Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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

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.
ReactomeiREACT_225978. 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
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 – 645Combined sources
Beta strandi68 – 714Combined sources
Beta strandi80 – 823Combined sources
Helixi84 – 9613Combined sources
Beta strandi101 – 1066Combined sources
Turni107 – 1104Combined sources
Helixi111 – 1133Combined sources
Helixi116 – 13015Combined sources
Turni131 – 1333Combined sources
Beta strandi134 – 1396Combined sources
Helixi145 – 15713Combined sources
Beta strandi161 – 1666Combined sources
Helixi175 – 1839Combined sources
Helixi186 – 1883Combined sources
Beta strandi191 – 1955Combined sources
Helixi197 – 2004Combined sources
Helixi206 – 2127Combined sources
Beta strandi218 – 2236Combined sources
Helixi227 – 2359Combined sources
Beta strandi240 – 2423Combined sources
Helixi245 – 2473Combined sources
Helixi248 – 2547Combined sources
Beta strandi259 – 2635Combined sources
Helixi264 – 2663Combined sources
Helixi269 – 2779Combined sources
Helixi282 – 29514Combined sources
Beta strandi297 – 2993Combined sources
Helixi302 – 3109Combined sources
Beta strandi316 – 3194Combined sources
Helixi327 – 34014Combined sources
Helixi342 – 3443Combined sources
Beta strandi345 – 3495Combined sources
Helixi356 – 3583Combined sources
Beta strandi360 – 3634Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
OMAiNVIPQEF.
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:
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_130106.2.
UniGeneiAt.12311.

Genome annotation databases

EnsemblPlantsiAT2G45440.1; AT2G45440.1; AT2G45440.
GeneIDi819152.
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_130106.2.
UniGeneiAt.12311.

3D structure databases

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

Protein-protein interaction databases

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

Proteomic databases

PaxDbiQ9FVC8.
PRIDEiQ9FVC8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

TAIRiAT2G45440.

Phylogenomic databases

eggNOGiCOG0329.
HOGENOMiHOG000173604.
InParanoidiQ9FVC8.
KOiK01714.
OMAiNVIPQEF.
PhylomeDBiQ9FVC8.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00017.
BioCyciARA:AT2G45440-MONOMER.
ReactomeiREACT_225978. Sialic acid metabolism.

Gene expression databases

ExpressionAtlasiQ9FVC8. baseline and differential.
GenevestigatoriQ9FVC8.

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]
ProtoNetiSearch...

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: January 7, 2015
This is version 107 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

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 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.