Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

O80452 (AMPD_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 99. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
AMP deaminase

Short name=AtAMPD
EC=3.5.4.6
Alternative name(s):
Protein EMBRYONIC FACTOR 1
Gene names
Name:AMPD
Synonyms:FAC1
Ordered Locus Names:At2g38280
ORF Names:F16M14.21
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length839 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Catalytic activity

AMP + H2O = IMP + NH3. Ref.11

Cofactor

Binds 1 zinc ion per subunit. Ref.11

Enzyme regulation

Activated by ATP. Activated by sulfate ions (in vitro). Inhibited by phosphate ions. Ref.11

Pathway

Purine metabolism; IMP biosynthesis via salvage pathway; IMP from AMP: step 1/1.

Subunit structure

Homodimer. Interacts with AHK4. Ref.8 Ref.11

Subcellular location

Membrane; Single-pass membrane protein. Microsome membrane. Note: Might be associated with the inner mitochondrial membrane By similarity. Ref.11

Tissue specificity

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

Developmental stage

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. Ref.1

Sequence similarities

Belongs to the adenosine and AMP deaminases family.

Biophysicochemical properties

Kinetic parameters:

KM=6.7 mM for AMP (in the absence of ATP) Ref.11

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)

Sequence caution

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

Binary interactions

With

Entry

#Exp.

IntAct

Notes

AHK4Q9C5U02EBI-1807679,EBI-1100775

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 839839AMP deaminase
PRO_0000238455

Regions

Transmembrane8 – 2821Helical; Potential
Nucleotide binding289 – 2968ATP Potential
Region462 – 4676Substrate binding
Region737 – 7404Substrate binding
Compositional bias86 – 927Poly-Gly
Compositional bias158 – 1614Poly-Asp

Sites

Active site6811Proton acceptor Probable
Metal binding3911Zinc; catalytic
Metal binding3931Zinc; catalytic
Metal binding6591Zinc; catalytic
Metal binding7361Zinc; catalytic
Binding site3931Substrate
Binding site6621Substrate

Amino acid modifications

Modified residue1341Phosphoserine Ref.7
Modified residue1401Phosphoserine Ref.7
Modified residue2031Phosphoserine Ref.7

Experimental info

Mutagenesis5981D → N in fac1-1; zygote-lethal phenotype. Ref.1
Sequence conflict3241D → G in BAH19646. Ref.5

Secondary structure

................................................................................................... 839
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O80452 [UniParc].

Last modified June 1, 2002. Version 2.
Checksum: 188F1F4A589A17DA

FASTA83995,130
        10         20         30         40         50         60 
MEPNIYQLAL AALFGASFVA VSGFFMHFKA LNLVLERGKE RKENPDGDEP QNPTLVRRRS 

        70         80         90        100        110        120 
QVRRKVNDQY GRSPASLPDA TPFTDGGGGG GGDTGRSNGH VYVDEIPPGL PRLHTPSEGR 

       130        140        150        160        170        180 
ASVHGASSIR KTGSFVRPIS PKSPVASASA FESVEESDDD DNLTNSEGLD ASYLQANGDN 

       190        200        210        220        230        240 
EMPADANEEQ ISMAASSMIR SHSVSGDLHG VQPDPIAADI LRKEPEQETF VRLNVPLEVP 

       250        260        270        280        290        300 
TSDEVEAYKC LQECLELRKR YVFQETVAPW EKEVISDPST PKPNTEPFAH YPQGKSDHCF 

       310        320        330        340        350        360 
EMQDGVVHVF ANKDAKEDLF PVADATAFFT DLHHVLKVIA AGNIRTLCHR RLVLLEQKFN 

       370        380        390        400        410        420 
LHLMLNADKE FLAQKSAPHR DFYNVRKVDT HVHHSACMNQ KHLLRFIKSK LRKEPDEVVI 

       430        440        450        460        470        480 
FRDGTYLTLR EVFESLDLTG YDLNVDLLDV HADKSTFHRF DKFNLKYNPC GQSRLREIFL 

       490        500        510        520        530        540 
KQDNLIQGRF LGEITKQVFS DLEASKYQMA EYRISIYGRK MSEWDQLASW IVNNDLYSEN 

       550        560        570        580        590        600 
VVWLIQLPRL YNIYKDMGIV TSFQNILDNI FIPLFEATVD PDSHPQLHVF LKQVVGFDLV 

       610        620        630        640        650        660 
DDESKPERRP TKHMPTPAQW TNAFNPAFSY YVYYCYANLY VLNKLRESKG MTTITLRPHS 

       670        680        690        700        710        720 
GEAGDIDHLA ATFLTCHSIA HGINLRKSPV LQYLYYLAQI GLAMSPLSNN SLFLDYHRNP 

       730        740        750        760        770        780 
FPVFFLRGLN VSLSTDDPLQ IHLTKEPLVE EYSIAASVWK LSACDLCEIA RNSVYQSGFS 

       790        800        810        820        830 
HALKSHWIGK DYYKRGPDGN DIHKTNVPHI RVEFRDTIWK EEMQQVYLGK AVISDEVVP 

« Hide

References

« Hide 'large scale' references
[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]"Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana."
Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D., Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V., Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S., Cronin L.A. expand/collapse author list , Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.
Nature 402:761-768(1999) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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. expand/collapse author list , 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]"Site-specific phosphorylation profiling of Arabidopsis proteins by mass spectrometry and peptide chip analysis."
de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E., Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J., Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.
J. Proteome Res. 7:2458-2470(2008) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRT01259.
RefSeqNP_565886.1. NM_129384.2.
NP_850294.1. NM_179963.2.
UniGeneAt.12466.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2A3LX-ray3.34A140-839[»]
ProteinModelPortalO80452.
SMRO80452. Positions 212-839.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid3750. 5 interactions.
IntActO80452. 2 interactions.

Proteomic databases

PaxDbO80452.
PRIDEO80452.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT2G38280.1; AT2G38280.1; AT2G38280.
AT2G38280.2; AT2G38280.2; AT2G38280.
GeneID818408.
KEGGath:AT2G38280.

Organism-specific databases

TAIRAT2G38280.

Phylogenomic databases

eggNOGCOG1816.
HOGENOMHOG000092200.
InParanoidO80452.
KOK01490.
OMAHRVYSDN.
PhylomeDBO80452.
ProtClustDBPLN02768.

Enzyme and pathway databases

BioCycARA:AT2G38280-MONOMER.
ARA:GQT-2641-MONOMER.
SABIO-RKO80452.
UniPathwayUPA00591; UER00663.

Gene expression databases

GenevestigatorO80452.

Family and domain databases

InterProIPR006650. A/AMP_deam_AS.
IPR001365. A/AMP_deaminase_dom.
IPR006329. AMP_deaminase.
[Graphical view]
PANTHERPTHR11359. PTHR11359. 1 hit.
PfamPF00962. A_deaminase. 1 hit.
[Graphical view]
TIGRFAMsTIGR01429. AMP_deaminase. 1 hit.
PROSITEPS00485. A_DEAMINASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO80452.
PROO80452.

Entry information

Entry nameAMPD_ARATH
AccessionPrimary (citable) accession number: O80452
Secondary accession number(s): B9DFX9, Q56XX1, Q93ZR9
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2006
Last sequence update: June 1, 2002
Last modified: April 16, 2014
This is version 99 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names