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Q9FVC8

- DAPA2_ARATH

UniProt

Q9FVC8 - DAPA2_ARATH

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Protein

4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic

Gene

DHDPS2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli

Functioni

Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).By similarity

Catalytic activityi

Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H2O.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei107 – 1071Part of a proton relay during catalysisBy similarity
Binding sitei108 – 1081PyruvateBy similarity
Sitei170 – 1701Part of a proton relay during catalysisBy similarity
Active sitei194 – 1941Proton donor/acceptorBy similarity
Active sitei222 – 2221Schiff-base intermediate with substrateBy similarity
Binding sitei261 – 2611Pyruvate; via carbonyl oxygenBy similarity

GO - Molecular functioni

  1. 4-hydroxy-tetrahydrodipicolinate synthase Source: TAIR

GO - Biological processi

  1. diaminopimelate biosynthetic process Source: UniProtKB-KW
  2. lysine biosynthetic process via diaminopimelate Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

Keywords - Ligandi

Schiff base

Enzyme and pathway databases

BioCyciARA:AT2G45440-MONOMER.
UniPathwayiUPA00034; UER00017.

Names & Taxonomyi

Protein namesi
Recommended name:
4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic (EC:4.3.3.7)
Short name:
HTPA synthase 2
Gene namesi
Name:DHDPS2
Ordered Locus Names:At2g45440
ORF Names:F4L23.5
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 2

Organism-specific databases

TAIRiAT2G45440.

Subcellular locationi

GO - Cellular componenti

  1. chloroplast Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3939ChloroplastSequence AnalysisAdd
BLAST
Chaini40 – 3653264-hydroxy-tetrahydrodipicolinate synthase 2, chloroplasticPRO_0000007198Add
BLAST

Proteomic databases

PaxDbiQ9FVC8.
PRIDEiQ9FVC8.

Expressioni

Gene expression databases

ExpressionAtlasiQ9FVC8. baseline and differential.
GenevestigatoriQ9FVC8.

Interactioni

Protein-protein interaction databases

BioGridi4488. 2 interactions.
STRINGi3702.AT2G45440.1-P.

Structurei

Secondary structure

1
365
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi60 – 645
Beta strandi68 – 714
Beta strandi80 – 823
Helixi84 – 9613
Beta strandi101 – 1066
Turni107 – 1104
Helixi111 – 1133
Helixi116 – 13015
Turni131 – 1333
Beta strandi134 – 1396
Helixi145 – 15713
Beta strandi161 – 1666
Helixi175 – 1839
Helixi186 – 1883
Beta strandi191 – 1955
Helixi197 – 2004
Helixi206 – 2127
Beta strandi218 – 2236
Helixi227 – 2359
Beta strandi240 – 2423
Helixi245 – 2473
Helixi248 – 2547
Beta strandi259 – 2635
Helixi264 – 2663
Helixi269 – 2779
Helixi282 – 29514
Beta strandi297 – 2993
Helixi302 – 3109
Beta strandi316 – 3194
Helixi327 – 34014
Helixi342 – 3443
Beta strandi345 – 3495
Helixi356 – 3583
Beta strandi360 – 3634

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4DPPX-ray2.00A/B39-365[»]
4DPQX-ray2.20A/B39-365[»]
ProteinModelPortaliQ9FVC8.
SMRiQ9FVC8. Positions 59-365.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the DapA family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0329.
HOGENOMiHOG000173604.
InParanoidiQ9FVC8.
KOiK01714.
OMAiMLYSGDD.
PhylomeDBiQ9FVC8.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00418. DapA.
InterProiIPR013785. Aldolase_TIM.
IPR005263. DapA.
IPR002220. DapA-like.
IPR020625. Dihydrodipicolinate_synth_AS.
IPR020624. Dihydrodipicolinate_synth_CS.
[Graphical view]
PANTHERiPTHR12128. PTHR12128. 1 hit.
PfamiPF00701. DHDPS. 1 hit.
[Graphical view]
PRINTSiPR00146. DHPICSNTHASE.
TIGRFAMsiTIGR00674. dapA. 1 hit.
PROSITEiPS00665. DHDPS_1. 1 hit.
PS00666. DHDPS_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9FVC8-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAALKGYGLC SMDSALQFPC PKLFNSYKRR SSKWVSPKAA VVPNFHLPMR
60 70 80 90 100
SLEVKNRTNT DDIKALRVIT AIKTPYLPDG RFDLEAYDDL VNIQIQNGAE
110 120 130 140 150
GVIVGGTTGE GQLMSWDEHI MLIGHTVNCF GGSIKVIGNT GSNSTREAIH
160 170 180 190 200
ATEQGFAVGM HAALHINPYY GKTSIEGLIA HFQSVLHMGP TIIYNVPGRT
210 220 230 240 250
GQDIPPRAIF KLSQNPNLAG VKECVGNKRV EEYTENGVVV WSGNDDECHD
260 270 280 290 300
SRWDYGATGV ISVTSNLVPG LMRKLMFEGR NSSLNSKLLP LMAWLFHEPN
310 320 330 340 350
PIGINTALAQ LGVSRPVFRL PYVPLPLSKR LEFVKLVKEI GREHFVGEKD
360
VQALDDDDFI LIGRY
Length:365
Mass (Da):40,292
Last modified:June 20, 2001 - v2
Checksum:i43BECEF1FC3E557A
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti26 – 261S → G in AAG28565. (PubMed:11069709)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF200325 Genomic DNA. Translation: AAG28565.1.
AC002387 Genomic DNA. Translation: AAB82620.1.
CP002685 Genomic DNA. Translation: AEC10554.1.
BT004823 mRNA. Translation: AAO44089.1.
PIRiE84890.
RefSeqiNP_182068.1. NM_130106.2.
UniGeneiAt.12311.

Genome annotation databases

EnsemblPlantsiAT2G45440.1; AT2G45440.1; AT2G45440.
GeneIDi819152.
KEGGiath:AT2G45440.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF200325 Genomic DNA. Translation: AAG28565.1 .
AC002387 Genomic DNA. Translation: AAB82620.1 .
CP002685 Genomic DNA. Translation: AEC10554.1 .
BT004823 mRNA. Translation: AAO44089.1 .
PIRi E84890.
RefSeqi NP_182068.1. NM_130106.2.
UniGenei At.12311.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
ProteinModelPortali Q9FVC8.
SMRi Q9FVC8. Positions 59-365.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 4488. 2 interactions.
STRINGi 3702.AT2G45440.1-P.

Proteomic databases

PaxDbi Q9FVC8.
PRIDEi Q9FVC8.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT2G45440.1 ; AT2G45440.1 ; AT2G45440 .
GeneIDi 819152.
KEGGi ath:AT2G45440.

Organism-specific databases

TAIRi AT2G45440.

Phylogenomic databases

eggNOGi COG0329.
HOGENOMi HOG000173604.
InParanoidi Q9FVC8.
KOi K01714.
OMAi MLYSGDD.
PhylomeDBi Q9FVC8.

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00017 .
BioCyci ARA:AT2G45440-MONOMER.

Gene expression databases

ExpressionAtlasi Q9FVC8. baseline and differential.
Genevestigatori Q9FVC8.

Family and domain databases

Gene3Di 3.20.20.70. 1 hit.
HAMAPi MF_00418. DapA.
InterProi IPR013785. Aldolase_TIM.
IPR005263. DapA.
IPR002220. DapA-like.
IPR020625. Dihydrodipicolinate_synth_AS.
IPR020624. Dihydrodipicolinate_synth_CS.
[Graphical view ]
PANTHERi PTHR12128. PTHR12128. 1 hit.
Pfami PF00701. DHDPS. 1 hit.
[Graphical view ]
PRINTSi PR00146. DHPICSNTHASE.
TIGRFAMsi TIGR00674. dapA. 1 hit.
PROSITEi PS00665. DHDPS_1. 1 hit.
PS00666. DHDPS_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiDAPA2_ARATH
AccessioniPrimary (citable) accession number: Q9FVC8
Secondary accession number(s): O22129
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 20, 2001
Last sequence update: June 20, 2001
Last modified: October 29, 2014
This is version 105 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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 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.Curated

Keywords - Technical termi

3D-structure, Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3