Reviewed, UniProtKB/Swiss-Prot P0A6L2 (DAPA_ECOLI)

Names and origin

Protein names

Recommended name:
    Dihydrodipicolinate synthase
      Short name=DHDPS
    EC=4.2.1.52

Gene names

Name:	dapA
Ordered Locus Names:	b2478, JW2463

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	292 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Catalytic activity	L-aspartate 4-semialdehyde + pyruvate = dihydrodipicolinate + 2 H2O. HAMAP MF_00418
Enzyme regulation	Sensitive to lysine inhibition. HAMAP MF_00418
Pathway	Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. HAMAP MF_00418
Subunit structure	Homotetramer. Ref.14
Subcellular location	Cytoplasm HAMAP MF_00418.
Sequence similarities	Belongs to the DHDPS family.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Diaminopimelate biosynthesis Lysine biosynthesis
Cellular component	Cytoplasm
Ligand	Schiff base
Molecular function	Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	diaminopimelate biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB
Molecular function	dihydrodipicolinate synthase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 292

292

Dihydrodipicolinate synthase HAMAP MF_00418

PRO_0000103110

Regions

Region

48 – 49

2

Pyruvate binding HAMAP MF_00418

Sites

Active site

161

1

Schiff-base intermediate with substrate Ref.8

Binding site

106

1

Pyruvate HAMAP MF_00418

Site

133

1

Involved in proton transfer during cleavage HAMAP MF_00418

Experimental info

Mutagenesis

44

1

T → V: Reduced Kcat by 99.9%.

Mutagenesis

107

1

Y → F: Reduced Kcat by 90%.

Mutagenesis

133

1

Y → F: Reduced Kcat by 99.7%. Reduced affinity for both substrates.

Mutagenesis

138

1

R → A or H: Strongly increased KM for L-aspartate 4-semialdehyde. No effect on KM for pyruvate. Reduced activity by 99.7%.

Sequence conflict

207

1

A → T in AAA23665. Ref.1

Sequence conflict

224

1

G → E in AAA23665. Ref.1

Secondary structure

1

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292

Helix Strand Turn

Details...

Beta strand

3 – 8

6

Beta strand

17 – 19

3

Helix

21 – 34

14

Beta strand

38 – 43

6

Helix

44 – 46

3

Helix

48 – 50

3

Helix

53 – 67

15

Beta strand

73 – 76

4

Helix

82 – 92

11

Turn

93 – 95

3

Beta strand

99 – 103

5

Helix

112 – 123

12

Beta strand

130 – 134

5

Helix

136 – 139

4

Helix

145 – 151

7

Beta strand

157 – 162

6

Helix

169 – 176

8

Beta strand

181 – 185

5

Helix

188 – 190

3

Helix

191 – 196

6

Beta strand

201 – 205

5

Helix

206 – 208

3

Helix

211 – 222

12

Helix

226 – 242

17

Beta strand

245 – 247

3

Helix

250 – 258

9

Beta strand

261 – 263

3

Helix

276 – 288

13

Sequences

	Sequence		Length	Mass (Da)
	P0A6L2-1 [UniParc]. Last modified May 10, 2005. Version 1. Checksum: 3970543296A77C08	FASTA	292	31,270
	10 20 30 40 50 60 MFTGSIVAIV TPMDEKGNVC RASLKKLIDY HVASGTSAIV SVGTTGESAT LNHDEHADVV 70 80 90 100 110 120 MMTLDLADGR IPVIAGTGAN ATAEAISLTQ RFNDSGIVGC LTVTPYYNRP SQEGLYQHFK 130 140 150 160 170 180 AIAEHTDLPQ ILYNVPSRTG CDLLPETVGR LAKVKNIIGI KEATGNLTRV NQIKELVSDD 190 200 210 220 230 240 FVLLSGDDAS ALDFMQLGGH GVISVTANVA ARDMAQMCKL AAEGHFAEAR VINQRLMPLH 250 260 270 280 290 NKLFVEPNPI PVKWACKELG LVATDTLRLP MTPITDSGRE TVRAALKHAG LL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Chromosomal location and nucleotide sequence of the Escherichia coli dapA gene." Richaud F., Richaud C., Ratet P., Patte J.-C. J. Bacteriol. 166:297-300(1986) [PubMed: 3514578] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed: 9205837] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F. Submitted (FEB-1996) to UniProtKB Cited for: PARTIAL PROTEIN SEQUENCE OF 1-11. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-12. Strain: K12 / EMG2.
[7]	"Protein identification with N and C-terminal sequence tags in proteome projects." Wilkins M.R., Gasteiger E., Tonella L., Ou K., Tyler M., Sanchez J.-C., Gooley A.A., Walsh B.J., Bairoch A., Appel R.D., Williams K.L., Hochstrasser D.F. J. Mol. Biol. 278:599-608(1998) [PubMed: 9600841] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-4. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]	"Escherichia coli dihydrodipicolinate synthase. Identification of the active site and crystallization." Laber B., Gomis-Rueth F.-X., Romao M.J., Huber R. Biochem. J. 288:691-695(1992) [PubMed: 1463470] [Abstract] Cited for: PROTEIN SEQUENCE OF 156-167, ACTIVE SITE.
[9]	"DNA sequence of the purC gene encoding 5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide synthetase and organization of the dapA-purC region of Escherichia coli K-12." Tiedemann A.A., Demarini D.J., Parker J., Smith J.M. J. Bacteriol. 172:6035-6041(1990) [PubMed: 2120198] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 288-292. Strain: K12.
[10]	"A gene for a new lipoprotein in the dapA-purC interval of the Escherichia coli chromosome." Bouvier J., Pugsley A.P., Stragier P. J. Bacteriol. 173:5523-5531(1991) [PubMed: 1885529] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 288-292. Strain: K12.
[11]	"The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5-A resolution." Mirwaldt C., Korndoerfer I., Huber R. J. Mol. Biol. 246:227-239(1995) [PubMed: 7853400] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
[12]	"Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy." Blicking S., Renner C., Laber B., Pohlenz H.-D., Holak T.A., Huber R. Biochemistry 36:24-33(1997) [PubMed: 8993314] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), CATALYTIC MECHANISM.
[13]	"The crystal structure of three site-directed mutants of Escherichia coli dihydrodipicolinate synthase: further evidence for a catalytic triad." Dobson R.C.J., Valegaard K., Gerrard J.A. J. Mol. Biol. 338:329-339(2004) [PubMed: 15066435] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF MUTANTS VAL-44; PHE-107 AND PHE-133.
[14]	"The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance." Dobson R.C.J., Griffin M.D.W., Jameson G.B., Gerrard J.A. Acta Crystallogr. D 61:1116-1124(2005) [PubMed: 16041077] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SUBUNIT.
[15]	"Role of arginine 138 in the catalysis and regulation of Escherichia coli dihydrodipicolinate synthase." Dobson R.C.J., Devenish S.R.A., Turner L.A., Clifford V.R., Pearce F.G., Jameson G.B., Gerrard J.A. Biochemistry 44:13007-13013(2005) [PubMed: 16185069] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF MUTANTS ALA-138 AND HIS-138.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M12844 Genomic DNA. Translation: AAA23665.1.
U00096 Genomic DNA. Translation: AAC75531.1.
AP009048 Genomic DNA. Translation: BAA16355.1.
M33928 Genomic DNA. No translation available.
X57402 Genomic DNA. Translation: CAA40660.1.

PIR

SYECDP. E65023.

RefSeq

AP_003064.1.
NP_416973.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DHP	X-ray	2.30	A/B	1-292	[»]
1S5T	X-ray	2.30	A/B	1-292	[»]
1S5V	X-ray	2.35	A/B	1-292	[»]
1S5W	X-ray	2.32	A/B	1-292	[»]
1YXC	X-ray	1.90	A/B	1-292	[»]
1YXD	X-ray	2.00	A/B	1-292	[»]
2A6L	X-ray	2.05	A/B	1-292	[»]
2A6N	X-ray	1.94	A/B	1-292	[»]
2ATS	X-ray	1.90	A/B	1-292	[»]
2OJP	X-ray	1.70	A/B	1-292	[»]
2PUR	X-ray	1.70	A/B	1-292	[»]
3C0J	X-ray	2.40	A/B	1-292	[»]
3DEN	X-ray	2.20	A/B	1-292	[»]
3DU0	X-ray	2.00	A/B	1-292	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

P0A6L2.

2-D gel databases

SWISS-2DPAGE

P0A6L2.

ECO2DBASE

G031.3. 6TH EDITION.

Genome annotation databases

GeneID

946952.

GenomeReviews

Gene locus JW2463 in contig AP009048_GR.
Gene locus b2478 in contig U00096_GR.

KEGG

ecj:JW2463.
eco:b2478.

Organism-specific databases

EchoBASE

EB0201.

EcoGene

EG10205. dapA.

CMR

Search...

Phylogenomic databases

eggNOG

COG0329.

HOGENOM

HBG358848.

OMA

EGTDGIV.

Enzyme and pathway databases

BioCyc

EcoCyc:DIHYDRODIPICSYN-MONOMER.
ECOL168927:B2478-MONOMER.
MetaCyc:DIHYDRODIPICSYN-MONOMER.

Gene expression databases

Genevestigator

P0A6L2.

Family and domain databases

HAMAP

MF_00418. DapA.
[Tree]

InterPro

IPR013785. Aldolase_TIM.
IPR005263. DapA_synth.
IPR002220. Dihydrodipicolinate_synth.
IPR020625. Dihydrodipicolinate_synth_AS.
IPR020624. Dihydrodipicolinate_synth_CS.
[Graphical view]

Gene3D

G3DSA:3.20.20.70. Aldolase_TIM. 1 hit.

PANTHER

PTHR12128. DHDPS. 1 hit.

Pfam

PF00701. DHDPS. 1 hit.
[Graphical view]

PRINTS

PR00146. DHPICSNTHASE.

TIGRFAMs

TIGR00674. dapA. 1 hit.

PROSITE

PS00665. DHDPS_1. 1 hit.
PS00666. DHDPS_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DAPA_ECOLI

Accession

Primary (citable) accession number: P0A6L2
Secondary accession number(s): P05640, P78223

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2005
Last sequence update:	May 10, 2005
Last modified:	February 9, 2010
This is version 54 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)