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Protein

Acetylornithine/succinyldiaminopimelate aminotransferase

Gene

argD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in both the arginine and lysine biosynthetic pathways.By similarity

Catalytic activityi

N(2)-acetyl-L-ornithine + 2-oxoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate.
N-succinyl-L-2,6-diaminoheptanedioate + 2-oxoglutarate = N-succinyl-2-L-amino-6-oxoheptanedioate + L-glutamate.

Cofactori

pyridoxal 5'-phosphate1 PublicationNote: Binds 1 pyridoxal phosphate per subunit.1 Publication

Enzyme regulationi

Inhibited by gabaculine (Gcn).1 Publication

Kineticsi

  1. KM=37 µM for N-acetylornithine (at pH 9.5 and 25 degrees Celsius)1 Publication
  2. KM=640 µM for ornithine (at pH 9.5 and 25 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 9.5. At pH 8.0, the activity is reduced by 50%.1 Publication

    Pathwayi: L-arginine biosynthesis

    This protein is involved in step 4 of the subpathway that synthesizes N(2)-acetyl-L-ornithine from L-glutamate.
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. Amino-acid acetyltransferase (argA)
    2. Acetylglutamate kinase (argB)
    3. N-acetyl-gamma-glutamyl-phosphate reductase (argC)
    4. Acetylornithine/succinyldiaminopimelate aminotransferase (argD)
    This subpathway is part of the pathway L-arginine biosynthesis, 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 N(2)-acetyl-L-ornithine from L-glutamate, the pathway L-arginine biosynthesis and in Amino-acid biosynthesis.

    Pathwayi: L-lysine biosynthesis via DAP pathway

    This protein is involved in step 2 of the subpathway that synthesizes LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (succinylase route).
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (dapD)
    2. Acetylornithine/succinyldiaminopimelate aminotransferase (argD)
    3. Succinyl-diaminopimelate desuccinylase (dapE)
    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 (succinylase route), the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei141Pyridoxal phosphate; via carbonyl oxygen1
    Binding sitei144N2-acetyl-L-ornithineBy similarity1
    Binding sitei283N2-acetyl-L-ornithineBy similarity1
    Binding sitei284Pyridoxal phosphateBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Aminotransferase, Transferase

    Keywords - Biological processi

    Amino-acid biosynthesis, Arginine biosynthesis, Lysine biosynthesis

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    SABIO-RKP40732.
    UniPathwayiUPA00034; UER00020.
    UPA00068; UER00109.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Acetylornithine/succinyldiaminopimelate aminotransferase (EC:2.6.1.11, EC:2.6.1.17)
    Short name:
    ACOAT
    Short name:
    DapATase
    Short name:
    Succinyldiaminopimelate transferase
    Gene namesi
    Name:argD
    Synonyms:dapC, dtu
    Ordered Locus Names:STM3468
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemovedBy similarity
    ChainiPRO_00001127772 – 405Acetylornithine/succinyldiaminopimelate aminotransferaseAdd BLAST404

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei255N6-(pyridoxal phosphate)lysine1

    Proteomic databases

    PaxDbiP40732.
    PRIDEiP40732.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    GO - Molecular functioni

    Protein-protein interaction databases

    STRINGi99287.STM3468.

    Structurei

    Secondary structure

    1405
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi13 – 16Combined sources4
    Beta strandi28 – 33Combined sources6
    Beta strandi35 – 38Combined sources4
    Beta strandi43 – 48Combined sources6
    Helixi49 – 52Combined sources4
    Helixi61 – 71Combined sources11
    Helixi84 – 96Combined sources13
    Beta strandi100 – 107Combined sources8
    Helixi108 – 126Combined sources19
    Beta strandi133 – 137Combined sources5
    Helixi146 – 151Combined sources6
    Helixi155 – 158Combined sources4
    Beta strandi161 – 163Combined sources3
    Beta strandi168 – 171Combined sources4
    Helixi176 – 182Combined sources7
    Beta strandi187 – 192Combined sources6
    Beta strandi194 – 196Combined sources3
    Turni197 – 200Combined sources4
    Beta strandi201 – 203Combined sources3
    Helixi206 – 219Combined sources14
    Beta strandi222 – 226Combined sources5
    Turni228 – 235Combined sources8
    Beta strandi236 – 239Combined sources4
    Helixi240 – 244Combined sources5
    Beta strandi249 – 253Combined sources5
    Helixi255 – 258Combined sources4
    Beta strandi264 – 268Combined sources5
    Helixi270 – 273Combined sources4
    Beta strandi284 – 286Combined sources3
    Helixi289 – 302Combined sources14
    Helixi305 – 329Combined sources25
    Beta strandi332 – 338Combined sources7
    Beta strandi341 – 346Combined sources6
    Helixi348 – 350Combined sources3
    Helixi354 – 363Combined sources10
    Beta strandi369 – 372Combined sources4
    Beta strandi375 – 378Combined sources4
    Helixi386 – 405Combined sources20

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2PB0X-ray1.96A/B1-405[»]
    2PB2X-ray1.91A/B1-405[»]
    4JEVX-ray1.67A/B1-405[»]
    4JEWX-ray1.48A/B1-405[»]
    4JEXX-ray1.43A/B1-405[»]
    4JEYX-ray1.55A/B1-405[»]
    4JEZX-ray1.55A/B1-405[»]
    4JF0X-ray2.10A/B1-405[»]
    4JF1X-ray1.28A/B1-405[»]
    ProteinModelPortaliP40732.
    SMRiP40732.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP40732.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni108 – 109Pyridoxal phosphate binding2
    Regioni226 – 229Pyridoxal phosphate binding4

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105C8Y. Bacteria.
    COG4992. LUCA.
    HOGENOMiHOG000020206.
    KOiK00821.
    OMAiDFEPLMP.
    PhylomeDBiP40732.

    Family and domain databases

    CDDicd00610. OAT_like. 1 hit.
    Gene3Di3.40.640.10. 1 hit.
    3.90.1150.10. 2 hits.
    HAMAPiMF_01107. ArgD_aminotrans_3. 1 hit.
    InterProiIPR017652. Ac/SucOrn_transaminase_bac.
    IPR004636. AcOrn/SuccOrn_fam.
    IPR005814. Aminotrans_3.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view]
    PANTHERiPTHR11986. PTHR11986. 1 hit.
    PfamiPF00202. Aminotran_3. 1 hit.
    [Graphical view]
    SUPFAMiSSF53383. SSF53383. 1 hit.
    TIGRFAMsiTIGR03246. arg_catab_astC. 1 hit.
    TIGR00707. argD. 1 hit.
    PROSITEiPS00600. AA_TRANSFER_CLASS_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P40732-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MATEQTAITR ATFDEVILPV YAPADFIPVK GKGSRVWDQQ GKEYIDFAGG
    60 70 80 90 100
    IAVTALGHCH PALVEALKSQ GETLWHTSNV FTNEPALRLG RKLIDATFAE
    110 120 130 140 150
    RVLFMNSGTE ANETAFKLAR HYACVRHSPF KTKIIAFHNA FHGRSLFTVS
    160 170 180 190 200
    VGGQPKYSDG FGPKPADIIH VPFNDLHAVK AVMDDHTCAV VVEPIQGEGG
    210 220 230 240 250
    VQAATPEFLK GLRDLCDEHQ ALLVFDEVQC GMGRTGDLFA YMHYGVTPDI
    260 270 280 290 300
    LTSAKALGGG FPVSAMLTTQ EIASAFHVGS HGSTYGGNPL ACAVAGAAFD
    310 320 330 340 350
    IINTPEVLQG IHTKRQQFVQ HLQAIDEQFD IFSDIRGMGL LIGAELKPKY
    360 370 380 390 400
    KGRARDFLYA GAEAGVMVLN AGADVMRFAP SLVVEEADIH EGMQRFAQAV

    GKVVA
    Length:405
    Mass (Da):43,670
    Last modified:January 23, 2007 - v3
    Checksum:i26A69C62831E986C
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti3T → I in AAA24265 (PubMed:2403545).Curated1
    Sequence conflicti3T → I in AAA27178 (PubMed:2403545).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE006468 Genomic DNA. Translation: AAL22330.1.
    M32354 Genomic DNA. Translation: AAA24265.1.
    M32355 Genomic DNA. Translation: AAA27178.1.
    RefSeqiNP_462371.1. NC_003197.1.
    WP_000190023.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL22330; AAL22330; STM3468.
    GeneIDi1254991.
    KEGGistm:STM3468.
    PATRICi32385735. VBISalEnt20916_3665.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE006468 Genomic DNA. Translation: AAL22330.1.
    M32354 Genomic DNA. Translation: AAA24265.1.
    M32355 Genomic DNA. Translation: AAA27178.1.
    RefSeqiNP_462371.1. NC_003197.1.
    WP_000190023.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2PB0X-ray1.96A/B1-405[»]
    2PB2X-ray1.91A/B1-405[»]
    4JEVX-ray1.67A/B1-405[»]
    4JEWX-ray1.48A/B1-405[»]
    4JEXX-ray1.43A/B1-405[»]
    4JEYX-ray1.55A/B1-405[»]
    4JEZX-ray1.55A/B1-405[»]
    4JF0X-ray2.10A/B1-405[»]
    4JF1X-ray1.28A/B1-405[»]
    ProteinModelPortaliP40732.
    SMRiP40732.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi99287.STM3468.

    Proteomic databases

    PaxDbiP40732.
    PRIDEiP40732.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL22330; AAL22330; STM3468.
    GeneIDi1254991.
    KEGGistm:STM3468.
    PATRICi32385735. VBISalEnt20916_3665.

    Phylogenomic databases

    eggNOGiENOG4105C8Y. Bacteria.
    COG4992. LUCA.
    HOGENOMiHOG000020206.
    KOiK00821.
    OMAiDFEPLMP.
    PhylomeDBiP40732.

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00020.
    UPA00068; UER00109.
    SABIO-RKP40732.

    Miscellaneous databases

    EvolutionaryTraceiP40732.

    Family and domain databases

    CDDicd00610. OAT_like. 1 hit.
    Gene3Di3.40.640.10. 1 hit.
    3.90.1150.10. 2 hits.
    HAMAPiMF_01107. ArgD_aminotrans_3. 1 hit.
    InterProiIPR017652. Ac/SucOrn_transaminase_bac.
    IPR004636. AcOrn/SuccOrn_fam.
    IPR005814. Aminotrans_3.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view]
    PANTHERiPTHR11986. PTHR11986. 1 hit.
    PfamiPF00202. Aminotran_3. 1 hit.
    [Graphical view]
    SUPFAMiSSF53383. SSF53383. 1 hit.
    TIGRFAMsiTIGR03246. arg_catab_astC. 1 hit.
    TIGR00707. argD. 1 hit.
    PROSITEiPS00600. AA_TRANSFER_CLASS_3. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiARGD_SALTY
    AccessioniPrimary (citable) accession number: P40732
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: January 23, 2007
    Last modified: November 2, 2016
    This is version 133 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The reaction catalyzed by ACOAT is highly reversible. This enzyme may also transaminate ornithine.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.