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)
3.40.50.720 : 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
3.30.360.10 : Dihydrodipicolinate Reductase; domain 2 T00219 D00003 D00010 D00017 D00023 D00027 D00028 D00476

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P04964 Meso-diaminopimelate D-dehydrogenase
DAPDH
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
15377
18009
28245
16134
16474
15378
PubChem 1549101
99290
22247451
962
5886
194695
222
5884
1038
1dapA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:NDP Unbound
1dapB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:NDP Unbound
2dapA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
3dapA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:NDP Unbound
3dapB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:NDP Unbound
1dapA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1dapB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
2dapA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:API Unbound Unbound Unbound Unbound Unbound
3dapA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
3dapB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dapB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2dapA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3dapA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3dapB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dapA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dapB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2dapA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3dapA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3dapB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Scheme 3
[1]

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