O80452 (AMPD_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	839 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	Nucleotide metabolism
Cellular component	Endoplasmic reticulum Membrane Microsome
Domain	Transmembrane Transmembrane helix
Ligand	ATP-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Hydrolase
PTM	Phosphoprotein
Technical term	3D-structure Allosteric enzyme Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	IMP salvage Inferred from electronic annotation. Source: UniProtKB-UniPathway embryo development ending in seed dormancy Inferred from mutant phenotype Ref.1. Source: TAIR response to abscisic acid stimulus Inferred from direct assay PubMed 20733066. Source: TAIR
Cellular_component	cytosol Inferred from direct assay Ref.7PubMed 21166475. Source: TAIR endoplasmic reticulum Inferred from electronic annotation. Source: UniProtKB-KW integral to mitochondrial outer membrane Inferred from direct assay PubMed 21896887. Source: TAIR nucleus Inferred from direct assay Ref.7. Source: TAIR
Molecular_function	AMP deaminase activity Inferred from genetic interaction Ref.1. Source: TAIR ATP binding Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
AHK4	Q9C5U0	2	EBI-1807679,EBI-1100775

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 839

839

AMP deaminase

PRO_0000238455

Regions

Transmembrane

8 – 28

21

Helical; Potential

Nucleotide binding

289 – 296

8

ATP Potential

Region

462 – 467

6

Substrate binding

Region

737 – 740

4

Substrate binding

Compositional bias

86 – 92

7

Poly-Gly

Compositional bias

158 – 161

4

Poly-Asp

Sites

Active site

681

1

Proton acceptor Probable

Metal binding

391

1

Zinc; catalytic

Metal binding

393

1

Zinc; catalytic

Metal binding

659

1

Zinc; catalytic

Metal binding

736

1

Zinc; catalytic

Binding site

393

1

Substrate

Binding site

662

1

Substrate

Amino acid modifications

Modified residue

128

1

Phosphoserine Ref.9

Modified residue

132

1

Phosphothreonine Ref.9

Modified residue

134

1

Phosphoserine Ref.7

Modified residue

140

1

Phosphoserine Ref.7 Ref.9

Modified residue

203

1

Phosphoserine Ref.7

Modified residue

279

1

Phosphoserine Ref.9

Experimental info

Mutagenesis

598

1

D → N in fac1-1; zygote-lethal phenotype. Ref.1

Sequence conflict

324

1

D → G in BAH19646. Ref.5

Secondary structure

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839

Helix Strand Turn

Details...

Turn

215 – 217

3

Turn

244 – 247

4

Helix

248 – 259

12

Helix

325 – 338

14

Helix

342 – 373

32

Helix

374 – 376

3

Turn

382 – 384

3

Beta strand

387 – 393

7

Turn

394 – 396

3

Helix

400 – 412

13

Beta strand

420 – 422

3

Beta strand

425 – 427

3

Helix

429 – 436

8

Beta strand

461 – 463

3

Helix

464 – 467

4

Helix

474 – 479

6

Beta strand

482 – 484

3

Turn

485 – 490

6

Helix

491 – 502

12

Beta strand

505 – 515

11

Beta strand

518 – 521

4

Helix

523 – 532

10

Turn

533 – 535

3

Beta strand

539 – 548

10

Helix

551 – 554

4

Beta strand

557 – 559

3

Helix

564 – 570

7

Helix

573 – 579

7

Helix

581 – 583

3

Turn

585 – 587

3

Helix

588 – 591

4

Beta strand

594 – 601

8

Turn

617 – 619

3

Beta strand

622 – 624

3

Helix

628 – 646

19

Turn

647 – 650

4

Beta strand

661 – 664

4

Helix

667 – 675

9

Helix

683 – 687

5

Helix

689 – 698

10

Beta strand

702 – 704

3

Helix

706 – 709

4

Turn

710 – 713

4

Helix

721 – 726

6

Beta strand

731 – 733

3

Helix

738 – 741

4

Beta strand

744 – 746

3

Helix

747 – 759

13

Helix

763 – 776

14

Helix

781 – 787

7

Turn

790 – 793

4

Beta strand

794 – 796

3

Helix

797 – 799

3

Helix

802 – 805

4

Helix

809 – 826

18

Turn

827 – 829

3

Sequences

	Sequence		Length	Mass (Da)
	O80452 [UniParc]. Last modified June 1, 2002. Version 2. Checksum: 188F1F4A589A17DA	FASTA	839	95,130
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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]	"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, MASS SPECTROMETRY. 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]	"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-128; THR-132; SER-140 AND SER-279, MASS SPECTROMETRY. Strain: cv. Columbia. Tissue: Seedling.
[10]	"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.
[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.
+	Additional computationally mapped references.

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.

IPI

IPI00546126.

PIR

T01259.

RefSeq

NP_565886.1. NM_129384.2.
NP_850294.1. NM_179963.2.

UniGene

At.12466.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2A3L	X-ray	3.34	A	140-839	[»]

ProteinModelPortal

O80452.

SMR

O80452. Positions 212-839.

ModBase

Search...

Protein-protein interaction databases

IntAct

O80452. 2 interactions.

Proteomic databases

PaxDb

O80452.

PRIDE

O80452.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT2G38280.1; AT2G38280.1; AT2G38280.
AT2G38280.2; AT2G38280.2; AT2G38280.

GeneID

818408.

KEGG

ath:AT2G38280.

Organism-specific databases

TAIR

At2g38280.

Phylogenomic databases

eggNOG

COG1816.

HOGENOM

HOG000092200.

InParanoid

O80452.

KO

K01490.

OMA

SLQNFCK.

PhylomeDB

O80452.

ProtClustDB

PLN02768.

Enzyme and pathway databases

SABIO-RK

O80452.

UniPathway

UPA00591; UER00663.

Gene expression databases

Genevestigator

O80452.

GermOnline

AT2G38280. Arabidopsis thaliana.

Family and domain databases

InterPro

IPR006650. A/AMP_deam_AS.
IPR001365. A/AMP_deaminase_dom.
IPR006329. AMP_deaminase.
[Graphical view]

PANTHER

PTHR11359. PTHR11359. 1 hit.

Pfam

PF00962. A_deaminase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01429. AMP_deaminase. 1 hit.

PROSITE

PS00485. A_DEAMINASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

O80452.

Entry information

Entry name

AMPD_ARATH

Accession

Primary (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:	May 1, 2013
This is version 91 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program