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Protein

Malate dehydrogenase

Gene

mdh

Organism
Thermus thermophilus
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible oxidation of malate to oxaloacetate.UniRule annotation

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei92 – 921SubstrateUniRule annotation
Binding sitei98 – 981SubstrateUniRule annotation
Binding sitei105 – 1051NADUniRule annotation
Binding sitei112 – 1121NADUniRule annotation1 Publication
Binding sitei131 – 1311SubstrateUniRule annotation
Binding sitei162 – 1621SubstrateUniRule annotation
Active sitei187 – 1871Proton acceptorUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi11 – 177NADUniRule annotation2 Publications
Nucleotide bindingi129 – 1313NADUniRule annotation2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Tricarboxylic acid cycle

Keywords - Ligandi

NAD

Enzyme and pathway databases

BRENDAi1.1.1.37. 2305.
SABIO-RKP10584.

Names & Taxonomyi

Protein namesi
Recommended name:
Malate dehydrogenaseUniRule annotation (EC:1.1.1.37UniRule annotation)
Gene namesi
Name:mdhUniRule annotation
OrganismiThermus thermophilus
Taxonomic identifieri274 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL4255.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 327327Malate dehydrogenasePRO_0000113400Add
BLAST

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi262724.TTC0168.

Chemistry

BindingDBiP10584.

Structurei

Secondary structure

1
327
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 117Combined sources
Helixi15 – 2511Combined sources
Turni26 – 305Combined sources
Beta strandi36 – 416Combined sources
Helixi44 – 463Combined sources
Helixi47 – 5812Combined sources
Turni59 – 613Combined sources
Beta strandi65 – 728Combined sources
Helixi74 – 774Combined sources
Turni78 – 803Combined sources
Beta strandi82 – 865Combined sources
Helixi98 – 11922Combined sources
Beta strandi125 – 1284Combined sources
Beta strandi130 – 1323Combined sources
Helixi133 – 14210Combined sources
Helixi149 – 1513Combined sources
Beta strandi152 – 1543Combined sources
Helixi157 – 17115Combined sources
Helixi175 – 1773Combined sources
Beta strandi182 – 1854Combined sources
Beta strandi192 – 1943Combined sources
Helixi205 – 2073Combined sources
Helixi211 – 2166Combined sources
Helixi218 – 23316Combined sources
Helixi238 – 25316Combined sources
Beta strandi262 – 2676Combined sources
Helixi271 – 2733Combined sources
Beta strandi278 – 28710Combined sources
Beta strandi290 – 2934Combined sources
Helixi301 – 32323Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BDMX-ray1.80A/B1-327[»]
1BMDX-ray1.90A/B1-327[»]
1IZ9X-ray2.00A/B1-327[»]
1WZEX-ray2.00A/B1-327[»]
1WZIX-ray2.00A/B1-327[»]
1Y7TX-ray1.65A/B1-327[»]
2CVQX-ray2.08A/B1-321[»]
4KDEX-ray1.80A/B1-327[»]
4KDFX-ray2.36A/B/C/D1-327[»]
ProteinModelPortaliP10584.
SMRiP10584. Positions 1-327.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP10584.

Family & Domainsi

Sequence similaritiesi

Belongs to the LDH/MDH superfamily. MDH type 2 family.UniRule annotationCurated

Phylogenomic databases

eggNOGiENOG4105D9Z. Bacteria.
COG0039. LUCA.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
HAMAPiMF_01517. Malate_dehydrog_2.
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.
IPR010945. Malate_DH_type2.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR23382. PTHR23382. 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.
TIGRFAMsiTIGR01759. MalateDH-SF1. 1 hit.
PROSITEiPS00068. MDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P10584-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKAPVRVAVT GAAGQIGYSL LFRIAAGEML GKDQPVILQL LEIPQAMKAL
60 70 80 90 100
EGVVMELEDC AFPLLAGLEA TDDPKVAFKD ADYALLVGAA PRKAGMERRD
110 120 130 140 150
LLQVNGKIFT EQGRALAEVA KKDVKVLVVG NPANTNALIA YKNAPGLNPR
160 170 180 190 200
NFTAMTRLDH NRAKAQLAKK TGTGVDRIRR MTVWGNHSST MFPDLFHAEV
210 220 230 240 250
DGRPALELVD MEWYEKVFIP TVAQRGAAII QARGASSAAS AANAAIEHIR
260 270 280 290 300
DWALGTPEGD WVSMAVPSQG EYGIPEGIVY SFPVTAKDGA YRVVEGLEIN
310 320
EFARKRMEIT AQELLDEMEQ VKALGLI
Length:327
Mass (Da):35,426
Last modified:July 1, 1989 - v1
Checksum:i31FA90DED2393DF2
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti190 – 1901T → I in strain: F428; produces a 2 to 3 times higher enzyme activity.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02598 Genomic DNA. Translation: AAA27499.1.
X54073 Genomic DNA. Translation: CAA38008.1.
X56033 Genomic DNA. Translation: CAA39508.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02598 Genomic DNA. Translation: AAA27499.1.
X54073 Genomic DNA. Translation: CAA38008.1.
X56033 Genomic DNA. Translation: CAA39508.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BDMX-ray1.80A/B1-327[»]
1BMDX-ray1.90A/B1-327[»]
1IZ9X-ray2.00A/B1-327[»]
1WZEX-ray2.00A/B1-327[»]
1WZIX-ray2.00A/B1-327[»]
1Y7TX-ray1.65A/B1-327[»]
2CVQX-ray2.08A/B1-321[»]
4KDEX-ray1.80A/B1-327[»]
4KDFX-ray2.36A/B/C/D1-327[»]
ProteinModelPortaliP10584.
SMRiP10584. Positions 1-327.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi262724.TTC0168.

Chemistry

BindingDBiP10584.
ChEMBLiCHEMBL4255.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105D9Z. Bacteria.
COG0039. LUCA.

Enzyme and pathway databases

BRENDAi1.1.1.37. 2305.
SABIO-RKP10584.

Miscellaneous databases

EvolutionaryTraceiP10584.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
HAMAPiMF_01517. Malate_dehydrog_2.
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.
IPR010945. Malate_DH_type2.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR23382. PTHR23382. 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.
TIGRFAMsiTIGR01759. MalateDH-SF1. 1 hit.
PROSITEiPS00068. MDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Nucleotide sequence of the malate dehydrogenase gene of Thermus flavus and its mutation directing an increase in enzyme activity."
    Nishiyama M., Matsubara N., Yamamoto K., Iijima S., Uozumi T., Beppu T.
    J. Biol. Chem. 261:14178-14183(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-37 AND 265-284.
    Strain: ATCC 33923 / DSM 674 / AT-62.
  2. "Characterization of an operon encoding succinyl-CoA synthetase and malate dehydrogenase from Thermus flavus AT-62 and its expression in Escherichia coli."
    Nishiyama M., Horinouchi S., Beppu T.
    Mol. Gen. Genet. 226:1-9(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 33923 / DSM 674 / AT-62.
  3. "Cloning and nucleotide sequences of the mdh and sucD genes from Thermus aquaticus B."
    Nicholls D.J., Sundaram T.K., Atkinson T., Minton N.P.
    FEMS Microbiol. Lett. 58:7-14(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: B / NCIB 11247.
  4. "Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus."
    Kelly C.A., Nishiyama M., Ohnishi Y., Beppu T., Birktoft J.J.
    Biochemistry 32:3913-3922(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH NAD.
    Strain: ATCC 33923 / DSM 674 / AT-62.
  5. "Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H)."
    Tomita T., Fushinobu S., Kuzuyama T., Nishiyama M.
    Biochem. Biophys. Res. Commun. 334:613-618(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH NADP.
  6. "Crystal structure of malate dehydrogenase from Thermus thermophilus HB8."
    RIKEN structural genomics initiative (RSGI)
    Submitted (OCT-2002) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

Entry informationi

Entry nameiMDH_THETH
AccessioniPrimary (citable) accession number: P10584
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: April 13, 2016
This is version 129 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, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.