MDH_AERPE
ID MDH_AERPE Reviewed; 308 AA.
AC Q9YEA1;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 26-JUN-2007, sequence version 2.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Malate dehydrogenase {ECO:0000303|PubMed:19555779};
DE EC=1.1.1.299 {ECO:0000269|PubMed:19555779};
GN Name=mdh; OrderedLocusNames=APE_0672.1;
OS Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 /
OS K1).
OC Archaea; Crenarchaeota; Thermoprotei; Desulfurococcales;
OC Desulfurococcaceae; Aeropyrum.
OX NCBI_TaxID=272557;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1;
RX PubMed=10382966; DOI=10.1093/dnares/6.2.83;
RA Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K.,
RA Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A.,
RA Fukui S., Nagai Y., Nishijima K., Nakazawa H., Takamiya M., Masuda S.,
RA Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A.,
RA Aoki K., Kubota K., Nakamura Y., Nomura N., Sako Y., Kikuchi H.;
RT "Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon,
RT Aeropyrum pernix K1.";
RL DNA Res. 6:83-101(1999).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.87 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=19555779; DOI=10.1016/j.bbapap.2009.06.014;
RA Kawakami R., Sakuraba H., Goda S., Tsuge H., Ohshima T.;
RT "Refolding, characterization and crystal structure of (S)-malate
RT dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix.";
RL Biochim. Biophys. Acta 1794:1496-1504(2009).
CC -!- FUNCTION: Catalyzes the reversible oxidation of malate to oxaloacetate.
CC Can also oxidize tartrate. Can utilize both NAD and NADP. Catalytic
CC efficiency for malate oxidation is 3-fold higher with NADP.
CC {ECO:0000269|PubMed:19555779}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-malate + NADP(+) = H(+) + NADPH + oxaloacetate;
CC Xref=Rhea:RHEA:10824, ChEBI:CHEBI:15378, ChEBI:CHEBI:15589,
CC ChEBI:CHEBI:16452, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349;
CC EC=1.1.1.299; Evidence={ECO:0000269|PubMed:19555779};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-malate + NAD(+) = H(+) + NADH + oxaloacetate;
CC Xref=Rhea:RHEA:21432, ChEBI:CHEBI:15378, ChEBI:CHEBI:15589,
CC ChEBI:CHEBI:16452, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC EC=1.1.1.299; Evidence={ECO:0000269|PubMed:19555779};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.12 mM for S-malate (in the presence of NAD)
CC {ECO:0000269|PubMed:19555779};
CC KM=0.019 mM for S-malate (in the presence of NADP)
CC {ECO:0000269|PubMed:19555779};
CC KM=1.2 mM for (2S,3S)-tartrate (in the presence of NAD)
CC {ECO:0000269|PubMed:19555779};
CC KM=23 mM for (2S,3S)-tartrate (in the presence of NADP)
CC {ECO:0000269|PubMed:19555779};
CC KM=0.2 mM for (2S,3R)-tartrate (in the presence of NAD)
CC {ECO:0000269|PubMed:19555779};
CC KM=5.8 mM for (2S,3R)-tartrate (in the presence of NADP)
CC {ECO:0000269|PubMed:19555779};
CC KM=0.87 mM for NAD (in the presence of malate)
CC {ECO:0000269|PubMed:19555779};
CC KM=0.0076 mM for NADP (in the presence of malate)
CC {ECO:0000269|PubMed:19555779};
CC Note=kcat is 2.6 sec(-1) for NAD-dependent malate oxidation. kcat is
CC 1.4 sec(-1) for NADP-dependent malate oxidation.
CC {ECO:0000269|PubMed:19555779};
CC pH dependence:
CC Optimum pH is 11 for malate oxidation. {ECO:0000269|PubMed:19555779};
CC Temperature dependence:
CC Optimum temperature is 95 degrees Celsius.
CC {ECO:0000269|PubMed:19555779};
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:19555779}.
CC -!- MISCELLANEOUS: Ala at position 30 is responsible for coenzyme
CC specificity. Asp or Glu is present at this position in most NAD-
CC specific enzymes. The next residue, Arg, is important for NADP binding.
CC {ECO:0000305|PubMed:19555779}.
CC -!- SIMILARITY: Belongs to the LDH/MDH superfamily. {ECO:0000305}.
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DR EMBL; BA000002; BAA79645.2; -; Genomic_DNA.
DR PIR; E72655; E72655.
DR PDB; 2D4A; X-ray; 2.87 A; A/B/C/D=1-308.
DR PDBsum; 2D4A; -.
DR AlphaFoldDB; Q9YEA1; -.
DR SMR; Q9YEA1; -.
DR STRING; 272557.APE_0672.1; -.
DR EnsemblBacteria; BAA79645; BAA79645; APE_0672.1.
DR KEGG; ape:APE_0672.1; -.
DR PATRIC; fig|272557.25.peg.482; -.
DR eggNOG; arCOG00246; Archaea.
DR BRENDA; 1.1.1.82; 171.
DR EvolutionaryTrace; Q9YEA1; -.
DR Proteomes; UP000002518; Chromosome.
DR GO; GO:0030060; F:L-malate dehydrogenase activity; IEA:RHEA.
DR GO; GO:0046554; F:malate dehydrogenase (NADP+) activity; IEA:RHEA.
DR GO; GO:0019752; P:carboxylic acid metabolic process; IEA:InterPro.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-KW.
DR CDD; cd01339; LDH-like_MDH; 1.
DR Gene3D; 3.90.110.10; -; 1.
DR InterPro; IPR001557; L-lactate/malate_DH.
DR InterPro; IPR022383; Lactate/malate_DH_C.
DR InterPro; IPR001236; Lactate/malate_DH_N.
DR InterPro; IPR015955; Lactate_DH/Glyco_Ohase_4_C.
DR InterPro; IPR011275; Malate_DH_type3.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF02866; Ldh_1_C; 1.
DR Pfam; PF00056; Ldh_1_N; 1.
DR PIRSF; PIRSF000102; Lac_mal_DH; 1.
DR PRINTS; PR00086; LLDHDRGNASE.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF56327; SSF56327; 1.
PE 1: Evidence at protein level;
KW 3D-structure; NAD; NADP; Oxidoreductase; Reference proteome;
KW Tricarboxylic acid cycle.
FT CHAIN 1..308
FT /note="Malate dehydrogenase"
FT /id="PRO_0000113479"
FT ACT_SITE 172
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P61889"
FT BINDING 6..11
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q60176"
FT BINDING 79
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P61889"
FT BINDING 85
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P61889"
FT BINDING 92
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q60176"
FT BINDING 115..117
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q60176"
FT BINDING 117
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P61889"
FT BINDING 148
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P61889"
FT STRAND 2..5
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 9..21
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 26..29
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 31..34
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 35..50
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 56..60
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 62..65
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 89..106
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 111..114
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 119..130
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 134..136
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 142..157
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 161..163
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 164..170
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 177..185
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 190..193
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 196..207
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 209..217
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 223..237
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 242..252
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 253..255
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 257..268
FT /evidence="ECO:0007829|PDB:2D4A"
FT STRAND 271..275
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 282..300
FT /evidence="ECO:0007829|PDB:2D4A"
FT HELIX 304..307
FT /evidence="ECO:0007829|PDB:2D4A"
SQ SEQUENCE 308 AA; 33490 MW; C2A14F224650B8CE CRC64;
MITILGAGKV GMATAVMLMM RGYDDLLLIA RTPGKPQGEA LDLAHAAAEL GVDIRISGSN
SYEDMRGSDI VLVTAGIGRK PGMTREQLLE ANANTMADLA EKIKAYAKDA IVVITTNPVD
AMTYVMYKKT GFPRERVIGF SGILDSARMA YYISQKLGVS FKSVNAIVLG MHGQKMFPVP
RLSSVGGVPL EHLMSKEEIE EVVSETVNAG AKITELRGYS SNYGPAAGLV LTVEAIKRDS
KRIYPYSLYL QGEYGYNDIV AEVPAVIGKS GIERIIELPL TEDEKRKFDE AVQAVKKLVE
TLPPQLRE
