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Protein

Probable LL-diaminopimelate aminotransferase, chloroplastic

Gene

AGD2

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

Functioni

Required for lysine biosynthesis. Catalyzes the direct conversion of tetrahydrodipicolinate to LL-diaminopimelate, a reaction that requires three enzymes in E.coli (By similarity).By similarity

Catalytic activityi

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

Cofactori

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. Probable LL-diaminopimelate aminotransferase, chloroplastic (AGD2)
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 sitei102Substrate; via amide nitrogenBy similarity1
Binding sitei132Pyridoxal phosphate; shared with dimeric partnerBy similarity1
Binding sitei135Substrate; shared with dimeric partnerBy similarity1
Binding sitei167SubstrateBy similarity1
Binding sitei190SubstrateBy similarity1
Binding sitei247Pyridoxal phosphateBy similarity1
Binding sitei247SubstrateBy similarity1
Binding sitei275Pyridoxal phosphateBy similarity1
Binding sitei278Pyridoxal phosphateBy similarity1
Binding sitei305Pyridoxal phosphateBy similarity1
Binding sitei307Pyridoxal phosphateBy similarity1
Binding sitei316Pyridoxal phosphateBy similarity1
Binding sitei347Substrate; shared with dimeric partnerBy similarity1
Binding sitei442SubstrateBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionAminotransferase, Transferase
LigandPyridoxal phosphate

Enzyme and pathway databases

UniPathwayi
UPA00034;UER00466

Names & Taxonomyi

Protein namesi
Recommended name:
Probable LL-diaminopimelate aminotransferase, chloroplastic (EC:2.6.1.83)
Short name:
DAP-AT
Short name:
DAP-aminotransferase
Short name:
LL-DAP-aminotransferase
Gene namesi
Name:AGD2
Ordered Locus Names:Os03g0299900, LOC_Os03g18810
ORF Names:OsJ_27598
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
Proteomesi
  • UP000059680 Componenti: Chromosome 3

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 39ChloroplastSequence analysisAdd BLAST39
ChainiPRO_000041686140 – 464Probable LL-diaminopimelate aminotransferase, chloroplasticAdd BLAST425

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei308N6-(pyridoxal phosphate)lysineBy similarity1

Proteomic databases

PaxDbiQ10MQ2
PRIDEiQ10MQ2

Expressioni

Gene expression databases

ExpressionAtlasiQ10MQ2 differential
GenevisibleiQ10MQ2 OS

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi39947.LOC_Os03g18810.1

Structurei

3D structure databases

ProteinModelPortaliQ10MQ2
SMRiQ10MQ2
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG0257 Eukaryota
COG0436 LUCA
InParanoidiQ10MQ2
KOiK10206
OMAiTGTRCAF
OrthoDBiEOG0936094D

Family and domain databases

Gene3Di3.40.640.10, 1 hit
3.90.1150.10, 2 hits
HAMAPiMF_01642 DapL_aminotrans_1, 1 hit
InterProiView protein in InterPro
IPR004839 Aminotransferase_I/II
IPR019942 DapL/ALD1
IPR015424 PyrdxlP-dep_Trfase
IPR015422 PyrdxlP-dep_Trfase_dom1
IPR015421 PyrdxlP-dep_Trfase_major
PANTHERiPTHR43144 PTHR43144, 1 hit
PfamiView protein in Pfam
PF00155 Aminotran_1_2, 1 hit
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.

Q10MQ2-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAASPAAGAA AATVSSFVSP SSFSSVKASK PDRLRPARRA AAVNVRCVSS
60 70 80 90 100
PPATETSFKT KVPRNANMAK LQAGYLFPEI ARRRAAHLLK FPDAKIISLG
110 120 130 140 150
IGDTTEPIPD VITNAMAKRA HALSTVDGYS GYGAEQGEKK LRAAIAATYY
160 170 180 190 200
ADLGIEETDI FVSDGAKCDI SRLQVLFGSN VKIAVQDPSY PAYVDSSVIM
210 220 230 240 250
GQTGLYQEDV QKYGNIEYMK CSPENGFFPD LSSVPRTDII FFCSPNNPTG
260 270 280 290 300
AAASRDQLTK LVKFAKDNGS IIVYDSAYAM YISDDSPKSI FEIPGAKEVA
310 320 330 340 350
IETASFSKYA GFTGVRLGWT VVPKELLFSD GHPVAKDFNR IVCTCFNGAS
360 370 380 390 400
NISQAGGLGC LSPEGLKAMS DVVGFYKENT KIIVDTFTSL GFNVYGAKNA
410 420 430 440 450
PYVWVHFPGR NSWDVFAEIL EKAHVVTTPG SGFGPGGEGF VRVSAFGHRE
460
NIIEAARRLK QLYK
Length:464
Mass (Da):49,858
Last modified:August 22, 2006 - v1
Checksum:i57F9B88788D75B75
GO

Sequence cautioni

The sequence ABF95474 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti8G → A in AAR01225 (PubMed:14729919).Curated1
Sequence conflicti118K → E in AAR01225 (PubMed:14729919).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY338235 mRNA Translation: AAR01225.1
DP000009 Genomic DNA Translation: ABF95473.1
DP000009 Genomic DNA Translation: ABF95474.1 Sequence problems.
AP008209 Genomic DNA Translation: BAF11766.1
AP014959 Genomic DNA Translation: BAS83755.1
CM000145 Genomic DNA Translation: EEE68826.1
AK069075 mRNA Translation: BAG91242.1
RefSeqiXP_015631441.1, XM_015775955.1
UniGeneiOs.4665

Genome annotation databases

EnsemblPlantsiOs03t0299900-01; Os03t0299900-01; Os03g0299900
GeneIDi4332563
GrameneiOs03t0299900-01; Os03t0299900-01; Os03g0299900
KEGGiosa:4332563

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY338235 mRNA Translation: AAR01225.1
DP000009 Genomic DNA Translation: ABF95473.1
DP000009 Genomic DNA Translation: ABF95474.1 Sequence problems.
AP008209 Genomic DNA Translation: BAF11766.1
AP014959 Genomic DNA Translation: BAS83755.1
CM000145 Genomic DNA Translation: EEE68826.1
AK069075 mRNA Translation: BAG91242.1
RefSeqiXP_015631441.1, XM_015775955.1
UniGeneiOs.4665

3D structure databases

ProteinModelPortaliQ10MQ2
SMRiQ10MQ2
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Os03g18810.1

Proteomic databases

PaxDbiQ10MQ2
PRIDEiQ10MQ2

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiOs03t0299900-01; Os03t0299900-01; Os03g0299900
GeneIDi4332563
GrameneiOs03t0299900-01; Os03t0299900-01; Os03g0299900
KEGGiosa:4332563

Phylogenomic databases

eggNOGiKOG0257 Eukaryota
COG0436 LUCA
InParanoidiQ10MQ2
KOiK10206
OMAiTGTRCAF
OrthoDBiEOG0936094D

Enzyme and pathway databases

UniPathwayi
UPA00034;UER00466

Gene expression databases

ExpressionAtlasiQ10MQ2 differential
GenevisibleiQ10MQ2 OS

Family and domain databases

Gene3Di3.40.640.10, 1 hit
3.90.1150.10, 2 hits
HAMAPiMF_01642 DapL_aminotrans_1, 1 hit
InterProiView protein in InterPro
IPR004839 Aminotransferase_I/II
IPR019942 DapL/ALD1
IPR015424 PyrdxlP-dep_Trfase
IPR015422 PyrdxlP-dep_Trfase_dom1
IPR015421 PyrdxlP-dep_Trfase_major
PANTHERiPTHR43144 PTHR43144, 1 hit
PfamiView protein in Pfam
PF00155 Aminotran_1_2, 1 hit
SUPFAMiSSF53383 SSF53383, 1 hit
TIGRFAMsiTIGR03542 DAPAT_plant, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDAPAT_ORYSJ
AccessioniPrimary (citable) accession number: Q10MQ2
Secondary accession number(s): A0A0P0VWF4, Q10MQ1, Q6VMN8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 18, 2012
Last sequence update: August 22, 2006
Last modified: May 23, 2018
This is version 91 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
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Main funding by: National Institutes of Health

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