MDH_THETH
ID MDH_THETH Reviewed; 327 AA.
AC P10584;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1989, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=Malate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_01517};
DE EC=1.1.1.37 {ECO:0000255|HAMAP-Rule:MF_01517};
GN Name=mdh {ECO:0000255|HAMAP-Rule:MF_01517};
OS Thermus thermophilus.
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=274;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 1-37 AND
RP 265-284.
RC STRAIN=ATCC 33923 / DSM 674 / AT-62;
RX PubMed=3771528; DOI=10.1016/s0021-9258(18)67000-0;
RA Nishiyama M., Matsubara N., Yamamoto K., Iijima S., Uozumi T., Beppu T.;
RT "Nucleotide sequence of the malate dehydrogenase gene of Thermus flavus and
RT its mutation directing an increase in enzyme activity.";
RL J. Biol. Chem. 261:14178-14183(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 33923 / DSM 674 / AT-62;
RX PubMed=2034208; DOI=10.1007/bf00273580;
RA Nishiyama M., Horinouchi S., Beppu T.;
RT "Characterization of an operon encoding succinyl-CoA synthetase and malate
RT dehydrogenase from Thermus flavus AT-62 and its expression in Escherichia
RT coli.";
RL Mol. Gen. Genet. 226:1-9(1991).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=B / NCIMB 11247;
RX PubMed=2204576; DOI=10.1016/0378-1097(90)90093-6;
RA Nicholls D.J., Sundaram T.K., Atkinson T., Minton N.P.;
RT "Cloning and nucleotide sequences of the mdh and sucD genes from Thermus
RT aquaticus B.";
RL FEMS Microbiol. Lett. 58:7-14(1990).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH NAD.
RC STRAIN=ATCC 33923 / DSM 674 / AT-62;
RX PubMed=8471603; DOI=10.1021/bi00066a010;
RA Kelly C.A., Nishiyama M., Ohnishi Y., Beppu T., Birktoft J.J.;
RT "Determinants of protein thermostability observed in the 1.9-A crystal
RT structure of malate dehydrogenase from the thermophilic bacterium Thermus
RT flavus.";
RL Biochemistry 32:3913-3922(1993).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH NADP.
RX PubMed=16009341; DOI=10.1016/j.bbrc.2005.06.133;
RA Tomita T., Fushinobu S., Kuzuyama T., Nishiyama M.;
RT "Crystal structure of NAD-dependent malate dehydrogenase complexed with
RT NADP(H).";
RL Biochem. Biophys. Res. Commun. 334:613-618(2005).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RG RIKEN structural genomics initiative (RSGI);
RT "Crystal structure of malate dehydrogenase from Thermus thermophilus HB8.";
RL Submitted (OCT-2002) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the reversible oxidation of malate to oxaloacetate.
CC {ECO:0000255|HAMAP-Rule:MF_01517}.
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; EC=1.1.1.37;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01517};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16009341}.
CC -!- SIMILARITY: Belongs to the LDH/MDH superfamily. MDH type 2 family.
CC {ECO:0000255|HAMAP-Rule:MF_01517, ECO:0000305}.
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DR EMBL; J02598; AAA27499.1; -; Genomic_DNA.
DR EMBL; X54073; CAA38008.1; -; Genomic_DNA.
DR EMBL; X56033; CAA39508.1; -; Genomic_DNA.
DR RefSeq; WP_011172623.1; NZ_LR027517.1.
DR PDB; 1BDM; X-ray; 1.80 A; A/B=1-327.
DR PDB; 1BMD; X-ray; 1.90 A; A/B=1-327.
DR PDB; 1IZ9; X-ray; 2.00 A; A/B=1-327.
DR PDB; 1WZE; X-ray; 2.00 A; A/B=1-327.
DR PDB; 1WZI; X-ray; 2.00 A; A/B=1-327.
DR PDB; 1Y7T; X-ray; 1.65 A; A/B=1-327.
DR PDB; 2CVQ; X-ray; 2.08 A; A/B=1-327.
DR PDB; 4KDE; X-ray; 1.80 A; A/B=1-327.
DR PDB; 4KDF; X-ray; 2.36 A; A/B/C/D=1-327.
DR PDBsum; 1BDM; -.
DR PDBsum; 1BMD; -.
DR PDBsum; 1IZ9; -.
DR PDBsum; 1WZE; -.
DR PDBsum; 1WZI; -.
DR PDBsum; 1Y7T; -.
DR PDBsum; 2CVQ; -.
DR PDBsum; 4KDE; -.
DR PDBsum; 4KDF; -.
DR AlphaFoldDB; P10584; -.
DR SMR; P10584; -.
DR BindingDB; P10584; -.
DR ChEMBL; CHEMBL4255; -.
DR DrugCentral; P10584; -.
DR GeneID; 3168364; -.
DR OMA; TKGMERG; -.
DR BRENDA; 1.1.1.37; 2305.
DR SABIO-RK; P10584; -.
DR EvolutionaryTrace; P10584; -.
DR GO; GO:0030060; F:L-malate dehydrogenase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006108; P:malate metabolic process; IEA:InterPro.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-UniRule.
DR Gene3D; 3.90.110.10; -; 1.
DR HAMAP; MF_01517; Malate_dehydrog_2; 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; IPR001252; Malate_DH_AS.
DR InterPro; IPR010945; Malate_DH_type2.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR PANTHER; PTHR23382; PTHR23382; 1.
DR Pfam; PF02866; Ldh_1_C; 1.
DR Pfam; PF00056; Ldh_1_N; 1.
DR PIRSF; PIRSF000102; Lac_mal_DH; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF56327; SSF56327; 1.
DR TIGRFAMs; TIGR01759; MalateDH-SF1; 1.
DR PROSITE; PS00068; MDH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; NAD; Oxidoreductase;
KW Tricarboxylic acid cycle.
FT CHAIN 1..327
FT /note="Malate dehydrogenase"
FT /id="PRO_0000113400"
FT ACT_SITE 187
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01517"
FT BINDING 11..17
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01517,
FT ECO:0000269|PubMed:16009341, ECO:0000269|PubMed:8471603"
FT BINDING 92
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01517"
FT BINDING 98
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01517"
FT BINDING 105
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01517"
FT BINDING 112
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01517,
FT ECO:0000269|PubMed:16009341"
FT BINDING 129..131
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01517,
FT ECO:0000269|PubMed:16009341, ECO:0000269|PubMed:8471603"
FT BINDING 131
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01517"
FT BINDING 162
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01517"
FT VARIANT 190
FT /note="T -> I (in strain: F428; produces a 2 to 3 times
FT higher enzyme activity)"
FT STRAND 5..11
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 15..25
FT /evidence="ECO:0007829|PDB:1Y7T"
FT TURN 26..30
FT /evidence="ECO:0007829|PDB:1Y7T"
FT STRAND 36..41
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 44..46
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 47..58
FT /evidence="ECO:0007829|PDB:1Y7T"
FT TURN 59..61
FT /evidence="ECO:0007829|PDB:1Y7T"
FT STRAND 65..72
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 74..77
FT /evidence="ECO:0007829|PDB:1Y7T"
FT TURN 78..80
FT /evidence="ECO:0007829|PDB:1Y7T"
FT STRAND 82..86
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 98..119
FT /evidence="ECO:0007829|PDB:1Y7T"
FT STRAND 125..128
FT /evidence="ECO:0007829|PDB:1Y7T"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 133..142
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 149..151
FT /evidence="ECO:0007829|PDB:1Y7T"
FT STRAND 152..154
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 157..171
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 175..177
FT /evidence="ECO:0007829|PDB:1Y7T"
FT STRAND 182..185
FT /evidence="ECO:0007829|PDB:1Y7T"
FT STRAND 192..194
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 205..207
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 211..216
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 218..233
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 238..253
FT /evidence="ECO:0007829|PDB:1Y7T"
FT STRAND 262..267
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 271..273
FT /evidence="ECO:0007829|PDB:1Y7T"
FT STRAND 278..287
FT /evidence="ECO:0007829|PDB:1Y7T"
FT STRAND 290..293
FT /evidence="ECO:0007829|PDB:1Y7T"
FT HELIX 301..323
FT /evidence="ECO:0007829|PDB:1Y7T"
SQ SEQUENCE 327 AA; 35426 MW; 31FA90DED2393DF2 CRC64;
MKAPVRVAVT GAAGQIGYSL LFRIAAGEML GKDQPVILQL LEIPQAMKAL EGVVMELEDC
AFPLLAGLEA TDDPKVAFKD ADYALLVGAA PRKAGMERRD LLQVNGKIFT EQGRALAEVA
KKDVKVLVVG NPANTNALIA YKNAPGLNPR NFTAMTRLDH NRAKAQLAKK TGTGVDRIRR
MTVWGNHSST MFPDLFHAEV DGRPALELVD MEWYEKVFIP TVAQRGAAII QARGASSAAS
AANAAIEHIR DWALGTPEGD WVSMAVPSQG EYGIPEGIVY SFPVTAKDGA YRVVEGLEIN
EFARKRMEIT AQELLDEMEQ VKALGLI
