ID MDH_METEA Reviewed; 320 AA.
AC Q84FY8; C5B049;
DT 16-AUG-2004, integrated into UniProtKB/Swiss-Prot.
DT 22-SEP-2009, sequence version 2.
DT 27-MAR-2024, entry version 131.
DE RecName: Full=Malate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_00487};
DE EC=1.1.1.37 {ECO:0000255|HAMAP-Rule:MF_00487};
GN Name=mdh {ECO:0000255|HAMAP-Rule:MF_00487};
GN OrderedLocusNames=MexAM1_META1p1537;
OS Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB
OS 9133 / AM1) (Methylobacterium extorquens).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Methylobacteriaceae; Methylorubrum.
OX NCBI_TaxID=272630;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=12730156; DOI=10.1128/jb.185.10.2980-2987.2003;
RA Chistoserdova L., Chen S.-W., Lapidus A., Lidstrom M.E.;
RT "Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of
RT view.";
RL J. Bacteriol. 185:2980-2987(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1;
RX PubMed=19440302; DOI=10.1371/journal.pone.0005584;
RA Vuilleumier S., Chistoserdova L., Lee M.-C., Bringel F., Lajus A., Zhou Y.,
RA Gourion B., Barbe V., Chang J., Cruveiller S., Dossat C., Gillett W.,
RA Gruffaz C., Haugen E., Hourcade E., Levy R., Mangenot S., Muller E.,
RA Nadalig T., Pagni M., Penny C., Peyraud R., Robinson D.G., Roche D.,
RA Rouy Z., Saenampechek C., Salvignol G., Vallenet D., Wu Z., Marx C.J.,
RA Vorholt J.A., Olson M.V., Kaul R., Weissenbach J., Medigue C.,
RA Lidstrom M.E.;
RT "Methylobacterium genome sequences: a reference blueprint to investigate
RT microbial metabolism of C1 compounds from natural and industrial sources.";
RL PLoS ONE 4:E5584-E5584(2009).
CC -!- FUNCTION: Catalyzes the reversible oxidation of malate to oxaloacetate.
CC {ECO:0000255|HAMAP-Rule:MF_00487}.
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_00487};
CC -!- SIMILARITY: Belongs to the LDH/MDH superfamily. MDH type 3 family.
CC {ECO:0000255|HAMAP-Rule:MF_00487}.
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DR EMBL; AY181040; AAO24626.1; -; Genomic_DNA.
DR EMBL; CP001510; ACS39399.1; -; Genomic_DNA.
DR RefSeq; WP_003599890.1; NC_012808.1.
DR PDB; 5UJK; X-ray; 1.53 A; A=1-320.
DR PDB; 5ULV; X-ray; 1.66 A; A=1-320.
DR PDBsum; 5UJK; -.
DR PDBsum; 5ULV; -.
DR AlphaFoldDB; Q84FY8; -.
DR SMR; Q84FY8; -.
DR STRING; 272630.MexAM1_META1p1537; -.
DR KEGG; mea:Mex_1p1537; -.
DR eggNOG; COG0039; Bacteria.
DR HOGENOM; CLU_045401_2_1_5; -.
DR OrthoDB; 9802969at2; -.
DR BioCyc; MetaCyc:MONOMER-4226; -.
DR BRENDA; 1.1.1.37; 3296.
DR Proteomes; UP000009081; Chromosome.
DR GO; GO:0030060; F:L-malate dehydrogenase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0019752; P:carboxylic acid metabolic process; IEA:InterPro.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-UniRule.
DR CDD; cd01339; LDH-like_MDH; 1.
DR Gene3D; 3.90.110.10; Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal; 1.
DR Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 1.
DR HAMAP; MF_00487; Malate_dehydrog_3; 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 NCBIfam; TIGR01763; MalateDH_bact; 1.
DR PANTHER; PTHR43128; L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)); 1.
DR PANTHER; PTHR43128:SF34; L-LACTATE DEHYDROGENASE; 1.
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; SSF56327; LDH C-terminal domain-like; 1.
DR SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1.
PE 1: Evidence at protein level;
KW 3D-structure; NAD; Oxidoreductase; Reference proteome;
KW Tricarboxylic acid cycle.
FT CHAIN 1..320
FT /note="Malate dehydrogenase"
FT /id="PRO_0000113457"
FT ACT_SITE 176
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00487"
FT BINDING 10..15
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00487"
FT BINDING 34
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00487"
FT BINDING 83
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00487"
FT BINDING 89
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00487"
FT BINDING 96
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00487"
FT BINDING 119..121
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00487"
FT BINDING 121
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00487"
FT BINDING 152
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00487"
FT CONFLICT 109
FT /note="E -> K (in Ref. 1; AAO24626)"
FT /evidence="ECO:0000305"
FT CONFLICT 120
FT /note="T -> A (in Ref. 1; AAO24626)"
FT /evidence="ECO:0000305"
FT STRAND 5..9
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 13..24
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 29..33
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:5ULV"
FT HELIX 39..54
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 60..65
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 66..69
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 73..77
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 89..110
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 123..134
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 141..143
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 146..161
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 165..167
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 172..174
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 177..179
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 180..182
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 194..199
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 205..216
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 218..226
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 227..229
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 233..247
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 252..262
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 263..265
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 267..278
FT /evidence="ECO:0007829|PDB:5UJK"
FT STRAND 281..285
FT /evidence="ECO:0007829|PDB:5UJK"
FT HELIX 292..314
FT /evidence="ECO:0007829|PDB:5UJK"
SQ SEQUENCE 320 AA; 33647 MW; B2CF23AAA0F032EC CRC64;
MARSKIALIG AGQIGGTLAH LAGLKELGDV VLFDIVDGVP QGKALDIAES APVDGFDAKY
SGASDYSAIA GADVVIVTAG VPRKPGMSRD DLIGINLKVM EAVGAGIKEH APDAFVICIT
NPLDAMVWAL QKFSGLPTNK VVGMAGVLDS ARFRHFLAEE FGVSVEDVTA FVLGGHGDDM
VPLTRYSTVA GVPLTDLVKL GWTTQEKLDA MVERTRKGGG EIVNLLKTGS AFYAPAASAI
AMAESYLRDK KRVLPCAAYL DGQYGIDGLY VGVPVVIGEN GVERVLEVTF NDDEKAMFEK
SVNSVKGLIE ACKSVNDKLA
//
