DB code: M00171
| CATH domain | 3.40.50.720 : Rossmann fold | |
|---|---|---|
| 3.90.110.10 : L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 | Catalytic domain | |
| 4.-.-.- : | Catalytic domain | |
| 4.-.-.- : | Catalytic domain | |
| E.C. | 1.1.1.82 | |
| CSA | ||
| M-CSA | ||
| MACiE | ||
| CATH domain | Related DB codes (homologues) |
|---|---|
| 3.40.50.720 : Rossmann fold | S00543 S00551 S00552 S00553 S00602 S00604 S00605 S00608 S00610 S00625 S00319 S00328 S00329 S00330 S00331 S00332 D00456 D00457 D00458 S00324 S00320 S00325 S00326 S00327 D00459 S00335 S00336 S00334 T00219 S00339 D00513 D00001 D00002 D00003 D00005 D00007 D00008 D00010 D00012 D00017 D00018 D00023 D00027 D00028 D00031 D00032 D00033 D00034 D00035 D00037 D00048 D00071 D00476 D00481 D00482 D00490 D00492 D00494 D00545 D00601 D00603 D00604 D00605 D00615 D00845 D00857 D00858 M00161 M00210 T00002 T00010 T00011 T00015 T00227 T00247 T00408 T00414 D00827 D00262 D00274 D00275 M00035 T00109 |
| 3.90.110.10 : L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 | D00005 D00008 D00827 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | Pfam | RefSeq |
|---|---|---|---|---|
| P46489 |
Malate dehydrogenase [NADP], chloroplastic
|
EC
1.1.1.82
NADP-MDH |
PF02866
(Ldh_1_C)
PF00056 (Ldh_1_N) [Graphical View] |
|
| P17606 |
Malate dehydrogenase [NADP] 1, chloroplastic
|
EC
1.1.1.82
NADP-MDH-1 |
PF02866
(Ldh_1_C)
PF00056 (Ldh_1_N) [Graphical View] |
XP_002445670.1
(Protein)
XM_002445625.1 (DNA/RNA sequence) |
| KEGG enzyme name |
|---|
|
malate dehydrogenase (NADP+)
NADP+-malic enzyme NADP+-malate dehydrogenase malic dehydrogenase (nicotinamide adenine dinucleotide phosphate) malate NADP+ dehydrogenase NADP+ malate dehydrogenase NADP+-linked malate dehydrogenase malate dehydrogenase (NADP+) |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| P46489 | MDHP_FLABI | (S)-malate + NADP(+) = oxaloacetate + NADPH. | Homodimer. | Plastid, chloroplast. | |
| P17606 | MDHP1_SORBI | (S)-malate + NADP(+) = oxaloacetate + NADPH. | Homodimer. | Plastid, chloroplast. |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|---|---|
| MAP00620 | Pyruvate metabolism | |
| MAP00710 | Carbon fixation in photosynthetic organisms |
| Compound table | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Substrates | Products | Intermediates | |||||||||
| KEGG-id | C00149 | C00006 | C00036 | C00005 | C00080 | ||||||
| E.C. | |||||||||||
| Compound | (S)-Malate | NADP+ | Oxaloacetate | NADPH | H+ | ||||||
| Type | carbohydrate,carboxyl group | amide group,amine group,nucleotide | carbohydrate,carboxyl group | amide group,amine group,nucleotide | others | ||||||
| ChEBI |
30797 30797 |
18009 18009 |
30744 30744 |
16474 16474 |
15378 15378 |
||||||
| PubChem |
222656 222656 |
5886 5886 |
970 970 |
5884 5884 |
1038 1038 |
||||||
| 1civA01 |
|
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|
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Unbound | Bound:NAP | Unbound | Unbound | ||
| 7mdhA01 |
|
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Unbound | Unbound | Unbound | Unbound | ||
| 7mdhB01 |
|
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|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhC01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhD01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 1civA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhB02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhC02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhD02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 1civA03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhA03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhB03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhC03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhD03 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 1civA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhA04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhB04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhC04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| 7mdhD04 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | ||
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| PDB;7mdh & Swiss-prot;P46489, P17606 & literature [9], [10] | ||
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1civA01 |
|
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|
|||||
| 7mdhA01 |
|
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|
|||||
| 7mdhB01 |
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|||||
| 7mdhC01 |
|
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| 7mdhD01 |
|
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|
|||||
| 1civA02 |
|
|
|
|
|
ASP 197;HIS 225;CYS 361 | ||||
| 7mdhA02 |
|
|
|
|
|
ASP 201;HIS 229;CYS 365 | ||||
| 7mdhB02 |
|
|
|
|
|
ASP 201;HIS 229;CYS 365 | ||||
| 7mdhC02 |
|
|
|
|
|
ASP 201;HIS 229;CYS 365 | ||||
| 7mdhD02 |
|
|
|
|
|
ASP 201;HIS 229;CYS 365 | ||||
| 1civA03 |
|
|
|
|
|
CYS 20;CYS 25 | ||||
| 7mdhA03 |
|
|
|
|
|
CYS 24;CYS 29 | ||||
| 7mdhB03 |
|
|
|
|
|
CYS 24;CYS 29 | ||||
| 7mdhC03 |
|
|
|
|
|
CYS 24;CYS 29 | ||||
| 7mdhD03 |
|
|
|
|
|
CYS 24;CYS 29 | ||||
| 1civA04 |
|
|
|
|
|
CYS 373 | ||||
| 7mdhA04 |
|
|
|
|
|
CYS 377 | ||||
| 7mdhB04 |
|
|
|
|
|
CYS 377 | ||||
| 7mdhC04 |
|
|
|
|
|
CYS 377 | ||||
| 7mdhD04 |
|
|
|
|
|
CYS 377 | ||||
| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
|
[4]
|
Fig.1, p.72-73 | |
|
[8]
|
Fig.8, p.3516-3517 | |
|
[10]
|
||
|
[11]
|
||
|
[14]
|
p.193 | |
|
[15]
|
p.33486-33487 | |
|
[16]
|
p.4325 | |
|
[18]
|
||
|
[19]
|
||
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 3586023 |
| Journal | J Mol Biol |
| Year | 1987 |
| Volume | 193 |
| Pages | 233-5 |
| Authors | Baker PJ, Thomas DH, Barton CH, Rice DW, Bailey E |
| Title | Crystallization of an NADP+-dependent malic enzyme from rat liver. |
| Related PDB | |
| Related UniProtKB | |
| [2] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 3341764 |
| Journal | Arch Biochem Biophys |
| Year | 1988 |
| Volume | 260 |
| Pages | 771-9 |
| Authors | Fickenscher K, Scheibe R |
| Title | Limited proteolysis of inactive tetrameric chloroplast NADP-malate dehydrogenase produces active dimers. |
| Related PDB | |
| Related UniProtKB | |
| [3] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 2351138 |
| Journal | Eur J Biochem |
| Year | 1990 |
| Volume | 189 |
| Pages | 581-7 |
| Authors | Scheibe R, Rudolph R, Reng W, Jaenicke R |
| Title | Structural and catalytic properties of oxidized and reduced chloroplast NADP-malate dehydrogenase upon denaturation and renaturation. |
| Related PDB | |
| Related UniProtKB | |
| [4] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 1678537 |
| Journal | Philos Trans R Soc Lond B Biol Sci |
| Year | 1991 |
| Volume | 332 |
| Pages | 177-84 |
| Authors | Dunn CR, Wilks HM, Halsall DJ, Atkinson T, Clarke AR, Muirhead H, Holbrook JJ |
| Title | Design and synthesis of new enzymes based on the lactate dehydrogenase framework. |
| Related PDB | |
| Related UniProtKB | |
| [5] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8444839 |
| Journal | J Biol Chem |
| Year | 1993 |
| Volume | 268 |
| Pages | 4656-60 |
| Authors | Nishiyama M, Birktoft JJ, Beppu T |
| Title | Alteration of coenzyme specificity of malate dehydrogenase from Thermus flavus by site-directed mutagenesis. |
| Related PDB | |
| Related UniProtKB | |
| [6] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8331658 |
| Journal | J Mol Biol |
| Year | 1993 |
| Volume | 232 |
| Pages | 213-22 |
| Authors | Hall MD, Banaszak LJ |
| Title | Crystal structure of a ternary complex of Escherichia coli malate dehydrogenase citrate and NAD at 1.9 A resolution. |
| Related PDB | |
| Related UniProtKB | |
| [7] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 7918997 |
| Journal | Biophys J |
| Year | 1994 |
| Volume | 67 |
| Pages | 29-35 |
| Authors | Li D, Stevens FJ, Schiffer M, Anderson LE |
| Title | Mechanism of light modulation: identification of potential redox-sensitive cysteines distal to catalytic site in light-activated chloroplast enzymes. |
| Related PDB | |
| Related UniProtKB | |
| [8] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8106392 |
| Journal | J Biol Chem |
| Year | 1994 |
| Volume | 269 |
| Pages | 3511-7 |
| Authors | Issakidis E, Saarinen M, Decottignies P, Jacquot JP, Cretin C, Gadal P, Miginiac-Maslow M |
| Title | Identification and characterization of the second regulatory disulfide bridge of recombinant sorghum leaf NADP-malate dehydrogenase. |
| Related PDB | |
| Related UniProtKB | |
| [9] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 7961639 |
| Journal | J Biol Chem |
| Year | 1994 |
| Volume | 269 |
| Pages | 27291-6 |
| Authors | Lemaire M, Schmitter JM, Issakidis E, Miginiac-Maslow M, Gadal P, Decottignies P |
| Title | Essential histidine at the active site of sorghum leaf NADP-dependent malate dehydrogenase. |
| Related PDB | |
| Related UniProtKB | |
| [10] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8665917 |
| Journal | Eur J Biochem |
| Year | 1996 |
| Volume | 236 |
| Pages | 947-52 |
| Authors | Lemaire M, Miginiac-Maslow M, Decottignies P |
| Title | The catalytic site of chloroplastic NADP-dependent malate dehydrogenase contains a His/Asp pair. |
| Related PDB | |
| Related UniProtKB | |
| [11] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8772188 |
| Journal | FEBS Lett |
| Year | 1996 |
| Volume | 392 |
| Pages | 121-4 |
| Authors | Issakidis E, Lemaire M, Decottignies P, Jacquot JP, Miginiac-Maslow M |
| Title | Direct evidence for the different roles of the N- and C-terminal regulatory disulfides of sorghum leaf NADP-malate dehydrogenase in its activation by reduced thioredoxin. |
| Related PDB | |
| Related UniProtKB | |
| [12] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8612735 |
| Journal | FEBS Lett |
| Year | 1996 |
| Volume | 382 |
| Pages | 137-40 |
| Authors | Lemaire M, Issakidis E, Ruelland E, Decottignies P, Miginiac-Maslow M |
| Title | An active-site cysteine of sorghum leaf NADP-malate dehydrogenase studied by site-directed mutagenesis. |
| Related PDB | |
| Related UniProtKB | |
| [13] | |
| Resource | |
| Comments | CRYSTALLIZATION. |
| Medline ID | |
| PubMed ID | 9761865 |
| Journal | Acta Crystallogr D Biol Crystallogr |
| Year | 1998 |
| Volume | 54 |
| Pages | 654-6 |
| Authors | MacPherson KH, Ashton AR, Carr PD, Trevanion SJ, Verger D, Ollis DL |
| Title | Crystallization and preliminary crystallographic studies of chloroplast NADP-dependent malate dehydrogenase from Flaveria bidentis. |
| Related PDB | |
| Related UniProtKB | P46489 |
| [14] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9692918 |
| Journal | Eur J Biochem |
| Year | 1998 |
| Volume | 255 |
| Pages | 185-95 |
| Authors | Krimm I, Lemaire S, Ruelland E, Miginiac-Maslow M, Jaquot JP, Hirasawa M, Knaff DB, Lancelin JM |
| Title | The single mutation Trp35-->Ala in the 35-40 redox site of Chlamydomonas reinhardtii thioredoxin h affects its biochemical activity and the pH dependence of C36-C39 1H-13C NMR. |
| Related PDB | |
| Related UniProtKB | |
| [15] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9837927 |
| Journal | J Biol Chem |
| Year | 1998 |
| Volume | 273 |
| Pages | 33482-8 |
| Authors | Ruelland E, Johansson K, Decottignies P, Djukic N, Miginiac-Maslow M |
| Title | The autoinhibition of sorghum NADP malate dehydrogenase is mediated by a C-terminal negative charge. |
| Related PDB | |
| Related UniProtKB | |
| [16] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS). |
| Medline ID | |
| PubMed ID | 10194350 |
| Journal | Biochemistry |
| Year | 1999 |
| Volume | 38 |
| Pages | 4319-26 |
| Authors | Johansson K, Ramaswamy S, Saarinen M, Lemaire-Chamley M, Issakidis-Bourguet E, Miginiac-Maslow M, Eklund H |
| Title | Structural basis for light activation of a chloroplast enzyme: the structure of sorghum NADP-malate dehydrogenase in its oxidized form. |
| Related PDB | 7mdh |
| Related UniProtKB | P17606 |
| [17] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10574915 |
| Journal | J Biol Chem |
| Year | 1999 |
| Volume | 274 |
| Pages | 34539-42 |
| Authors | Krimm I, Goyer A, Issakidis-Bourguet E, Miginiac-Maslow M, Lancelin JM |
| Title | Direct NMR observation of the thioredoxin-mediated reduction of the chloroplast NADP-malate dehydrogenase provides a structural basis for the relief of autoinhibition. |
| Related PDB | |
| Related UniProtKB | |
| [18] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS). |
| Medline ID | |
| PubMed ID | 10196131 |
| Journal | Structure Fold Des |
| Year | 1999 |
| Volume | 7 |
| Pages | 461-75 |
| Authors | Carr PD, Verger D, Ashton AR, Ollis DL |
| Title | Chloroplast NADP-malate dehydrogenase: structural basis of light-dependent regulation of activity by thiol oxidation and reduction. |
| Related PDB | 1civ |
| Related UniProtKB | P46489 |
| [19] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10913357 |
| Journal | Biochem Biophys Res Commun |
| Year | 2000 |
| Volume | 274 |
| Pages | 440-4 |
| Authors | Yang Z, Batra R, Floyd DL, Hung HC, Chang GG, Tong L |
| Title | Potent and competitive inhibition of malic enzymes by lanthanide ions. |
| Related PDB | |
| Related UniProtKB | |
| [20] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10767431 |
| Journal | FEBS Lett |
| Year | 2000 |
| Volume | 471 |
| Pages | 240-4 |
| Authors | Schepens I, Decottignies P, Ruelland E, Johansson K, Miginiac-Maslow M |
| Title | The dimer contact area of sorghum NADP-malate dehydrogenase: role of aspartate 101 in dimer stability and catalytic activity. |
| Related PDB | |
| Related UniProtKB | |
| [21] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10801830 |
| Journal | J Biol Chem |
| Year | 2000 |
| Volume | 275 |
| Pages | 20996-1001 |
| Authors | Schepens I, Johansson K, Decottignies P, Gillibert M, Hirasawa M, Knaff DB, Miginiac-Maslow M |
| Title | Inhibition of the thioredoxin-dependent activation of the NADP-malate dehydrogenase and cofactor specificity. |
| Related PDB | |
| Related UniProtKB | |
| [22] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10958800 |
| Journal | J Biol Chem |
| Year | 2000 |
| Volume | 275 |
| Pages | 35792-8 |
| Authors | Schepens I, Ruelland E, Miginiac-Maslow M, Le Marechal P, Decottignies P |
| Title | The role of active site arginines of sorghum NADP-malate dehydrogenase in thioredoxin-dependent activation and activity. |
| Related PDB | |
| Related UniProtKB | |
| [23] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11025545 |
| Journal | Proteins |
| Year | 2000 |
| Volume | 41 |
| Pages | 334-49 |
| Authors | Lancelin JM, Guilhaudis L, Krimm I, Blackledge MJ, Marion D, Jacquot JP |
| Title | NMR structures of thioredoxin m from the green alga Chlamydomonas reinhardtii. |
| Related PDB | |
| Related UniProtKB | |
| [24] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11172800 |
| Journal | FEBS Lett |
| Year | 2001 |
| Volume | 490 |
| Pages | 1-6 |
| Authors | Drincovich MF, Casati P, Andreo CS |
| Title | NADP-malic enzyme from plants: a ubiquitous enzyme involved in different metabolic pathways. |
| Related PDB | |
| Related UniProtKB | |
| [25] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11576537 |
| Journal | FEBS Lett |
| Year | 2001 |
| Volume | 505 |
| Pages | 405-8 |
| Authors | Goyer A, Decottignies P, Issakidis-Bourguet E, Miginiac-Maslow M |
| Title | Sites of interaction of thioredoxin with sorghum NADP-malate dehydrogenase. |
| Related PDB | |
| Related UniProtKB | |
| [26] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12562758 |
| Journal | J Biol Chem |
| Year | 2003 |
| Volume | 278 |
| Pages | 13757-64 |
| Authors | Detarsio E, Wheeler MC, Campos Bermudez VA, Andreo CS, Drincovich MF |
| Title |
Maize C4 NADP-malic enzyme. |
| Related PDB | |
| Related UniProtKB | |
| Comments |
|---|
|
Although this enzyme is assigned only two domains in the CATH classification, There seem to be three distinct active sites, |
| Created | Updated |
|---|---|
| 2004-03-16 | 2009-02-26 |