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O80452

- AMPD_ARATH

UniProt

O80452 - AMPD_ARATH

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Protein
AMP deaminase
Gene
AMPD, FAC1, At2g38280, F16M14.21
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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)

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

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

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 acceptor Inferred
Metal bindingi736 – 7361Zinc; catalytic

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi289 – 2968ATP Reviewed prediction

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

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

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei8 – 2821Helical; Reviewed prediction
Add
BLAST

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
Complete GO annotation...

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 deaminase
PRO_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 AHK4.2 Publications

Binary interactionsi

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

Protein-protein interaction databases

BioGridi3750. 5 interactions.
IntActiO80452. 2 interactions.

Structurei

Secondary structure

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.

Miscellaneous databases

EvolutionaryTraceiO80452.

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.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti324 – 3241D → G in BAH19646. 1 Publication

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 103 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

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