DB code: D00034
| CATH domain | 3.40.50.720 : Rossmann fold | Catalytic domain |
|---|---|---|
| 3.30.360.10 : Dihydrodipicolinate Reductase; domain 2 | Catalytic domain | |
| E.C. | 1.4.1.16 | |
| CSA | ||
| M-CSA | ||
| MACiE | ||
| CATH domain | Related DB codes (homologues) |
|---|---|
| 3.30.360.10 : Dihydrodipicolinate Reductase; domain 2 | T00219 D00003 D00010 D00017 D00023 D00027 D00028 D00476 |
| 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 D00035 D00037 D00048 D00071 D00476 D00481 D00482 D00490 D00492 D00494 D00545 D00601 D00603 D00604 D00605 D00615 D00845 D00857 D00858 M00161 M00171 M00210 T00002 T00010 T00011 T00015 T00227 T00247 T00408 T00414 D00827 D00262 D00274 D00275 M00035 T00109 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | RefSeq | Pfam |
|---|---|---|---|---|
| P04964 |
Meso-diaminopimelate D-dehydrogenase
|
Meso-DAP dehydrogenase
EC 1.4.1.16 |
NP_601818.2
(Protein)
NC_003450.3 (DNA/RNA sequence) YP_226858.1 (Protein) NC_006958.1 (DNA/RNA sequence) |
PF01113
(DapB_N)
[Graphical View] |
| KEGG enzyme name |
|---|
|
diaminopimelate dehydrogenase
meso-alpha,epsilon-diaminopimelate dehydrogenase meso-diaminopimelate dehydrogenase |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| P04964 | DDH_CORGL | Meso-2,6-diaminoheptanedioate + H(2)O + NADP(+) = L-2-amino-6-oxoheptanedioate + NH(3) + NADPH. |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|---|---|
| MAP00300 | Lysine biosynthesis |
| Compound table | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Substrates | Products | Intermediates | |||||||||||
| KEGG-id | C00680 | C00001 | C00006 | C03871 | C00014 | C00005 | C00080 | ||||||
| E.C. | |||||||||||||
| Compound | meso-2,6-Diaminoheptanedioate | H2O | NADP+ | L-2-Amino-6-oxoheptanedioate | NH3 | NADPH | H+ | ||||||
| Type | amino acids | H2O | amide group,amine group,nucleotide | amino acids,carbohydrate,carboxyl group,lipid | amine group,organic ion | amide group,amine group,nucleotide | others | ||||||
| ChEBI |
16488 57791 16488 57791 |
15377 15377 |
18009 18009 |
28245 28245 |
16134 16134 |
16474 16474 |
15378 15378 |
||||||
| PubChem |
1549101 99290 1549101 99290 |
22247451 962 22247451 962 |
5886 5886 |
194695 194695 |
222 222 |
5884 5884 |
1038 1038 |
||||||
| 1dapA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Bound:NDP | Unbound | ||
| 1dapB01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Bound:NDP | Unbound | ||
| 2dapA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 3dapA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Bound:NDP | Unbound | ||
| 3dapB01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Bound:NDP | Unbound | ||
| 1dapA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 1dapB02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 2dapA02 |
|
|
|
|
|
Bound:API | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 3dapA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | ||
| 3dapB02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DA3 | ||
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1dapA01 |
|
|
|
|
|
|||||
| 1dapB01 |
|
|
|
|
|
|||||
| 2dapA01 |
|
|
|
|
|
|||||
| 3dapA01 |
|
|
|
|
|
|||||
| 3dapB01 |
|
|
|
|
|
|||||
| 1dapA02 |
|
|
|
|
|
|||||
| 1dapB02 |
|
|
|
|
|
|||||
| 2dapA02 |
|
|
|
|
|
|||||
| 3dapA02 |
|
|
|
|
|
|||||
| 3dapB02 |
|
|
|
|
|
|||||
| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
|
[1]
|
||
|
[2]
|
Scheme 3 | |
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) |
| Medline ID | 97040520 |
| PubMed ID | 8885833 |
| Journal | Biochemistry |
| Year | 1996 |
| Volume | 35 |
| Pages | 13540-51 |
| Authors | Scapin G, Reddy SG, Blanchard JS |
| Title | Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum. |
| Related PDB | 1dap |
| Related UniProtKB | P04964 |
| [2] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) |
| Medline ID | 98198036 |
| PubMed ID | 9521647 |
| Journal | Biochemistry |
| Year | 1998 |
| Volume | 37 |
| Pages | 3278-85 |
| Authors | Scapin G, Cirilli M, Reddy SG, Gao Y, Vederas JC, Blanchard JS |
| Title | Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase. |
| Related PDB | 2dap 3dap |
| Related UniProtKB | P04964 |
| [3] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11106178 |
| Journal | Protein Sci |
| Year | 2000 |
| Volume | 9 |
| Pages | 2034-7 |
| Authors | Cirilli M, Scapin G, Sutherland A, Vederas JC, Blanchard JS |
| Title | The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate. |
| Related PDB | |
| Related UniProtKB | |
| Comments |
|---|
| Created | Updated |
|---|---|
| 2004-03-17 | 2009-02-26 |