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Protein

Malate dehydrogenase

Gene

mdh

Organism
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible oxidation of malate to oxaloacetate. Can also oxidize tartrate. Can utilize both NAD and NADP. Has a preference for NADP.1 Publication

Catalytic activityi

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

Kineticsi

  1. KM=0.019 mM for S-malate (in the presence of NADP)1 Publication
  2. KM=0.12 mM for S-malate (in the presence of NAD)1 Publication
  3. KM=1.2 mM for (2S,3S)-tartrate (in the presence of NAD)1 Publication
  4. KM=23 mM for (2S,3S)-tartrate (in the presence of NADP)1 Publication
  5. KM=5.8 mM for (2S,3R)-tartrate (in the presence of NADP)1 Publication
  6. KM=0.2 mM for (2S,3R)-tartrate (in the presence of NAD)1 Publication
  7. KM=0.87 mM for NAD (in the presence of malate)1 Publication
  8. KM=0.0076 mM for NAD (in the presence of malate)1 Publication

pH dependencei

Optimum pH is 11 for malate oxidation.1 Publication

Temperature dependencei

Optimum temperature is 95 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei79 – 791SubstrateBy similarity
Binding sitei85 – 851SubstrateBy similarity
Binding sitei92 – 921NADBy similarity
Binding sitei117 – 1171SubstrateBy similarity
Binding sitei148 – 1481SubstrateBy similarity
Active sitei172 – 1721Proton acceptorBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi6 – 116NADBy similarity
Nucleotide bindingi115 – 1173NADBy similarity

GO - Molecular functioni

  1. L-malate dehydrogenase activity Source: UniProtKB-HAMAP
  2. malate dehydrogenase (NADP+) activity Source: UniProtKB-EC

GO - Biological processi

  1. cellular carbohydrate metabolic process Source: InterPro
  2. malate metabolic process Source: InterPro
  3. tricarboxylic acid cycle Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Tricarboxylic acid cycle

Keywords - Ligandi

NAD, NADP

Enzyme and pathway databases

BioCyciAPER272557:GJD6-489-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Malate dehydrogenase (EC:1.1.1.37, EC:1.1.1.82)
Gene namesi
Name:mdh
Ordered Locus Names:APE_0672.1
OrganismiAeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Taxonomic identifieri272557 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesDesulfurococcaceaeAeropyrum
ProteomesiUP000002518: Chromosome

Subcellular locationi

Cytoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 308308Malate dehydrogenasePRO_0000113479Add
BLAST

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

STRINGi272557.APE_0672.1.

Structurei

Secondary structure

1
308
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 54Combined sources
Helixi9 – 2113Combined sources
Beta strandi26 – 294Combined sources
Beta strandi31 – 344Combined sources
Helixi35 – 5016Combined sources
Beta strandi56 – 605Combined sources
Helixi62 – 654Combined sources
Beta strandi69 – 735Combined sources
Helixi89 – 10618Combined sources
Beta strandi111 – 1144Combined sources
Beta strandi116 – 1183Combined sources
Helixi119 – 13012Combined sources
Helixi134 – 1363Combined sources
Beta strandi137 – 1393Combined sources
Helixi142 – 15716Combined sources
Helixi161 – 1633Combined sources
Beta strandi164 – 1707Combined sources
Beta strandi177 – 1859Combined sources
Helixi190 – 1934Combined sources
Helixi196 – 20712Combined sources
Helixi209 – 2179Combined sources
Helixi223 – 23715Combined sources
Beta strandi242 – 25211Combined sources
Helixi253 – 2553Combined sources
Beta strandi257 – 26812Combined sources
Beta strandi271 – 2755Combined sources
Helixi282 – 30019Combined sources
Helixi304 – 3074Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2D4AX-ray2.87A/B/C/D1-308[»]
ProteinModelPortaliQ9YEA1.
SMRiQ9YEA1. Positions 1-308.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9YEA1.

Family & Domainsi

Sequence similaritiesi

Belongs to the LDH/MDH superfamily. MDH type 3 family.Curated

Phylogenomic databases

eggNOGiCOG0039.
HOGENOMiHOG000213794.
KOiK00024.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
HAMAPiMF_00487. Malate_dehydrog_3.
InterProiIPR001557. L-lactate/malate_DH.
IPR022383. Lactate/malate_DH_C.
IPR001236. Lactate/malate_DH_N.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR011275. Malate_DH_type3.
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.
SUPFAMiSSF56327. SSF56327. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9YEA1-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MITILGAGKV GMATAVMLMM RGYDDLLLIA RTPGKPQGEA LDLAHAAAEL
60 70 80 90 100
GVDIRISGSN SYEDMRGSDI VLVTAGIGRK PGMTREQLLE ANANTMADLA
110 120 130 140 150
EKIKAYAKDA IVVITTNPVD AMTYVMYKKT GFPRERVIGF SGILDSARMA
160 170 180 190 200
YYISQKLGVS FKSVNAIVLG MHGQKMFPVP RLSSVGGVPL EHLMSKEEIE
210 220 230 240 250
EVVSETVNAG AKITELRGYS SNYGPAAGLV LTVEAIKRDS KRIYPYSLYL
260 270 280 290 300
QGEYGYNDIV AEVPAVIGKS GIERIIELPL TEDEKRKFDE AVQAVKKLVE

TLPPQLRE
Length:308
Mass (Da):33,490
Last modified:June 26, 2007 - v2
Checksum:iC2A14F224650B8CE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000002 Genomic DNA. Translation: BAA79645.2.
PIRiE72655.
RefSeqiNP_147405.2. NC_000854.2.
WP_010865893.1. NC_000854.2.

Genome annotation databases

EnsemblBacteriaiBAA79645; BAA79645; APE_0672.1.
GeneIDi1444806.
KEGGiape:APE_0672.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000002 Genomic DNA. Translation: BAA79645.2.
PIRiE72655.
RefSeqiNP_147405.2. NC_000854.2.
WP_010865893.1. NC_000854.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2D4AX-ray2.87A/B/C/D1-308[»]
ProteinModelPortaliQ9YEA1.
SMRiQ9YEA1. Positions 1-308.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272557.APE_0672.1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA79645; BAA79645; APE_0672.1.
GeneIDi1444806.
KEGGiape:APE_0672.1.

Phylogenomic databases

eggNOGiCOG0039.
HOGENOMiHOG000213794.
KOiK00024.

Enzyme and pathway databases

BioCyciAPER272557:GJD6-489-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9YEA1.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
HAMAPiMF_00487. Malate_dehydrog_3.
InterProiIPR001557. L-lactate/malate_DH.
IPR022383. Lactate/malate_DH_C.
IPR001236. Lactate/malate_DH_N.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR011275. Malate_DH_type3.
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.
SUPFAMiSSF56327. SSF56327. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1.
  2. "Refolding, characterization and crystal structure of (S)-malate dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix."
    Kawakami R., Sakuraba H., Goda S., Tsuge H., Ohshima T.
    Biochim. Biophys. Acta 1794:1496-1504(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.87 ANGSTROMS), SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, FUNCTION, CATALYTIC ACTIVITY.

Entry informationi

Entry nameiMDH_AERPE
AccessioniPrimary (citable) accession number: Q9YEA1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: June 26, 2007
Last modified: January 7, 2015
This is version 103 of the entry and version 2 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.