPro
  • defense response to bacterium Source: TAIR
  • malate metabolic process Source: InterPro
  • response to cadmium ion Source: TAIR
  • response to cold Source: TAIR
  • response to salt stress Source: TAIR
  • tricarboxylic acid cycle Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Tricarboxylic acid cycle

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciARA:AT1G53240-MONOMER.
MetaCyc:AT1G53240-MONOMER.
BRENDAi1.1.1.37. 399.
ReactomeiR-ATH-70263. Gluconeogenesis.
R-ATH-71403. Citric acid cycle (TCA cycle).

Names & Taxonomyi

Protein namesi
Recommended name:
Malate dehydrogenase 1, mitochondrialCurated (EC:1.1.1.371 Publication)
Alternative name(s):
Mitochondrial MDH11 Publication
Short name:
mMDH11 Publication
Mitochondrial NAD-dependent malate dehydrogenase 1Curated
Short name:
mNAD-MDH 1Curated
Short name:
mtNAD-MDH11 Publication
Gene namesi
Ordered Locus Names:At1g53240
ORF Names:F12M16.14
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G53240.

Subcellular locationi

GO - Cellular componenti

  • apoplast Source: TAIR
  • cell wall Source: TAIR
  • chloroplast Source: TAIR
  • mitochondrial matrix Source: UniProtKB-SubCell
  • mitochondrion Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Disruption phenotypei

Slight reduction of rosette leaf size and reduction by 50 percents in fresh weight and seed production (PubMed:26889011). The double mutant plants mmdh1 and mmdh2 have decreased germination rate, grow slowly, are small, have increased photorespiration and die before producing seeds (PubMed:20876337).2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 22Mitochondrion1 PublicationAdd BLAST22
ChainiPRO_000001862223 – 341Malate dehydrogenase 1, mitochondrialAdd BLAST319

Post-translational modificationi

Forms intramolecular disulfide bonds.1 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiQ9ZP06.
PRIDEiQ9ZP06.

2D gel databases

SWISS-2DPAGEQ9ZP06.

PTM databases

iPTMnetiQ9ZP06.

Expressioni

Tissue specificityi

Expressed in rosette leaves.1 Publication

Gene expression databases

GenevisibleiQ9ZP06. AT.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

BioGridi26982. 2 interactors.
IntActiQ9ZP06. 1 interactor.
STRINGi3702.AT1G53240.1.

Structurei

3D structure databases

ProteinModelPortaliQ9ZP06.
SMRiQ9ZP06.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the LDH/MDH superfamily. MDH type 1 family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG1494. Eukaryota.
COG0039. LUCA.
HOGENOMiHOG000213792.
InParanoidiQ9ZP06.
KOiK00026.
OMAiNDMERNQ.
OrthoDBiEOG09360H2H.
PhylomeDBiQ9ZP06.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
InterProiIPR001557. L-lactate/malate_DH.
IPR022383. Lactate/malate_DH_C.
IPR001236. Lactate/malate_DH_N.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR001252. Malate_DH_AS.
IPR010097. Malate_DH_type1.
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.
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF56327. SSF56327. 1 hit.
TIGRFAMsiTIGR01772. MDH_euk_gproteo. 1 hit.
PROSITEiPS00068. MDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q9ZP06-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFRSMLVRSS ASAKQAVIRR SFSSGSVPER KVAILGAAGG IGQPLALLMK
60 70 80 90 100
LNPLVSSLSL YDIANTPGVA ADVGHINTRS EVVGYMGDDN LAKALEGADL
110 120 130 140 150
VIIPAGVPRK PGMTRDDLFN INAGIVKNLC TAIAKYCPHA LINMISNPVN
160 170 180 190 200
STVPIAAEIF KKAGMYDEKK LFGVTTLDVV RARTFYAGKA NVPVAEVNVP
210 220 230 240 250
VIGGHAGVTI LPLFSQATPQ ANLSSDILTA LTKRTQDGGT EVVEAKAGKG
260 270 280 290 300
SATLSMAYAG ALFADACLKG LNGVPDVIEC SYVQSTITEL PFFASKVRLG
310 320 330 340
KNGVEEVLDL GPLSDFEKEG LEALKPELKS SIEKGVKFAN Q
Length:341
Mass (Da):35,804
Last modified:May 1, 1999 - v1
Checksum:iD035C4C38785BE57
GO

Sequence cautioni

The sequence AAF69549 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti17V → A in AAM64855 (Ref. 5) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ131205 mRNA. Translation: CAA10320.1.
AC008007 Genomic DNA. Translation: AAF69549.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE32910.1.
AF324670 mRNA. Translation: AAG40021.1.
AF339684 mRNA. Translation: AAK00366.1.
AY062580 mRNA. Translation: AAL32658.1.
AY128783 mRNA. Translation: AAM91183.1.
AY087304 mRNA. Translation: AAM64855.1.
PIRiT51311.
RefSeqiNP_564625.1. NM_104202.3.
UniGeneiAt.23771.

Genome annotation databases

EnsemblPlantsiAT1G53240.1; AT1G53240.1; AT1G53240.
GeneIDi841757.
GrameneiAT1G53240.1; AT1G53240.1; AT1G53240.
KEGGiath:AT1G53240.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ131205 mRNA. Translation: CAA10320.1.
AC008007 Genomic DNA. Translation: AAF69549.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE32910.1.
AF324670 mRNA. Translation: AAG40021.1.
AF339684 mRNA. Translation: AAK00366.1.
AY062580 mRNA. Translation: AAL32658.1.
AY128783 mRNA. Translation: AAM91183.1.
AY087304 mRNA. Translation: AAM64855.1.
PIRiT51311.
RefSeqiNP_564625.1. NM_104202.3.
UniGeneiAt.23771.

3D structure databases

ProteinModelPortaliQ9ZP06.
SMRiQ9ZP06.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi26982. 2 interactors.
IntActiQ9ZP06. 1 interactor.
STRINGi3702.AT1G53240.1.

PTM databases

iPTMnetiQ9ZP06.

2D gel databases

SWISS-2DPAGEQ9ZP06.

Proteomic databases

PaxDbiQ9ZP06.
PRIDEiQ9ZP06.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G53240.1; AT1G53240.1; AT1G53240.
GeneIDi841757.
GrameneiAT1G53240.1; AT1G53240.1; AT1G53240.
KEGGiath:AT1G53240.

Organism-specific databases

TAIRiAT1G53240.

Phylogenomic databases

eggNOGiKOG1494. Eukaryota.
COG0039. LUCA.
HOGENOMiHOG000213792.
InParanoidiQ9ZP06.
KOiK00026.
OMAiNDMERNQ.
OrthoDBiEOG09360H2H.
PhylomeDBiQ9ZP06.

Enzyme and pathway databases

BioCyciARA:AT1G53240-MONOMER.
MetaCyc:AT1G53240-MONOMER.
BRENDAi1.1.1.37. 399.
ReactomeiR-ATH-70263. Gluconeogenesis.
R-ATH-71403. Citric acid cycle (TCA cycle).

Miscellaneous databases

PROiQ9ZP06.

Gene expression databases

GenevisibleiQ9ZP06. AT.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
InterProiIPR001557. L-lactate/malate_DH.
IPR022383. Lactate/malate_DH_C.
IPR001236. Lactate/malate_DH_N.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR001252. Malate_DH_AS.
IPR010097. Malate_DH_type1.
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.
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF56327. SSF56327. 1 hit.
TIGRFAMsiTIGR01772. MDH_euk_gproteo. 1 hit.
PROSITEiPS00068. MDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiMDHM1_ARATH
AccessioniPrimary (citable) accession number: Q9ZP06
Secondary accession number(s): Q8LBB9, Q9MAH7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: May 1, 1999
Last modified: November 30, 2016
This is version 152 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. 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.