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Protein

AMP deaminase

Gene

AMPD

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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

Zn2+1 PublicationNote: 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
  1. Vmax=17 µmol/min/mg enzyme (in the absence of ATP)1 Publication
  2. Vmax=375 µmol/min/mg enzyme (in the presence of 1 mM ATP)1 Publication

Pathwayi: IMP biosynthesis via salvage pathway

This protein is involved in step 1 of the subpathway that synthesizes IMP from AMP.
Proteins known to be involved in this subpathway in this organism are:
  1. AMP deaminase (AMPD)
This subpathway is part of the pathway IMP biosynthesis via salvage pathway, which is itself part of Purine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes IMP from AMP, the pathway IMP biosynthesis via salvage pathway and in Purine metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi391Zinc; catalytic1
Metal bindingi393Zinc; catalytic1
Binding sitei393Substrate1
Metal bindingi659Zinc; catalytic1
Binding sitei662Substrate1
Active sitei681Proton acceptorCurated1
Metal bindingi736Zinc; catalytic1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi289 – 296ATPSequence analysis8

GO - Molecular functioni

  • AMP deaminase activity Source: UniProtKB-EC
  • ATP binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • protein histidine kinase binding Source: UniProtKB

GO - Biological processi

  • embryo development ending in seed dormancy Source: TAIR
  • IMP salvage Source: UniProtKB-UniPathway
  • 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.
BRENDAi3.5.4.6. 399.
ReactomeiR-ATH-6798695. Neutrophil degranulation.
R-ATH-74217. Purine salvage.
SABIO-RKO80452.
UniPathwayiUPA00591; UER00663.

Names & Taxonomyi

Protein namesi
Recommended name:
AMP deaminase1 Publication (EC:3.5.4.6Curated)
Short name:
AtAMPD1 Publication
Alternative name(s):
Protein EMBRYONIC FACTOR 11 Publication
Gene namesi
Name:AMPD1 Publication
Synonyms:FAC11 Publication
Ordered Locus Names:At2g38280Imported
ORF Names:F16M14.21Imported
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G38280.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei8 – 28HelicalSequence analysisAdd BLAST21

GO - Cellular componenti

  • cytosol Source: TAIR
  • endoplasmic reticulum Source: UniProtKB-KW
  • integral component of mitochondrial outer membrane Source: TAIR
  • intracellular membrane-bounded organelle Source: TAIR
  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane, Microsome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi598D → N in fac1-1; zygote-lethal phenotype. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL2366458.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002384551 – 839AMP deaminaseAdd BLAST839

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei134PhosphoserineCombined sources1
Modified residuei140PhosphoserineCombined sources1
Modified residuei203PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiO80452.

PTM databases

iPTMnetiO80452.

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

GenevisibleiO80452. AT.

Interactioni

Subunit structurei

Homodimer. Interacts with AHK4. Interacts with EER5 (PubMed:19843313).4 Publications

Binary interactionsi

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

GO - Molecular functioni

  • protein histidine kinase binding Source: UniProtKB

Protein-protein interaction databases

BioGridi3750. 5 interactors.
IntActiO80452. 2 interactors.
STRINGi3702.AT2G38280.1.

Chemistry databases

BindingDBiO80452.

Structurei

Secondary structure

1839
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni215 – 217Combined sources3
Turni244 – 247Combined sources4
Helixi248 – 259Combined sources12
Helixi325 – 338Combined sources14
Helixi342 – 373Combined sources32
Helixi374 – 376Combined sources3
Turni382 – 384Combined sources3
Beta strandi387 – 393Combined sources7
Turni394 – 396Combined sources3
Helixi400 – 412Combined sources13
Beta strandi420 – 422Combined sources3
Beta strandi425 – 427Combined sources3
Helixi429 – 436Combined sources8
Beta strandi461 – 463Combined sources3
Helixi464 – 467Combined sources4
Helixi474 – 479Combined sources6
Beta strandi482 – 484Combined sources3
Turni485 – 490Combined sources6
Helixi491 – 502Combined sources12
Beta strandi505 – 515Combined sources11
Beta strandi518 – 521Combined sources4
Helixi523 – 532Combined sources10
Turni533 – 535Combined sources3
Beta strandi539 – 548Combined sources10
Helixi551 – 554Combined sources4
Beta strandi557 – 559Combined sources3
Helixi564 – 570Combined sources7
Helixi573 – 579Combined sources7
Helixi581 – 583Combined sources3
Turni585 – 587Combined sources3
Helixi588 – 591Combined sources4
Beta strandi594 – 601Combined sources8
Turni617 – 619Combined sources3
Beta strandi622 – 624Combined sources3
Helixi628 – 646Combined sources19
Turni647 – 650Combined sources4
Beta strandi661 – 664Combined sources4
Helixi667 – 675Combined sources9
Helixi683 – 687Combined sources5
Helixi689 – 698Combined sources10
Beta strandi702 – 704Combined sources3
Helixi706 – 709Combined sources4
Turni710 – 713Combined sources4
Helixi721 – 726Combined sources6
Beta strandi731 – 733Combined sources3
Helixi738 – 741Combined sources4
Beta strandi744 – 746Combined sources3
Helixi747 – 759Combined sources13
Helixi763 – 776Combined sources14
Helixi781 – 787Combined sources7
Turni790 – 793Combined sources4
Beta strandi794 – 796Combined sources3
Helixi797 – 799Combined sources3
Helixi802 – 805Combined sources4
Helixi809 – 826Combined sources18
Turni827 – 829Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2A3LX-ray3.34A139-839[»]
ProteinModelPortaliO80452.
SMRiO80452.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO80452.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni462 – 467Substrate binding6
Regioni737 – 740Substrate binding4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi86 – 92Poly-Gly7
Compositional biasi158 – 161Poly-Asp4

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG1096. Eukaryota.
COG1816. LUCA.
HOGENOMiHOG000092200.
InParanoidiO80452.
KOiK01490.
OMAiYPQGKSD.
OrthoDBiEOG093602O5.
PhylomeDBiO80452.

Family and domain databases

CDDicd01319. AMPD. 1 hit.
InterProiIPR006650. A/AMP_deam_AS.
IPR001365. A/AMP_deaminase_dom.
IPR006329. AMPD.
IPR032466. Metal_Hydrolase.
[Graphical view]
PANTHERiPTHR11359. PTHR11359. 1 hit.
PfamiPF00962. A_deaminase. 1 hit.
[Graphical view]
SUPFAMiSSF51556. SSF51556. 1 hit.
TIGRFAMsiTIGR01429. AMP_deaminase. 1 hit.
PROSITEiPS00485. A_DEAMINASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O80452-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEPNIYQLAL AALFGASFVA VSGFFMHFKA LNLVLERGKE RKENPDGDEP
60 70 80 90 100
QNPTLVRRRS QVRRKVNDQY GRSPASLPDA TPFTDGGGGG GGDTGRSNGH
110 120 130 140 150
VYVDEIPPGL PRLHTPSEGR ASVHGASSIR KTGSFVRPIS PKSPVASASA
160 170 180 190 200
FESVEESDDD DNLTNSEGLD ASYLQANGDN EMPADANEEQ ISMAASSMIR
210 220 230 240 250
SHSVSGDLHG VQPDPIAADI LRKEPEQETF VRLNVPLEVP TSDEVEAYKC
260 270 280 290 300
LQECLELRKR YVFQETVAPW EKEVISDPST PKPNTEPFAH YPQGKSDHCF
310 320 330 340 350
EMQDGVVHVF ANKDAKEDLF PVADATAFFT DLHHVLKVIA AGNIRTLCHR
360 370 380 390 400
RLVLLEQKFN LHLMLNADKE FLAQKSAPHR DFYNVRKVDT HVHHSACMNQ
410 420 430 440 450
KHLLRFIKSK LRKEPDEVVI FRDGTYLTLR EVFESLDLTG YDLNVDLLDV
460 470 480 490 500
HADKSTFHRF DKFNLKYNPC GQSRLREIFL KQDNLIQGRF LGEITKQVFS
510 520 530 540 550
DLEASKYQMA EYRISIYGRK MSEWDQLASW IVNNDLYSEN VVWLIQLPRL
560 570 580 590 600
YNIYKDMGIV TSFQNILDNI FIPLFEATVD PDSHPQLHVF LKQVVGFDLV
610 620 630 640 650
DDESKPERRP TKHMPTPAQW TNAFNPAFSY YVYYCYANLY VLNKLRESKG
660 670 680 690 700
MTTITLRPHS GEAGDIDHLA ATFLTCHSIA HGINLRKSPV LQYLYYLAQI
710 720 730 740 750
GLAMSPLSNN SLFLDYHRNP FPVFFLRGLN VSLSTDDPLQ IHLTKEPLVE
760 770 780 790 800
EYSIAASVWK LSACDLCEIA RNSVYQSGFS HALKSHWIGK DYYKRGPDGN
810 820 830
DIHKTNVPHI RVEFRDTIWK EEMQQVYLGK AVISDEVVP
Length:839
Mass (Da):95,130
Last modified:June 1, 2002 - v2
Checksum:i188F1F4A589A17DA
GO

Sequence cautioni

The sequence BAD94943 differs from that shown. Intron retention.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti324D → G in BAH19646 (PubMed:19423640).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_129384.3.
NP_850294.1. NM_179963.3.
UniGeneiAt.12466.

Genome annotation databases

EnsemblPlantsiAT2G38280.1; AT2G38280.1; AT2G38280.
AT2G38280.2; AT2G38280.2; AT2G38280.
GeneIDi818408.
GrameneiAT2G38280.1; AT2G38280.1; AT2G38280.
AT2G38280.2; AT2G38280.2; AT2G38280.
KEGGiath:AT2G38280.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_129384.3.
NP_850294.1. NM_179963.3.
UniGeneiAt.12466.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2A3LX-ray3.34A139-839[»]
ProteinModelPortaliO80452.
SMRiO80452.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi3750. 5 interactors.
IntActiO80452. 2 interactors.
STRINGi3702.AT2G38280.1.

Chemistry databases

BindingDBiO80452.
ChEMBLiCHEMBL2366458.

PTM databases

iPTMnetiO80452.

Proteomic databases

PaxDbiO80452.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G38280.1; AT2G38280.1; AT2G38280.
AT2G38280.2; AT2G38280.2; AT2G38280.
GeneIDi818408.
GrameneiAT2G38280.1; AT2G38280.1; AT2G38280.
AT2G38280.2; AT2G38280.2; AT2G38280.
KEGGiath:AT2G38280.

Organism-specific databases

TAIRiAT2G38280.

Phylogenomic databases

eggNOGiKOG1096. Eukaryota.
COG1816. LUCA.
HOGENOMiHOG000092200.
InParanoidiO80452.
KOiK01490.
OMAiYPQGKSD.
OrthoDBiEOG093602O5.
PhylomeDBiO80452.

Enzyme and pathway databases

UniPathwayiUPA00591; UER00663.
BioCyciARA:AT2G38280-MONOMER.
BRENDAi3.5.4.6. 399.
ReactomeiR-ATH-6798695. Neutrophil degranulation.
R-ATH-74217. Purine salvage.
SABIO-RKO80452.

Miscellaneous databases

EvolutionaryTraceiO80452.
PROiO80452.

Gene expression databases

GenevisibleiO80452. AT.

Family and domain databases

CDDicd01319. AMPD. 1 hit.
InterProiIPR006650. A/AMP_deam_AS.
IPR001365. A/AMP_deaminase_dom.
IPR006329. AMPD.
IPR032466. Metal_Hydrolase.
[Graphical view]
PANTHERiPTHR11359. PTHR11359. 1 hit.
PfamiPF00962. A_deaminase. 1 hit.
[Graphical view]
SUPFAMiSSF51556. SSF51556. 1 hit.
TIGRFAMsiTIGR01429. AMP_deaminase. 1 hit.
PROSITEiPS00485. A_DEAMINASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 30, 2016
This is version 118 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

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.