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Protein

LL-diaminopimelate aminotransferase, chloroplastic

Gene

DAP

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

Functioni

Required for lysine biosynthesis. Catalyzes the direct conversion of tetrahydrodipicolinate to LL-diaminopimelate, a reaction that requires three enzymes in E.coli. Not active with meso-diaminopimelate, lysine or ornithine as substrates.4 Publications

Catalytic activityi

LL-2,6-diaminoheptanedioate + 2-oxoglutarate = (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + L-glutamate + H2O.2 Publications

Cofactori

pyridoxal 5'-phosphate2 Publications

Kineticsi

  1. KM=47 µM for LL-2,6-diaminopimelate1 Publication
  2. KM=67 µM for LL-2,6-diaminopimelate1 Publication
  3. KM=8.7 mM for 2-oxoglutarate1 Publication
  4. KM=38 µM for L-2,3,4,5-tetrahydrodipicolinate1 Publication
  5. KM=1.9 mM for glutamatic acid1 Publication
  1. Vmax=22.3 µmol/min/mg enzyme for the forward reaction1 Publication
  2. Vmax=0.38 µmol/min/mg enzyme for the reverse reaction1 Publication

pH dependencei

Optimum pH is 7.9 in Tris buffer and 7.6 in HEPES buffer.1 Publication

Temperature dependencei

Optimum temperature is 36 degrees Celsius.1 Publication

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (aminotransferase route).
Proteins known to be involved in this subpathway in this organism are:
  1. LL-diaminopimelate aminotransferase, chloroplastic (DAP)
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 LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (aminotransferase route), the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei72 – 721Substrate1 Publication
Binding sitei99 – 991Substrate; via amide nitrogen2 Publications
Binding sitei129 – 1291Pyridoxal phosphate2 Publications
Binding sitei164 – 1641Substrate2 Publications
Binding sitei187 – 1871Pyridoxal phosphate1 Publication
Binding sitei187 – 1871Substrate2 Publications
Binding sitei244 – 2441Pyridoxal phosphate2 Publications
Binding sitei244 – 2441Substrate2 Publications
Binding sitei275 – 2751Pyridoxal phosphate2 Publications
Binding sitei313 – 3131Pyridoxal phosphate2 Publications
Binding sitei344 – 3441Pyridoxal phosphate2 Publications
Binding sitei344 – 3441Substrate2 Publications
Binding sitei439 – 4391Substrate2 Publications

GO - Molecular functioni

  • copper ion binding Source: TAIR
  • L,L-diaminopimelate aminotransferase activity Source: TAIR
  • pyridoxal phosphate binding Source: InterPro
  • transaminase activity Source: TAIR

GO - Biological processi

  • lysine biosynthetic process via diaminopimelate Source: UniProtKB-UniPathway
  • response to cytokinin Source: TAIR
  • systemic acquired resistance, salicylic acid mediated signaling pathway Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Aminotransferase, Transferase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciARA:AT4G33680-MONOMER.
MetaCyc:AT4G33680-MONOMER.
BRENDAi2.6.1.83. 399.
SABIO-RKQ93ZN9.
UniPathwayiUPA00034; UER00466.

Names & Taxonomyi

Protein namesi
Recommended name:
LL-diaminopimelate aminotransferase, chloroplastic (EC:2.6.1.832 Publications)
Short name:
AtDAP-AT
Short name:
DAP-AT
Short name:
DAP-aminotransferase
Short name:
LL-DAP-aminotransferase
Alternative name(s):
Protein ABERRANT GROWTH AND DEATH 2
Gene namesi
Name:DAP
Synonyms:AGD2
Ordered Locus Names:At4g33680
ORF Names:T16L1.170
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G33680.

Subcellular locationi

  • Plastidchloroplast 1 Publication

GO - Cellular componenti

  • chloroplast Source: TAIR
  • chloroplast stroma Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

Pathology & Biotechi

Disruption phenotypei

Embryonic lethality.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi305 – 3051K → N: Loss of LL-DAP-aminotransferase activity. 1 Publication
Mutagenesisi305 – 3051K → Q: Loss of LL-DAP-aminotransferase activity. 1 Publication
Mutagenesisi398 – 3981P → S in agd2-1; reduced activity and increased resistance to pathogen. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3636ChloroplastSequence analysisAdd
BLAST
Chaini37 – 461425LL-diaminopimelate aminotransferase, chloroplasticPRO_0000306914Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei305 – 3051N6-(pyridoxal phosphate)lysine1 Publication1 Publication

Proteomic databases

PaxDbiQ93ZN9.
PRIDEiQ93ZN9.

Expressioni

Tissue specificityi

Highly expressed in seedlings, roots, stems, flowers and leaves. Lower expression in siliques.1 Publication

Developmental stagei

Down-regulated during senescence.1 Publication

Inductioni

Not induced by pathogen infection, but down-regulated by dark treatment.1 Publication

Gene expression databases

GenevisibleiQ93ZN9. AT.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

BioGridi14792. 1 interaction.
STRINGi3702.AT4G33680.1.

Structurei

Secondary structure

1
461
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi63 – 675Combined sources
Helixi73 – 8715Combined sources
Helixi107 – 11913Combined sources
Turni123 – 1253Combined sources
Helixi136 – 14712Combined sources
Turni148 – 1514Combined sources
Helixi154 – 1563Combined sources
Beta strandi157 – 1615Combined sources
Helixi163 – 17412Combined sources
Beta strandi180 – 1856Combined sources
Helixi189 – 1979Combined sources
Turni205 – 2084Combined sources
Beta strandi214 – 2174Combined sources
Helixi220 – 2223Combined sources
Helixi228 – 2303Combined sources
Beta strandi235 – 2428Combined sources
Turni244 – 2463Combined sources
Helixi252 – 26514Combined sources
Beta strandi268 – 2725Combined sources
Helixi276 – 2783Combined sources
Helixi287 – 2893Combined sources
Helixi293 – 2953Combined sources
Beta strandi297 – 3037Combined sources
Helixi304 – 3074Combined sources
Turni309 – 3124Combined sources
Beta strandi315 – 3184Combined sources
Helixi331 – 34111Combined sources
Helixi348 – 35710Combined sources
Helixi360 – 38627Combined sources
Beta strandi391 – 3933Combined sources
Beta strandi395 – 4039Combined sources
Helixi409 – 42012Combined sources
Helixi427 – 4304Combined sources
Helixi432 – 4343Combined sources
Beta strandi437 – 4415Combined sources
Helixi446 – 46015Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z1ZX-ray2.40A/B36-461[»]
2Z20X-ray1.95A/B36-461[»]
3EI5X-ray2.05A/B36-461[»]
3EI6X-ray1.90A/B36-461[»]
3EI7X-ray1.99A/B36-461[»]
3EI8X-ray1.60A/B36-461[»]
3EI9X-ray1.55A/B36-461[»]
3EIAX-ray1.85A/B36-461[»]
3EIBX-ray1.85A/B36-461[»]
ProteinModelPortaliQ93ZN9.
SMRiQ93ZN9. Positions 54-461.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ93ZN9.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni163 – 1642Pyridoxal phosphate binding2 Publications
Regioni302 – 3043Pyridoxal phosphate binding2 Publications

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG0257. Eukaryota.
COG0436. LUCA.
HOGENOMiHOG000223061.
InParanoidiQ93ZN9.
KOiK10206.
OMAiRCAFTVV.
OrthoDBiEOG0936094D.
PhylomeDBiQ93ZN9.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_01642. DapL_aminotrans_1. 1 hit.
InterProiIPR004839. Aminotransferase_I/II.
IPR019942. DapL_aminotrans.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PANTHERiPTHR11751:SF376. PTHR11751:SF376. 1 hit.
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
TIGRFAMsiTIGR03542. DAPAT_plant. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q93ZN9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSTHQLVSS MISSSSSTFL APSNFNLRTR NACLPMAKRV NTCKCVATPQ
60 70 80 90 100
EKIEYKTKVS RNSNMSKLQA GYLFPEIARR RSAHLLKYPD AQVISLGIGD
110 120 130 140 150
TTEPIPEVIT SAMAKKAHEL STIEGYSGYG AEQGAKPLRA AIAKTFYGGL
160 170 180 190 200
GIGDDDVFVS DGAKCDISRL QVMFGSNVTI AVQDPSYPAY VDSSVIMGQT
210 220 230 240 250
GQFNTDVQKY GNIEYMRCTP ENGFFPDLST VGRTDIIFFC SPNNPTGAAA
260 270 280 290 300
TREQLTQLVE FAKKNGSIIV YDSAYAMYMS DDNPRSIFEI PGAEEVAMET
310 320 330 340 350
ASFSKYAGFT GVRLGWTVIP KKLLYSDGFP VAKDFNRIIC TCFNGASNIS
360 370 380 390 400
QAGALACLTP EGLEAMHKVI GFYKENTNII IDTFTSLGYD VYGGKNAPYV
410 420 430 440 450
WVHFPNQSSW DVFAEILEKT HVVTTPGSGF GPGGEGFVRV SAFGHRENIL
460
EACRRFKQLY K
Length:461
Mass (Da):50,396
Last modified:December 1, 2001 - v1
Checksum:i9F49DE08EEDCEC3D
GO

Sequence cautioni

The sequence CAA20581 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAB80085 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY518701 mRNA. Translation: AAR99909.1.
AL031394 Genomic DNA. Translation: CAA20581.1. Sequence problems.
AL161584 Genomic DNA. Translation: CAB80085.1. Sequence problems.
CP002687 Genomic DNA. Translation: AEE86265.1.
AY056423 mRNA. Translation: AAL08279.1.
AY065256 mRNA. Translation: AAL38732.1.
AY117246 mRNA. Translation: AAM51321.1.
PIRiT04985.
RefSeqiNP_567934.1. NM_119526.3.
UniGeneiAt.2456.

Genome annotation databases

EnsemblPlantsiAT4G33680.1; AT4G33680.1; AT4G33680.
GeneIDi829510.
GrameneiAT4G33680.1; AT4G33680.1; AT4G33680.
KEGGiath:AT4G33680.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY518701 mRNA. Translation: AAR99909.1.
AL031394 Genomic DNA. Translation: CAA20581.1. Sequence problems.
AL161584 Genomic DNA. Translation: CAB80085.1. Sequence problems.
CP002687 Genomic DNA. Translation: AEE86265.1.
AY056423 mRNA. Translation: AAL08279.1.
AY065256 mRNA. Translation: AAL38732.1.
AY117246 mRNA. Translation: AAM51321.1.
PIRiT04985.
RefSeqiNP_567934.1. NM_119526.3.
UniGeneiAt.2456.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z1ZX-ray2.40A/B36-461[»]
2Z20X-ray1.95A/B36-461[»]
3EI5X-ray2.05A/B36-461[»]
3EI6X-ray1.90A/B36-461[»]
3EI7X-ray1.99A/B36-461[»]
3EI8X-ray1.60A/B36-461[»]
3EI9X-ray1.55A/B36-461[»]
3EIAX-ray1.85A/B36-461[»]
3EIBX-ray1.85A/B36-461[»]
ProteinModelPortaliQ93ZN9.
SMRiQ93ZN9. Positions 54-461.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi14792. 1 interaction.
STRINGi3702.AT4G33680.1.

Proteomic databases

PaxDbiQ93ZN9.
PRIDEiQ93ZN9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G33680.1; AT4G33680.1; AT4G33680.
GeneIDi829510.
GrameneiAT4G33680.1; AT4G33680.1; AT4G33680.
KEGGiath:AT4G33680.

Organism-specific databases

TAIRiAT4G33680.

Phylogenomic databases

eggNOGiKOG0257. Eukaryota.
COG0436. LUCA.
HOGENOMiHOG000223061.
InParanoidiQ93ZN9.
KOiK10206.
OMAiRCAFTVV.
OrthoDBiEOG0936094D.
PhylomeDBiQ93ZN9.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00466.
BioCyciARA:AT4G33680-MONOMER.
MetaCyc:AT4G33680-MONOMER.
BRENDAi2.6.1.83. 399.
SABIO-RKQ93ZN9.

Miscellaneous databases

EvolutionaryTraceiQ93ZN9.
PROiQ93ZN9.

Gene expression databases

GenevisibleiQ93ZN9. AT.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_01642. DapL_aminotrans_1. 1 hit.
InterProiIPR004839. Aminotransferase_I/II.
IPR019942. DapL_aminotrans.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PANTHERiPTHR11751:SF376. PTHR11751:SF376. 1 hit.
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
TIGRFAMsiTIGR03542. DAPAT_plant. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiDAPAT_ARATH
AccessioniPrimary (citable) accession number: Q93ZN9
Secondary accession number(s): O81885
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 2, 2007
Last sequence update: December 1, 2001
Last modified: September 7, 2016
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

The expected covalent binding of pyridoxal phosphate by Lys-305 has not been observed in the 3D-structure.

Keywords - Technical termi

3D-structure, 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.