Q9FVC8 (DAPA2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic
Short name=HTPA synthase 2
EC=4.3.3.7

Gene names

Name:	DHDPS2
Ordered Locus Names:	At2g45440
ORF Names:	F4L23.5

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	365 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA) By similarity.
Catalytic activity	Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H2O.
Pathway	Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4.
Subcellular location	Plastid › chloroplast.
Sequence similarities	Belongs to the DapA family.
Caution	Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli (PubMed:8993314 and PubMed:20503968) that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB (PubMed:20503968).

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Diaminopimelate biosynthesis Lysine biosynthesis
Cellular component	Chloroplast Plastid
Domain	Transit peptide
Ligand	Schiff base
Molecular function	Lyase
Technical term	3D-structure Allosteric enzyme Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	diaminopimelate biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW lysine biosynthetic process via diaminopimelate Inferred from electronic annotation. Source: UniProtKB-UniPathway
Cellular_component	chloroplast Inferred from direct assay PubMed 18431481. Source: TAIR
Molecular_function	4-hydroxy-tetrahydrodipicolinate synthase Inferred from mutant phenotype Ref.1. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 39

39

Chloroplast Potential

Chain

40 – 365

326

4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic

PRO_0000007198

Sites

Active site

194

1

Proton donor/acceptor By similarity

Active site

222

1

Schiff-base intermediate with substrate By similarity

Binding site

108

1

Pyruvate By similarity

Binding site

261

1

Pyruvate; via carbonyl oxygen By similarity

Site

107

1

Part of a proton relay during catalysis By similarity

Site

170

1

Part of a proton relay during catalysis By similarity

Experimental info

Sequence conflict

26

1

S → G in AAG28565. Ref.1

Secondary structure

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365

Helix Strand Turn

Details...

Helix

60 – 64

5

Beta strand

68 – 71

4

Beta strand

80 – 82

3

Helix

84 – 96

13

Beta strand

101 – 106

6

Turn

107 – 110

4

Helix

111 – 113

3

Helix

116 – 130

15

Turn

131 – 133

3

Beta strand

134 – 139

6

Helix

145 – 157

13

Beta strand

161 – 166

6

Helix

175 – 183

9

Helix

186 – 188

3

Beta strand

191 – 195

5

Helix

197 – 200

4

Helix

206 – 212

7

Beta strand

218 – 223

6

Helix

227 – 235

9

Beta strand

240 – 242

3

Helix

245 – 247

3

Helix

248 – 254

7

Beta strand

259 – 263

5

Helix

264 – 266

3

Helix

269 – 277

9

Helix

282 – 295

14

Beta strand

297 – 299

3

Helix

302 – 310

9

Beta strand

316 – 319

4

Helix

327 – 340

14

Helix

342 – 344

3

Beta strand

345 – 349

5

Helix

356 – 358

3

Beta strand

360 – 363

4

Sequences

	Sequence		Length	Mass (Da)
	Q9FVC8 [UniParc]. Last modified June 20, 2001. Version 2. Checksum: 43BECEF1FC3E557A	FASTA	365	40,292
	10 20 30 40 50 60 MAALKGYGLC SMDSALQFPC PKLFNSYKRR SSKWVSPKAA VVPNFHLPMR SLEVKNRTNT 70 80 90 100 110 120 DDIKALRVIT AIKTPYLPDG RFDLEAYDDL VNIQIQNGAE GVIVGGTTGE GQLMSWDEHI 130 140 150 160 170 180 MLIGHTVNCF GGSIKVIGNT GSNSTREAIH ATEQGFAVGM HAALHINPYY GKTSIEGLIA 190 200 210 220 230 240 HFQSVLHMGP TIIYNVPGRT GQDIPPRAIF KLSQNPNLAG VKECVGNKRV EEYTENGVVV 250 260 270 280 290 300 WSGNDDECHD SRWDYGATGV ISVTSNLVPG LMRKLMFEGR NSSLNSKLLP LMAWLFHEPN 310 320 330 340 350 360 PIGINTALAQ LGVSRPVFRL PYVPLPLSKR LEFVKLVKEI GREHFVGEKD VQALDDDDFI LIGRY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of an Arabidopsis thaliana mutant accumulating threonine resulting from mutation in a new dihydrodipicolinate synthase gene." Sarrobert C., Thibaud M.-C., Contard-David P., Gineste S., Bechtold N., Robaglia C., Nussaume L. Plant J. 24:357-367(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: cv. Wassilewskija.
[2]	"Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana." Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D., Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V., Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S., Cronin L.A. , Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C. Nature 402:761-768(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF200325 Genomic DNA. Translation: AAG28565.1.
AC002387 Genomic DNA. Translation: AAB82620.1.
CP002685 Genomic DNA. Translation: AEC10554.1.
BT004823 mRNA. Translation: AAO44089.1.

IPI

IPI00541031.

PIR

E84890.

RefSeq

NP_182068.1. NM_130106.2.

UniGene

At.12311.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4DPP	X-ray	2.00	A/B	39-365	[»]
4DPQ	X-ray	2.20	A/B	39-365	[»]

ProteinModelPortal

Q9FVC8.

SMR

Q9FVC8. Positions 59-365.

ModBase

Search...

Protein-protein interaction databases

STRING

3702.AT2G45440.1-P.

Proteomic databases

PaxDb

Q9FVC8.

PRIDE

Q9FVC8.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT2G45440.1; AT2G45440.1; AT2G45440.

GeneID

819152.

KEGG

ath:AT2G45440.

Organism-specific databases

TAIR

At2g45440.

Phylogenomic databases

eggNOG

COG0329.

HOGENOM

HOG000173604.

InParanoid

Q9FVC8.

KO

K01714.

OMA

ADAILCV.

PhylomeDB

Q9FVC8.

ProtClustDB

PLN02417.

Enzyme and pathway databases

UniPathway

UPA00034; UER00017.

Gene expression databases

ArrayExpress

Q9FVC8.

Genevestigator

Q9FVC8.

GermOnline

AT2G45440. Arabidopsis thaliana.

Family and domain databases

Gene3D

3.20.20.70. 1 hit.

InterPro

IPR013785. Aldolase_TIM.
IPR002220. Dihydrodipicolinate_synth-like.
IPR020625. Dihydrodipicolinate_synth_AS.
IPR020624. Dihydrodipicolinate_synth_CS.
IPR005263. Dihydrodipicolinate_synth_DapA.
[Graphical view]

PANTHER

PTHR12128. PTHR12128. 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

DAPA2_ARATH

Accession

Primary (citable) accession number: Q9FVC8
Secondary accession number(s): O22129

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 20, 2001
Last sequence update:	June 20, 2001
Last modified:	May 1, 2013
This is version 95 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program