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O80452

- AMPD_ARATH

UniProt

O80452 - AMPD_ARATH

Protein

AMP deaminase

Gene

AMPD

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 2 (01 Jun 2002)
      Previous versions | rss
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    Functioni

    AMP deaminase plays a critical role in energy metabolism. Essential for the transition from zygote to embryo.1 Publication

    Catalytic activityi

    AMP + H2O = IMP + NH3.1 Publication

    Cofactori

    Binds 1 zinc ion per subunit.1 Publication

    Enzyme regulationi

    Activated by ATP. Activated by sulfate ions (in vitro). Inhibited by phosphate ions.1 Publication

    Kineticsi

    1. KM=6.7 mM for AMP (in the absence of ATP)1 Publication
    2. KM=0.26 mM for AMP (in the presence of 1 mM ATP)1 Publication

    Vmax=17 µmol/min/mg enzyme (in the absence of ATP)1 Publication

    Vmax=375 µmol/min/mg enzyme (in the presence of 1 mM ATP)1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi391 – 3911Zinc; catalytic
    Metal bindingi393 – 3931Zinc; catalytic
    Binding sitei393 – 3931Substrate
    Metal bindingi659 – 6591Zinc; catalytic
    Binding sitei662 – 6621Substrate
    Active sitei681 – 6811Proton acceptorCurated
    Metal bindingi736 – 7361Zinc; catalytic

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi289 – 2968ATPSequence Analysis

    GO - Molecular functioni

    1. AMP deaminase activity Source: TAIR
    2. ATP binding Source: UniProtKB-KW
    3. metal ion binding Source: UniProtKB-KW
    4. protein binding Source: IntAct
    5. protein histidine kinase binding Source: UniProtKB

    GO - Biological processi

    1. embryo development ending in seed dormancy Source: TAIR
    2. IMP salvage Source: UniProtKB-UniPathway
    3. response to abscisic acid Source: TAIR

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Nucleotide metabolism

    Keywords - Ligandi

    ATP-binding, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciARA:AT2G38280-MONOMER.
    ARA:GQT-2641-MONOMER.
    SABIO-RKO80452.
    UniPathwayiUPA00591; UER00663.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    AMP deaminase (EC:3.5.4.6)
    Short name:
    AtAMPD
    Alternative name(s):
    Protein EMBRYONIC FACTOR 1
    Gene namesi
    Name:AMPD
    Synonyms:FAC1
    Ordered Locus Names:At2g38280
    ORF Names:F16M14.21
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 2

    Organism-specific databases

    TAIRiAT2G38280.

    Subcellular locationi

    Membrane 1 Publication; Single-pass membrane protein 1 Publication. Microsome membrane 1 Publication
    Note: Might be associated with the inner mitochondrial membrane.By similarity

    GO - Cellular componenti

    1. cytosol Source: TAIR
    2. endoplasmic reticulum Source: UniProtKB-KW
    3. integral component of mitochondrial outer membrane Source: TAIR
    4. intracellular membrane-bounded organelle Source: TAIR
    5. nucleus Source: TAIR

    Keywords - Cellular componenti

    Endoplasmic reticulum, Membrane, Microsome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi598 – 5981D → N in fac1-1; zygote-lethal phenotype. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 839839AMP deaminasePRO_0000238455Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei134 – 1341Phosphoserine1 Publication
    Modified residuei140 – 1401Phosphoserine1 Publication
    Modified residuei203 – 2031Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiO80452.
    PRIDEiO80452.

    Expressioni

    Tissue specificityi

    Expressed in seedlings, roots, leaves, flowers, pollen grains, pollen tubes and siliques, and at a lower level in stems.1 Publication

    Developmental stagei

    Expressed in both male and female gametophytes, at the zygote stage, in the endosperm, and during early embryo development. Observed in cotyledonary embryos and in the basal part of the embryo, but not in the suspensor or in mature embryos. Also expressed during somatic embryogenesis.1 Publication

    Gene expression databases

    GenevestigatoriO80452.

    Interactioni

    Subunit structurei

    Homodimer. Interacts with AHK4.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    AHK4Q9C5U02EBI-1807679,EBI-1100775

    Protein-protein interaction databases

    BioGridi3750. 5 interactions.
    IntActiO80452. 2 interactions.

    Structurei

    Secondary structure

    1
    839
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni215 – 2173
    Turni244 – 2474
    Helixi248 – 25912
    Helixi325 – 33814
    Helixi342 – 37332
    Helixi374 – 3763
    Turni382 – 3843
    Beta strandi387 – 3937
    Turni394 – 3963
    Helixi400 – 41213
    Beta strandi420 – 4223
    Beta strandi425 – 4273
    Helixi429 – 4368
    Beta strandi461 – 4633
    Helixi464 – 4674
    Helixi474 – 4796
    Beta strandi482 – 4843
    Turni485 – 4906
    Helixi491 – 50212
    Beta strandi505 – 51511
    Beta strandi518 – 5214
    Helixi523 – 53210
    Turni533 – 5353
    Beta strandi539 – 54810
    Helixi551 – 5544
    Beta strandi557 – 5593
    Helixi564 – 5707
    Helixi573 – 5797
    Helixi581 – 5833
    Turni585 – 5873
    Helixi588 – 5914
    Beta strandi594 – 6018
    Turni617 – 6193
    Beta strandi622 – 6243
    Helixi628 – 64619
    Turni647 – 6504
    Beta strandi661 – 6644
    Helixi667 – 6759
    Helixi683 – 6875
    Helixi689 – 69810
    Beta strandi702 – 7043
    Helixi706 – 7094
    Turni710 – 7134
    Helixi721 – 7266
    Beta strandi731 – 7333
    Helixi738 – 7414
    Beta strandi744 – 7463
    Helixi747 – 75913
    Helixi763 – 77614
    Helixi781 – 7877
    Turni790 – 7934
    Beta strandi794 – 7963
    Helixi797 – 7993
    Helixi802 – 8054
    Helixi809 – 82618
    Turni827 – 8293

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2A3LX-ray3.34A139-839[»]
    ProteinModelPortaliO80452.
    SMRiO80452. Positions 212-839.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO80452.

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei8 – 2821HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni462 – 4676Substrate binding
    Regioni737 – 7404Substrate binding

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi86 – 927Poly-Gly
    Compositional biasi158 – 1614Poly-Asp

    Sequence similaritiesi

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiCOG1816.
    HOGENOMiHOG000092200.
    InParanoidiO80452.
    KOiK01490.
    OMAiHRVYSDN.
    PhylomeDBiO80452.

    Family and domain databases

    InterProiIPR006650. A/AMP_deam_AS.
    IPR001365. A/AMP_deaminase_dom.
    IPR006329. AMPD.
    [Graphical view]
    PANTHERiPTHR11359. PTHR11359. 1 hit.
    PfamiPF00962. A_deaminase. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01429. AMP_deaminase. 1 hit.
    PROSITEiPS00485. A_DEAMINASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O80452-1 [UniParc]FASTAAdd to Basket

    « Hide

    MEPNIYQLAL AALFGASFVA VSGFFMHFKA LNLVLERGKE RKENPDGDEP    50
    QNPTLVRRRS QVRRKVNDQY GRSPASLPDA TPFTDGGGGG GGDTGRSNGH 100
    VYVDEIPPGL PRLHTPSEGR ASVHGASSIR KTGSFVRPIS PKSPVASASA 150
    FESVEESDDD DNLTNSEGLD ASYLQANGDN EMPADANEEQ ISMAASSMIR 200
    SHSVSGDLHG VQPDPIAADI LRKEPEQETF VRLNVPLEVP TSDEVEAYKC 250
    LQECLELRKR YVFQETVAPW EKEVISDPST PKPNTEPFAH YPQGKSDHCF 300
    EMQDGVVHVF ANKDAKEDLF PVADATAFFT DLHHVLKVIA AGNIRTLCHR 350
    RLVLLEQKFN LHLMLNADKE FLAQKSAPHR DFYNVRKVDT HVHHSACMNQ 400
    KHLLRFIKSK LRKEPDEVVI FRDGTYLTLR EVFESLDLTG YDLNVDLLDV 450
    HADKSTFHRF DKFNLKYNPC GQSRLREIFL KQDNLIQGRF LGEITKQVFS 500
    DLEASKYQMA EYRISIYGRK MSEWDQLASW IVNNDLYSEN VVWLIQLPRL 550
    YNIYKDMGIV TSFQNILDNI FIPLFEATVD PDSHPQLHVF LKQVVGFDLV 600
    DDESKPERRP TKHMPTPAQW TNAFNPAFSY YVYYCYANLY VLNKLRESKG 650
    MTTITLRPHS GEAGDIDHLA ATFLTCHSIA HGINLRKSPV LQYLYYLAQI 700
    GLAMSPLSNN SLFLDYHRNP FPVFFLRGLN VSLSTDDPLQ IHLTKEPLVE 750
    EYSIAASVWK LSACDLCEIA RNSVYQSGFS HALKSHWIGK DYYKRGPDGN 800
    DIHKTNVPHI RVEFRDTIWK EEMQQVYLGK AVISDEVVP 839
    Length:839
    Mass (Da):95,130
    Last modified:June 1, 2002 - v2
    Checksum:i188F1F4A589A17DA
    GO

    Sequence cautioni

    The sequence BAD94943.1 differs from that shown. Reason: Intron retention.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti324 – 3241D → G in BAH19646. (PubMed:19423640)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC003028 Genomic DNA. Translation: AAC27176.2.
    CP002685 Genomic DNA. Translation: AEC09516.1.
    CP002685 Genomic DNA. Translation: AEC09517.1.
    AY056301 mRNA. Translation: AAL07150.1.
    AY133852 mRNA. Translation: AAM91786.1.
    AK316943 mRNA. Translation: BAH19646.1.
    AK221552 mRNA. Translation: BAD94943.1. Sequence problems.
    PIRiT01259.
    RefSeqiNP_565886.1. NM_129384.2.
    NP_850294.1. NM_179963.2.
    UniGeneiAt.12466.

    Genome annotation databases

    EnsemblPlantsiAT2G38280.1; AT2G38280.1; AT2G38280.
    AT2G38280.2; AT2G38280.2; AT2G38280.
    GeneIDi818408.
    KEGGiath:AT2G38280.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC003028 Genomic DNA. Translation: AAC27176.2 .
    CP002685 Genomic DNA. Translation: AEC09516.1 .
    CP002685 Genomic DNA. Translation: AEC09517.1 .
    AY056301 mRNA. Translation: AAL07150.1 .
    AY133852 mRNA. Translation: AAM91786.1 .
    AK316943 mRNA. Translation: BAH19646.1 .
    AK221552 mRNA. Translation: BAD94943.1 . Sequence problems.
    PIRi T01259.
    RefSeqi NP_565886.1. NM_129384.2.
    NP_850294.1. NM_179963.2.
    UniGenei At.12466.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2A3L X-ray 3.34 A 139-839 [» ]
    ProteinModelPortali O80452.
    SMRi O80452. Positions 212-839.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 3750. 5 interactions.
    IntActi O80452. 2 interactions.

    Proteomic databases

    PaxDbi O80452.
    PRIDEi O80452.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT2G38280.1 ; AT2G38280.1 ; AT2G38280 .
    AT2G38280.2 ; AT2G38280.2 ; AT2G38280 .
    GeneIDi 818408.
    KEGGi ath:AT2G38280.

    Organism-specific databases

    TAIRi AT2G38280.

    Phylogenomic databases

    eggNOGi COG1816.
    HOGENOMi HOG000092200.
    InParanoidi O80452.
    KOi K01490.
    OMAi HRVYSDN.
    PhylomeDBi O80452.

    Enzyme and pathway databases

    UniPathwayi UPA00591 ; UER00663 .
    BioCyci ARA:AT2G38280-MONOMER.
    ARA:GQT-2641-MONOMER.
    SABIO-RK O80452.

    Miscellaneous databases

    EvolutionaryTracei O80452.
    PROi O80452.

    Gene expression databases

    Genevestigatori O80452.

    Family and domain databases

    InterProi IPR006650. A/AMP_deam_AS.
    IPR001365. A/AMP_deaminase_dom.
    IPR006329. AMPD.
    [Graphical view ]
    PANTHERi PTHR11359. PTHR11359. 1 hit.
    Pfami PF00962. A_deaminase. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR01429. AMP_deaminase. 1 hit.
    PROSITEi PS00485. A_DEAMINASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "EMBRYONIC FACTOR 1 encodes an AMP deaminase and is essential for the zygote to embryo transition in Arabidopsis."
      Xu J., Zhang H.-Y., Xie C.-H., Xue H.-W., Dijkhuis P., Liu C.-M.
      Plant J. 42:743-756(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF ASP-598, FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
      Strain: cv. Landsberg erecta.
    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.
    5. "Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs."
      Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K.
      DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    6. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
      Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
      , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
      Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-357.
      Strain: cv. Columbia.
    7. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-134; SER-140 AND SER-203, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Root.
    8. "Toward an interaction map of the two-component signaling pathway of Arabidopsis thaliana."
      Dortay H., Gruhn N., Pfeifer A., Schwerdtner M., Schmuelling T., Heyl A.
      J. Proteome Res. 7:3649-3660(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH AHK4.
    9. "Crystallization and preliminary X-ray crystallographic analysis of adenosine 5'-monophosphate deaminase (AMPD) from Arabidopsis thaliana in complex with coformycin 5'-phosphate."
      Han B.W., Bingman C.A., Mahnke D.K., Sabina R.L., Phillips G.N. Jr.
      Acta Crystallogr. F 61:740-742(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: CRYSTALLIZATION, X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF 140-839 IN COMPLEX WITH COFORMYCIN 5'-PHOSPHATE AND ZINC IONS.
    10. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
      Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
      Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "Membrane association, mechanism of action, and structure of Arabidopsis embryonic factor 1 (FAC1)."
      Han B.W., Bingman C.A., Mahnke D.K., Bannen R.M., Bednarek S.Y., Sabina R.L., Phillips G.N. Jr.
      J. Biol. Chem. 281:14939-14947(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF 140-839 IN COMPLEX WITH COFORMYCIN 5'-PHOSPHATE; PHOSPHATE AND ZINC IONS, CATALYTIC ACTIVITY, SUBUNIT, COFACTOR, SUBCELLULAR LOCATION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.

    Entry informationi

    Entry nameiAMPD_ARATH
    AccessioniPrimary (citable) accession number: O80452
    Secondary accession number(s): B9DFX9, Q56XX1, Q93ZR9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2006
    Last sequence update: June 1, 2002
    Last modified: October 1, 2014
    This is version 104 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    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