EzCatDB: D00034
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DB codeD00034
CATH domainDomain 13.40.50.720 : Rossmann foldCatalytic domain
Domain 23.30.360.10 : Dihydrodipicolinate Reductase; domain 2Catalytic domain
E.C.1.4.1.16

CATH domainRelated DB codes (homologues)
3.30.360.10 : Dihydrodipicolinate Reductase; domain 2T00219,D00003,D00010,D00017,D00023,D00027,D00028,D00476
3.40.50.720 : Rossmann foldS00543,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

Enzyme Name
UniProtKBKEGG

P04964
Protein nameMeso-diaminopimelate D-dehydrogenasediaminopimelate dehydrogenase
meso-alpha,epsilon-diaminopimelate dehydrogenase
meso-diaminopimelate dehydrogenase
SynonymsMeso-DAP dehydrogenase
EC 1.4.1.16
RefSeqNP_601818.2 (Protein)
NC_003450.3 (DNA/RNA sequence)
YP_226858.1 (Protein)
NC_006958.1 (DNA/RNA sequence)
PfamPF01113 (DapB_N)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00300Lysine biosynthesis

UniProtKB:Accession NumberP04964
Entry nameDDH_CORGL
ActivityMeso-2,6-diaminoheptanedioate + H(2)O + NADP(+) = L-2-amino-6-oxoheptanedioate + NH(3) + NADPH.
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00680C00001C00006C03871C00014C00005C00080
Compoundmeso-2,6-DiaminoheptanedioateH2ONADP+L-2-Amino-6-oxoheptanedioateNH3NADPHH+
Typeamino acidsH2Oamide group,amine group,nucleotideamino acids,carbohydrate,carboxyl group,lipidamine group,organic ionamide group,amine group,nucleotideothers
ChEBI16488
57791
15377
18009
28245
16134
16474
15378

PubChem99290
1549101
962
22247451
5886
194695
222
5884
1038

                
1dapA01Unbound UnboundUnboundUnboundBound:NDP Unbound
1dapB01Unbound UnboundUnboundUnboundBound:NDP Unbound
2dapA01Unbound UnboundUnboundUnboundUnbound Unbound
3dapA01Unbound UnboundUnboundUnboundBound:NDP Unbound
3dapB01Unbound UnboundUnboundUnboundBound:NDP Unbound
1dapA02Unbound UnboundUnboundUnboundUnbound Unbound
1dapB02Unbound UnboundUnboundUnboundUnbound Unbound
2dapA02Bound:API UnboundUnboundUnboundUnbound Unbound
3dapA02Unbound UnboundUnboundUnboundUnbound Unbound
3dapB02Unbound UnboundUnboundUnboundUnbound Intermediate-analogue:DA3

Active-site residues
pdb
        
1dapA01
1dapB01
2dapA01
3dapA01
3dapB01
1dapA02
1dapB02
2dapA02
3dapA02
3dapB02

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]

[2]Scheme 3

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID97040520
PubMed ID8885833
JournalBiochemistry
Year1996
Volume35
Pages13540-51
AuthorsScapin G, Reddy SG, Blanchard JS
TitleThree-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum.
Related PDB1dap
Related UniProtKBP04964
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID98198036
PubMed ID9521647
JournalBiochemistry
Year1998
Volume37
Pages3278-85
AuthorsScapin G, Cirilli M, Reddy SG, Gao Y, Vederas JC, Blanchard JS
TitleSubstrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase.
Related PDB2dap,3dap
Related UniProtKBP04964
[3]
PubMed ID11106178
JournalProtein Sci
Year2000
Volume9
Pages2034-7
AuthorsCirilli M, Scapin G, Sutherland A, Vederas JC, Blanchard JS
TitleThe three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate.


createdupdated
2004-03-172009-02-26


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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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