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Q9YEA1

- MDH_AERPE

UniProt

Q9YEA1 - MDH_AERPE

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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: 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-KW
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 – 54
Helixi9 – 2113
Beta strandi26 – 294
Beta strandi31 – 344
Helixi35 – 5016
Beta strandi56 – 605
Helixi62 – 654
Beta strandi69 – 735
Helixi89 – 10618
Beta strandi111 – 1144
Beta strandi116 – 1183
Helixi119 – 13012
Helixi134 – 1363
Beta strandi137 – 1393
Helixi142 – 15716
Helixi161 – 1633
Beta strandi164 – 1707
Beta strandi177 – 1859
Helixi190 – 1934
Helixi196 – 20712
Helixi209 – 2179
Helixi223 – 23715
Beta strandi242 – 25211
Helixi253 – 2553
Beta strandi257 – 26812
Beta strandi271 – 2755
Helixi282 – 30019
Helixi304 – 3074

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
BA000002 Genomic DNA. Translation: BAA79645.2 .
PIRi E72655.
RefSeqi NP_147405.2. NC_000854.2.
WP_010865893.1. NC_000854.2.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2D4A X-ray 2.87 A/B/C/D 1-308 [» ]
ProteinModelPortali Q9YEA1.
SMRi Q9YEA1. Positions 1-308.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 272557.APE_0672.1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAA79645 ; BAA79645 ; APE_0672.1 .
GeneIDi 1444806.
KEGGi ape:APE_0672.1.

Phylogenomic databases

eggNOGi COG0039.
HOGENOMi HOG000213794.
KOi K00024.

Enzyme and pathway databases

BioCyci APER272557:GJD6-489-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q9YEA1.

Family and domain databases

Gene3Di 3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
HAMAPi MF_00487. Malate_dehydrog_3.
InterProi IPR001557. 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 ]
PANTHERi PTHR11540. PTHR11540. 1 hit.
Pfami PF02866. Ldh_1_C. 1 hit.
PF00056. Ldh_1_N. 1 hit.
[Graphical view ]
PIRSFi PIRSF000102. Lac_mal_DH. 1 hit.
PRINTSi PR00086. LLDHDRGNASE.
SUPFAMi SSF56327. SSF56327. 1 hit.
ProtoNeti Search...

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: October 29, 2014
This is version 101 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