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

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)DescriptionActionsGraphical viewLength
Binding sitei72Substrate1 Publication1
Binding sitei99Substrate; via amide nitrogen2 Publications1
Binding sitei129Pyridoxal phosphate2 Publications1
Binding sitei164Substrate2 Publications1
Binding sitei187Pyridoxal phosphate1 Publication1
Binding sitei187Substrate2 Publications1
Binding sitei244Pyridoxal phosphate2 Publications1
Binding sitei244Substrate2 Publications1
Binding sitei275Pyridoxal phosphate2 Publications1
Binding sitei313Pyridoxal phosphate2 Publications1
Binding sitei344Pyridoxal phosphate2 Publications1
Binding sitei344Substrate2 Publications1
Binding sitei439Substrate2 Publications1

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)DescriptionActionsGraphical viewLength
Mutagenesisi305K → N: Loss of LL-DAP-aminotransferase activity. 1 Publication1
Mutagenesisi305K → Q: Loss of LL-DAP-aminotransferase activity. 1 Publication1
Mutagenesisi398P → S in agd2-1; reduced activity and increased resistance to pathogen. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 36ChloroplastSequence analysisAdd BLAST36
ChainiPRO_000030691437 – 461LL-diaminopimelate aminotransferase, chloroplasticAdd BLAST425

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei305N6-(pyridoxal phosphate)lysine1 Publication1 Publication1

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 interactor.
STRINGi3702.AT4G33680.1.

Structurei

Secondary structure

1461
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi63 – 67Combined sources5
Helixi73 – 87Combined sources15
Helixi107 – 119Combined sources13
Turni123 – 125Combined sources3
Helixi136 – 147Combined sources12
Turni148 – 151Combined sources4
Helixi154 – 156Combined sources3
Beta strandi157 – 161Combined sources5
Helixi163 – 174Combined sources12
Beta strandi180 – 185Combined sources6
Helixi189 – 197Combined sources9
Turni205 – 208Combined sources4
Beta strandi214 – 217Combined sources4
Helixi220 – 222Combined sources3
Helixi228 – 230Combined sources3
Beta strandi235 – 242Combined sources8
Turni244 – 246Combined sources3
Helixi252 – 265Combined sources14
Beta strandi268 – 272Combined sources5
Helixi276 – 278Combined sources3
Helixi287 – 289Combined sources3
Helixi293 – 295Combined sources3
Beta strandi297 – 303Combined sources7
Helixi304 – 307Combined sources4
Turni309 – 312Combined sources4
Beta strandi315 – 318Combined sources4
Helixi331 – 341Combined sources11
Helixi348 – 357Combined sources10
Helixi360 – 386Combined sources27
Beta strandi391 – 393Combined sources3
Beta strandi395 – 403Combined sources9
Helixi409 – 420Combined sources12
Helixi427 – 430Combined sources4
Helixi432 – 434Combined sources3
Beta strandi437 – 441Combined sources5
Helixi446 – 460Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ93ZN9.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni163 – 164Pyridoxal phosphate binding2 Publications2
Regioni302 – 304Pyridoxal phosphate binding2 Publications3

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_119526.4.
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_119526.4.
UniGeneiAt.2456.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi14792. 1 interactor.
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: November 30, 2016
This is version 105 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.