P04964 (DDH_CORGL) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Meso-diaminopimelate D-dehydrogenase
Short name=Meso-DAP dehydrogenase
EC=1.4.1.16

Gene names

Name:	ddh
Ordered Locus Names:	Cgl2617, cg2900

Organism

Corynebacterium glutamicum (Brevibacterium flavum)

Taxonomic identifier

1718 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Corynebacteriaceae › Corynebacterium

Protein attributes

Sequence length	320 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	Meso-2,6-diaminoheptanedioate + H2O + NADP+ = L-2-amino-6-oxoheptanedioate + NH3 + NADPH.
Pathway	Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; DL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate: step 1/1.

Ontologies

Keywords
Ligand	NADP
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	lysine biosynthetic process via diaminopimelate Inferred from electronic annotation. Source: InterPro
Molecular function	diaminopimelate dehydrogenase activity Inferred from electronic annotation. Source: EC dihydrodipicolinate reductase activity Inferred from electronic annotation. Source: InterPro nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 320

320

Meso-diaminopimelate D-dehydrogenase

PRO_0000079848

Secondary structure

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320

Helix Strand Turn

Details...

Beta strand

4 – 9

6

Helix

13 – 22

10

Beta strand

26 – 38

13

Beta strand

46 – 48

3

Helix

49 – 55

7

Turn

56 – 58

3

Beta strand

60 – 64

5

Turn

68 – 70

3

Helix

71 – 79

9

Turn

80 – 82

3

Beta strand

83 – 86

4

Helix

92 – 94

3

Helix

95 – 109

15

Beta strand

112 – 116

5

Turn

119 – 122

4

Helix

123 – 134

12

Beta strand

135 – 137

3

Beta strand

139 – 144

6

Beta strand

146 – 148

3

Helix

150 – 157

8

Beta strand

164 – 171

8

Helix

173 – 180

8

Helix

189 – 192

4

Beta strand

193 – 200

8

Helix

203 – 205

3

Helix

206 – 214

9

Turn

217 – 222

6

Beta strand

225 – 229

5

Helix

232 – 238

7

Beta strand

244 – 256

13

Beta strand

258 – 268

11

Helix

270 – 290

21

Beta strand

295 – 298

4

Helix

299 – 301

3

Helix

304 – 307

4

Helix

312 – 319

8

Sequences

	Sequence		Length	Mass (Da)
	P04964 [UniParc]. Last modified August 13, 1987. Version 1. Checksum: D29D3EB6DFDA35DE	FASTA	320	35,199
	10 20 30 40 50 60 MTNIRVAIVG YGNLGRSVEK LIAKQPDMDL VGIFSRRATL DTKTPVFDVA DVDKHADDVD 70 80 90 100 110 120 VLFLCMGSAT DIPEQAPKFA QFACTVDTYD NHRDIPRHRQ VMNEAATAAG NVALVSTGWD 130 140 150 160 170 180 PGMFSINRVY AAAVLAEHQQ HTFWGPGLSQ GHSDALRRIP GVQKAVQYTL PSEDALEKAR 190 200 210 220 230 240 RGEAGDLTGK QTHKRQCFVV ADAADHERIE NDIRTMPDYF VGYEVEVNFI DEATFDSEHT 250 260 270 280 290 300 GMPHGGHVIT TGDTGGFNHT VEYILKLDRN PDFTASSQIA FGRAAHRMKQ QGQSGAFTVL 310 320 EVAPYLLSPE NLDDLIARDV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the meso-diaminopimelate D-dehydrogenase gene from Corynebacterium glutamicum." Ishino S., Mizukami T., Yamaguchi K., Katsumata R., Araki K. Nucleic Acids Res. 15:3917-3917(1987) [PubMed: 3588313] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: KY 10755.
[2]	"Complete genomic sequence of Corynebacterium glutamicum ATCC 13032." Nakagawa S. Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
[3]	"The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins." Kalinowski J., Bathe B., Bartels D., Bischoff N., Bott M., Burkovski A., Dusch N., Eggeling L., Eikmanns B.J., Gaigalat L., Goesmann A., Hartmann M., Huthmacher K., Kraemer R., Linke B., McHardy A.C., Meyer F., Moeckel B. , Pfefferle W., Puehler A., Rey D.A., Rueckert C., Rupp O., Sahm H., Wendisch V.F., Wiegraebe I., Tauch A. J. Biotechnol. 104:5-25(2003) [PubMed: 12948626] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
[4]	"Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum." Scapin G., Reddy S.G., Blanchard J.S. Biochemistry 35:13540-13551(1996) [PubMed: 8885833] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS). Strain: KY 10755.
[5]	"Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase." Scapin G., Cirilli M., Reddy S.G., Gao Y., Vederas J.C., Blanchard J.S. Biochemistry 37:3278-3285(1998) [PubMed: 9521647] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Y00151 Genomic DNA. Translation: CAA68346.1.
BA000036 Genomic DNA. Translation: BAC00011.1.
BX927155 Genomic DNA. Translation: CAF21279.1.

PIR

S07384.

RefSeq

NP_601818.2. NC_003450.3.
YP_226858.1. NC_006958.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DAP	X-ray	2.20	A/B	1-320	[»]
1F06	X-ray	2.10	A/B	1-320	[»]
2DAP	X-ray	2.20	A	1-320	[»]
3DAP	X-ray	2.20	A/B	1-320	[»]

ProteinModelPortal

P04964.

SMR

P04964. Positions 1-320.

ModBase

Search...

2D gel databases

World-2DPAGE

0001:P04964.

Proteomic databases

PRIDE

P04964.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1020564.
3344238.

GenomeReviews

Gene locus Cgl2617 in contig BA000036_GR.
Gene locus cg2900 in contig BX927147_GR.

KEGG

cgb:cg2900.
cgl:NCgl2528.

PATRIC

21497280. VBICorGlu203724_2553.

Phylogenomic databases

HOGENOM

HBG730618.

OMA

DSFDTHA.

ProtClustDB

CLSK904830.

Enzyme and pathway databases

BioCyc

CGLU196627:CG2900-MONOMER.
MetaCyc:MONOMER-6621.

Family and domain databases

InterPro

IPR000846. DapB_N.
IPR010190. Diaminopimelate_DH_Ddh.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Gene3D

G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.

KO

K03340.

Pfam

PF01113. DapB_N. 1 hit.
[Graphical view]

PIRSF

PIRSF025648. DDH. 1 hit.

TIGRFAMs

TIGR01921. DAP-DH. 1 hit.

ProtoNet

Search...

Entry information

Entry name

DDH_CORGL

Accession

Primary (citable) accession number: P04964

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	August 13, 1987
Last modified:	January 25, 2012
This is version 94 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program