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Protein

4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic

Gene

DHDPS2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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: L-lysine biosynthesis via DAP pathway

This protein is involved in step 3 of the subpathway that synthesizes (S)-tetrahydrodipicolinate from L-aspartate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. AK1 (AXX17_At5g12690), Aspartokinase 2, chloroplastic (AK2), Aspartokinase (AXX17_At5g13510), Aspartokinase 1, chloroplastic (AK1), Aspartokinase 3, chloroplastic (AK3), Aspartokinase (AXX17_At3g01160), Bifunctional aspartokinase/homoserine dehydrogenase 2, chloroplastic (AKHSDH2), Aspartokinase (AXX17_At3g01160), Aspartokinase (AXX17_At3g01160), Bifunctional aspartokinase/homoserine dehydrogenase 1, chloroplastic (AKHSDH1)
  2. no protein annotated in this organism
  3. 4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic (DHDPS1), 4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic (DHDPS2)
  4. 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic (DAPB2), 4-hydroxy-tetrahydrodipicolinate reductase 1, chloroplastic (DAPB1)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes (S)-tetrahydrodipicolinate from L-aspartate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei107Part of a proton relay during catalysisBy similarity1
Binding sitei108PyruvateBy similarity1
Sitei170Part of a proton relay during catalysisBy similarity1
Active sitei194Proton donor/acceptorBy similarity1
Active sitei222Schiff-base intermediate with substrateBy similarity1
Binding sitei261Pyruvate; via carbonyl oxygenBy similarity1

GO - Molecular functioni

  • 4-hydroxy-tetrahydrodipicolinate synthase Source: CACAO

GO - Biological processi

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.
ReactomeiR-ATH-4085001. Sialic acid metabolism.
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
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G45440.

Subcellular locationi

GO - Cellular componenti

  • chloroplast Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 39ChloroplastSequence analysisAdd BLAST39
ChainiPRO_000000719840 – 3654-hydroxy-tetrahydrodipicolinate synthase 2, chloroplasticAdd BLAST326

Proteomic databases

PaxDbiQ9FVC8.

Expressioni

Gene expression databases

ExpressionAtlasiQ9FVC8. baseline and differential.
GenevisibleiQ9FVC8. AT.

Interactioni

Protein-protein interaction databases

BioGridi4488. 2 interactors.
STRINGi3702.AT2G45440.1.

Structurei

Secondary structure

1365
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi60 – 64Combined sources5
Beta strandi68 – 71Combined sources4
Beta strandi80 – 82Combined sources3
Helixi84 – 96Combined sources13
Beta strandi101 – 106Combined sources6
Turni107 – 110Combined sources4
Helixi111 – 113Combined sources3
Helixi116 – 130Combined sources15
Turni131 – 133Combined sources3
Beta strandi134 – 139Combined sources6
Helixi145 – 157Combined sources13
Beta strandi161 – 166Combined sources6
Helixi175 – 183Combined sources9
Helixi186 – 188Combined sources3
Beta strandi191 – 195Combined sources5
Helixi197 – 200Combined sources4
Helixi206 – 212Combined sources7
Beta strandi218 – 223Combined sources6
Helixi227 – 235Combined sources9
Beta strandi240 – 242Combined sources3
Helixi245 – 247Combined sources3
Helixi248 – 254Combined sources7
Beta strandi259 – 263Combined sources5
Helixi264 – 266Combined sources3
Helixi269 – 277Combined sources9
Helixi282 – 295Combined sources14
Beta strandi297 – 299Combined sources3
Helixi302 – 310Combined sources9
Beta strandi316 – 319Combined sources4
Helixi327 – 340Combined sources14
Helixi342 – 344Combined sources3
Beta strandi345 – 349Combined sources5
Helixi356 – 358Combined sources3
Beta strandi360 – 363Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4DPPX-ray2.00A/B39-365[»]
4DPQX-ray2.20A/B39-365[»]
ProteinModelPortaliQ9FVC8.
SMRiQ9FVC8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the DapA family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiENOG410IJ4Q. Eukaryota.
COG0329. LUCA.
HOGENOMiHOG000173604.
InParanoidiQ9FVC8.
KOiK01714.
OMAiFDSVLPM.
OrthoDBiEOG09360ENI.
PhylomeDBiQ9FVC8.

Family and domain databases

CDDicd00950. DHDPS. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00418. DapA. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR005263. DapA.
IPR002220. DapA-like.
IPR020625. Schiff_base-form_aldolases_AS.
IPR020624. Schiff_base-form_aldolases_CS.
[Graphical view]
PANTHERiPTHR12128. PTHR12128. 1 hit.
PfamiPF00701. DHDPS. 1 hit.
[Graphical view]
PRINTSiPR00146. DHPICSNTHASE.
SMARTiSM01130. DHDPS. 1 hit.
[Graphical view]
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)DescriptionActionsGraphical viewLength
Sequence conflicti26S → G in AAG28565 (PubMed:11069709).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_130106.3.
UniGeneiAt.12311.

Genome annotation databases

EnsemblPlantsiAT2G45440.1; AT2G45440.1; AT2G45440.
GeneIDi819152.
GrameneiAT2G45440.1; AT2G45440.1; AT2G45440.
KEGGiath:AT2G45440.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_130106.3.
UniGeneiAt.12311.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4DPPX-ray2.00A/B39-365[»]
4DPQX-ray2.20A/B39-365[»]
ProteinModelPortaliQ9FVC8.
SMRiQ9FVC8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4488. 2 interactors.
STRINGi3702.AT2G45440.1.

Proteomic databases

PaxDbiQ9FVC8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G45440.1; AT2G45440.1; AT2G45440.
GeneIDi819152.
GrameneiAT2G45440.1; AT2G45440.1; AT2G45440.
KEGGiath:AT2G45440.

Organism-specific databases

TAIRiAT2G45440.

Phylogenomic databases

eggNOGiENOG410IJ4Q. Eukaryota.
COG0329. LUCA.
HOGENOMiHOG000173604.
InParanoidiQ9FVC8.
KOiK01714.
OMAiFDSVLPM.
OrthoDBiEOG09360ENI.
PhylomeDBiQ9FVC8.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00017.
BioCyciARA:AT2G45440-MONOMER.
ReactomeiR-ATH-4085001. Sialic acid metabolism.

Miscellaneous databases

PROiQ9FVC8.

Gene expression databases

ExpressionAtlasiQ9FVC8. baseline and differential.
GenevisibleiQ9FVC8. AT.

Family and domain databases

CDDicd00950. DHDPS. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00418. DapA. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR005263. DapA.
IPR002220. DapA-like.
IPR020625. Schiff_base-form_aldolases_AS.
IPR020624. Schiff_base-form_aldolases_CS.
[Graphical view]
PANTHERiPTHR12128. PTHR12128. 1 hit.
PfamiPF00701. DHDPS. 1 hit.
[Graphical view]
PRINTSiPR00146. DHPICSNTHASE.
SMARTiSM01130. DHDPS. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00674. dapA. 1 hit.
PROSITEiPS00665. DHDPS_1. 1 hit.
PS00666. DHDPS_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 30, 2016
This is version 119 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.