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Protein

Malate dehydrogenase 2, peroxisomal

Gene

PMDH2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Catalyzes a reversible NAD-dependent dehydrogenase reaction involved in central metabolism and redox homeostasis between organelle compartments (Probable). Peroxisomal NAD-dependent malate dehydrogenase involved in fatty acid beta-oxidation. Reoxidizes NADH from the beta-oxidation and provides NAD for the conversion of fatty acyl-CoA to acetyl-CoA. Does not participate directly in the glyoxylate cycle (PubMed:17376163, PubMed:19812894). Required for maintenance of photosynthetic rates under photorespiratory conditions, and carbon flow during photorespiration. Supplies NADH reductant to the peroxisomal hydroxypyruvate reductase (HPR), which reduces hydroxypyruvate into glycerate in the photorespiratory cycle (PubMed:18685043).1 Publication3 Publications

Catalytic activityi

(S)-malate + NAD+ = oxaloacetate + NADH.PROSITE-ProRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei75NADBy similarity1
Binding sitei122SubstrateBy similarity1
Binding sitei128SubstrateBy similarity1
Binding sitei135NADBy similarity1
Binding sitei160SubstrateBy similarity1
Binding sitei194SubstrateBy similarity1
Active sitei218Proton acceptorBy similarity1
Binding sitei269NADBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi49 – 55NADBy similarity7
Nucleotide bindingi158 – 160NADBy similarity3

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glyoxylate bypass, Tricarboxylic acid cycle

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciMetaCyc:AT5G09660-MONOMER.
ReactomeiR-ATH-70263. Gluconeogenesis.
R-ATH-71403. Citric acid cycle (TCA cycle).

Names & Taxonomyi

Protein namesi
Recommended name:
Malate dehydrogenase 2, peroxisomalCurated (EC:1.1.1.37)
Alternative name(s):
Microbody NAD-dependent malate dehydrogenase1 Publication
Short name:
mbNAD-MDH1 Publication
Peroxisomal NAD-dependent malate dehydrogenase 2Curated
Short name:
pxNAD-MDH21 Publication
Peroxisomal malate dehydrogenase 21 Publication
Short name:
Peroxisomal MDH2Curated
Gene namesi
Name:PMDH21 Publication
Ordered Locus Names:At5g09660
ORF Names:F17I14_150, MTH16.8
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G09660.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Peroxisome

Pathology & Biotechi

Disruption phenotypei

No visible phenotype under normal growth conditions, but the double mutant plants pmdh1 and pmdh2 show seedling growth arrest 5 days after seed imbibition.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000186341 – 354Malate dehydrogenase 2, peroxisomalAdd BLAST354

Proteomic databases

PaxDbiQ9ZP05.
PRIDEiQ9ZP05.

Expressioni

Tissue specificityi

Expressed in rosette leaves.1 Publication

Gene expression databases

ExpressionAtlasiQ9ZP05. baseline and differential.
GenevisibleiQ9ZP05. AT.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

BioGridi16103. 1 interactor.
STRINGi3702.AT5G09660.4.

Structurei

3D structure databases

ProteinModelPortaliQ9ZP05.
SMRiQ9ZP05.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni10 – 18Peroxisomal targeting signal PTS21 Publication9

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG1494. Eukaryota.
COG0039. LUCA.
HOGENOMiHOG000213792.
InParanoidiQ9ZP05.
KOiK00026.
PhylomeDBiQ9ZP05.

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.

This entry describes 1 isoform i produced by alternative splicing. AlignAdd to basket

Note: A number of isoforms are produced. According to EST sequences.
Isoform 1 (identifier: Q9ZP05-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MEFRGDANQR IARISAHLTP QMEAKNSVIG RENCRAKGGN PGFKVAILGA
60 70 80 90 100
AGGIGQSLSL LMKMNPLVSL LHLYDVVNAP GVTADVSHMD TGAVVRGFLG
110 120 130 140 150
AKQLEDALTG MDLVIIPAGI PRKPGMTRDD LFKINAGIVK TLCEGVAKCC
160 170 180 190 200
PNAIVNLISN PVNSTVPIAA EVFKKAGTYD PKKLLGVTTL DVARANTFVA
210 220 230 240 250
EVLGLDPREV DVPVVGGHAG VTILPLLSQV KPPSSFTPQE IEYLTNRIQN
260 270 280 290 300
GGTEVVEAKA GAGSATLSMA YAAAKFADAC LRGLRGDANV VECSFVASQV
310 320 330 340 350
TELAFFATKV RLGRTGAEEV YQLGPLNEYE RIGLEKAKDE LAGSIQKGVE

FIRK
Length:354
Mass (Da):37,369
Last modified:May 1, 1999 - v1
Checksum:iAC56EAC7AB025288
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti166V → I in AAL15313 (PubMed:14593172).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ131206 mRNA. Translation: CAA10321.1.
AB020752 Genomic DNA. Translation: BAB09521.1.
AL353994 Genomic DNA. Translation: CAB89364.1.
CP002688 Genomic DNA. Translation: AED91422.1.
AF428373 mRNA. Translation: AAL16303.1.
AY037252 mRNA. Translation: AAK59853.1.
AY057682 mRNA. Translation: AAL15313.1.
AY077653 mRNA. Translation: AAL76131.1.
PIRiPA0040.
T49932.
RefSeqiNP_196528.1. NM_121003.4. [Q9ZP05-1]
UniGeneiAt.40751.
At.47611.

Genome annotation databases

EnsemblPlantsiAT5G09660.1; AT5G09660.1; AT5G09660. [Q9ZP05-1]
GeneIDi830825.
GrameneiAT5G09660.1; AT5G09660.1; AT5G09660.
KEGGiath:AT5G09660.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ131206 mRNA. Translation: CAA10321.1.
AB020752 Genomic DNA. Translation: BAB09521.1.
AL353994 Genomic DNA. Translation: CAB89364.1.
CP002688 Genomic DNA. Translation: AED91422.1.
AF428373 mRNA. Translation: AAL16303.1.
AY037252 mRNA. Translation: AAK59853.1.
AY057682 mRNA. Translation: AAL15313.1.
AY077653 mRNA. Translation: AAL76131.1.
PIRiPA0040.
T49932.
RefSeqiNP_196528.1. NM_121003.4. [Q9ZP05-1]
UniGeneiAt.40751.
At.47611.

3D structure databases

ProteinModelPortaliQ9ZP05.
SMRiQ9ZP05.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi16103. 1 interactor.
STRINGi3702.AT5G09660.4.

Proteomic databases

PaxDbiQ9ZP05.
PRIDEiQ9ZP05.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G09660.1; AT5G09660.1; AT5G09660. [Q9ZP05-1]
GeneIDi830825.
GrameneiAT5G09660.1; AT5G09660.1; AT5G09660.
KEGGiath:AT5G09660.

Organism-specific databases

TAIRiAT5G09660.

Phylogenomic databases

eggNOGiKOG1494. Eukaryota.
COG0039. LUCA.
HOGENOMiHOG000213792.
InParanoidiQ9ZP05.
KOiK00026.
PhylomeDBiQ9ZP05.

Enzyme and pathway databases

BioCyciMetaCyc:AT5G09660-MONOMER.
ReactomeiR-ATH-70263. Gluconeogenesis.
R-ATH-71403. Citric acid cycle (TCA cycle).

Miscellaneous databases

PROiQ9ZP05.

Gene expression databases

ExpressionAtlasiQ9ZP05. baseline and differential.
GenevisibleiQ9ZP05. 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 nameiMDHX2_ARATH
AccessioniPrimary (citable) accession number: Q9ZP05
Secondary accession number(s): Q93ZA7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: May 1, 1999
Last modified: November 30, 2016
This is version 140 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, 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.