AMY3_ARATH
ID AMY3_ARATH Reviewed; 887 AA.
AC Q94A41; Q9CAR6;
DT 05-SEP-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Alpha-amylase 3, chloroplastic {ECO:0000303|PubMed:15637061};
DE Short=AtAMY3 {ECO:0000303|PubMed:15637061};
DE EC=3.2.1.1 {ECO:0000269|PubMed:24089528};
DE AltName: Full=1,4-alpha-D-glucan glucanohydrolase;
DE Flags: Precursor;
GN Name=AMY3 {ECO:0000303|PubMed:15637061};
GN OrderedLocusNames=At1g69830 {ECO:0000312|Araport:AT1G69830};
GN ORFNames=T17F3.14 {ECO:0000312|EMBL:AAG52558.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP INDUCTION.
RX PubMed=15347792; DOI=10.1104/pp.104.044347;
RA Smith S.M., Fulton D.C., Chia T., Thorneycroft D., Chapple A., Dunstan H.,
RA Hylton C., Zeeman S.C., Smith A.M.;
RT "Diurnal changes in the transcriptome encoding enzymes of starch metabolism
RT provide evidence for both transcriptional and posttranscriptional
RT regulation of starch metabolism in Arabidopsis leaves.";
RL Plant Physiol. 136:2687-2699(2004).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, INDUCTION, DOMAIN, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=15637061; DOI=10.1074/jbc.m413638200;
RA Yu T.S., Zeeman S.C., Thorneycroft D., Fulton D.C., Dunstan H., Lue W.L.,
RA Hegemann B., Tung S.Y., Umemoto T., Chapple A., Tsai D.L., Wang S.M.,
RA Smith A.M., Chen J., Smith S.M.;
RT "alpha-Amylase is not required for breakdown of transitory starch in
RT Arabidopsis leaves.";
RL J. Biol. Chem. 280:9773-9779(2005).
RN [6]
RP TISSUE SPECIFICITY.
RX PubMed=15927942; DOI=10.1093/pcp/pci141;
RA Kim Y.C., Nakajima M., Nakayama A., Yamaguchi I.;
RT "Contribution of gibberellins to the formation of Arabidopsis seed coat
RT through starch degradation.";
RL Plant Cell Physiol. 46:1317-1325(2005).
RN [7]
RP FUNCTION.
RX PubMed=19074683; DOI=10.1105/tpc.108.063487;
RA Streb S., Delatte T., Umhang M., Eicke S., Schorderet M., Reinhardt D.,
RA Zeeman S.C.;
RT "Starch granule biosynthesis in Arabidopsis is abolished by removal of all
RT debranching enzymes but restored by the subsequent removal of an
RT endoamylase.";
RL Plant Cell 20:3448-3466(2008).
RN [8]
RP FUNCTION.
RX PubMed=19141707; DOI=10.1105/tpc.108.064360;
RA Koetting O., Santelia D., Edner C., Eicke S., Marthaler T., Gentry M.S.,
RA Comparot-Moss S., Chen J., Smith A.M., Steup M., Ritte G., Zeeman S.C.;
RT "STARCH-EXCESS4 is a laforin-like Phosphoglucan phosphatase required for
RT starch degradation in Arabidopsis thaliana.";
RL Plant Cell 21:334-346(2009).
RN [9]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=21294843; DOI=10.1111/j.1742-4658.2011.08043.x;
RA Glaring M.A., Baumann M.J., Abou Hachem M., Nakai H., Nakai N.,
RA Santelia D., Sigurskjold B.W., Zeeman S.C., Blennow A., Svensson B.;
RT "Starch-binding domains in the CBM45 family--low-affinity domains from
RT glucan, water dikinase and alpha-amylase involved in plastidial starch
RT metabolism.";
RL FEBS J. 278:1175-1185(2011).
RN [10]
RP FUNCTION, MUTAGENESIS OF CYS-285; CYS-363; CYS-499; CYS-587; CYS-652 AND
RP ASP-666, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVITY
RP REGULATION.
RX PubMed=24089528; DOI=10.1074/jbc.m113.514794;
RA Seung D., Thalmann M., Sparla F., Abou Hachem M., Lee S.K.,
RA Issakidis-Bourguet E., Svensson B., Zeeman S.C., Santelia D.;
RT "Arabidopsis thaliana AMY3 is a unique redox-regulated chloroplastic alpha-
RT amylase.";
RL J. Biol. Chem. 288:33620-33633(2013).
RN [11]
RP FUNCTION, AND INDUCTION BY MANNITOL AND ABSCISIC ACID.
RX PubMed=27436713; DOI=10.1105/tpc.16.00143;
RA Thalmann M., Pazmino D., Seung D., Horrer D., Nigro A., Meier T.,
RA Koelling K., Pfeifhofer H.W., Zeeman S.C., Santelia D.;
RT "Regulation of leaf starch degradation by abscisic acid is important for
RT osmotic stress tolerance in plants.";
RL Plant Cell 28:1860-1878(2016).
CC -!- FUNCTION: Possesses endoamylolytic activity in vitro, but seems not
CC required for breakdown of transitory starch in leaves. May be involved
CC in the determination of the final structure of glucans by shortening
CC long linear phospho-oligosaccharides in the chloroplast stroma. Can act
CC on both soluble and insoluble glucan substrates to release small linear
CC and branched malto-oligosaccharides (PubMed:24089528). Works
CC synergistically with beta-amylase toward efficient starch degradation
CC (PubMed:24089528). Has activity against p-nitrophenyl maltoheptaoside
CC (BPNP-G7), amylopectin and beta-limit dextrin (PubMed:24089528).
CC Involved in stress-induced starch degradation (PubMed:27436713).
CC {ECO:0000269|PubMed:15637061, ECO:0000269|PubMed:19074683,
CC ECO:0000269|PubMed:19141707, ECO:0000269|PubMed:21294843,
CC ECO:0000269|PubMed:24089528, ECO:0000269|PubMed:27436713}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in
CC polysaccharides containing three or more (1->4)-alpha-linked D-
CC glucose units.; EC=3.2.1.1; Evidence={ECO:0000269|PubMed:24089528};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000250|UniProtKB:P00693};
CC -!- ACTIVITY REGULATION: Redox-regulated, with the highest activity under
CC reducing conditions. The midpoint redox potential is -329 mV. The
CC disulfide bridge between Cys-499 and Cys-587 inhibits catalysis.
CC Inhibited by CuCl(2) and H(2)O(2). {ECO:0000269|PubMed:24089528}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7.5 with p-nitrophenyl maltoheptaoside or amylopectin
CC as substrate. {ECO:0000269|PubMed:24089528};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:15637061, ECO:0000269|PubMed:21294843}.
CC -!- TISSUE SPECIFICITY: Expressed in developing siliques.
CC {ECO:0000269|PubMed:15927942}.
CC -!- INDUCTION: Circadian-regulation. Expression increases during the light
CC phase and decreases during the dark phase. Up-regulated during osmotic
CC stress and by abscisic acid (PubMed:27436713).
CC {ECO:0000269|PubMed:15347792, ECO:0000269|PubMed:15637061,
CC ECO:0000269|PubMed:27436713}.
CC -!- DOMAIN: The N-terminal domain is not required for endoamylolytic
CC activity. {ECO:0000269|PubMed:15637061}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions. {ECO:0000269|PubMed:15637061}.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 13 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG52558.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AC010675; AAG52558.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE34983.1; -; Genomic_DNA.
DR EMBL; AY050398; AAK91414.1; -; mRNA.
DR EMBL; BT000643; AAN18209.1; -; mRNA.
DR PIR; E96720; E96720.
DR RefSeq; NP_564977.1; NM_105651.5.
DR AlphaFoldDB; Q94A41; -.
DR SMR; Q94A41; -.
DR BioGRID; 28540; 3.
DR STRING; 3702.AT1G69830.1; -.
DR CAZy; CBM45; Carbohydrate-Binding Module Family 45.
DR CAZy; GH13; Glycoside Hydrolase Family 13.
DR iPTMnet; Q94A41; -.
DR MetOSite; Q94A41; -.
DR PaxDb; Q94A41; -.
DR PRIDE; Q94A41; -.
DR ProMEX; Q94A41; -.
DR ProteomicsDB; 244443; -.
DR EnsemblPlants; AT1G69830.1; AT1G69830.1; AT1G69830.
DR GeneID; 843319; -.
DR Gramene; AT1G69830.1; AT1G69830.1; AT1G69830.
DR KEGG; ath:AT1G69830; -.
DR Araport; AT1G69830; -.
DR TAIR; locus:2196759; AT1G69830.
DR eggNOG; KOG0471; Eukaryota.
DR HOGENOM; CLU_018421_0_0_1; -.
DR InParanoid; Q94A41; -.
DR OMA; IPGKWIL; -.
DR OrthoDB; 665362at2759; -.
DR PhylomeDB; Q94A41; -.
DR BioCyc; ARA:AT1G69830-MON; -.
DR PRO; PR:Q94A41; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q94A41; baseline and differential.
DR Genevisible; Q94A41; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0004556; F:alpha-amylase activity; IDA:TAIR.
DR GO; GO:0005509; F:calcium ion binding; IEA:InterPro.
DR GO; GO:0005983; P:starch catabolic process; TAS:TAIR.
DR GO; GO:0005987; P:sucrose catabolic process; IBA:GO_Central.
DR Gene3D; 2.60.40.1180; -; 1.
DR InterPro; IPR012850; A-amylase_bs_C.
DR InterPro; IPR006047; Glyco_hydro_13_cat_dom.
DR InterPro; IPR013780; Glyco_hydro_b.
DR InterPro; IPR017853; Glycoside_hydrolase_SF.
DR Pfam; PF07821; Alpha-amyl_C2; 1.
DR Pfam; PF00128; Alpha-amylase; 1.
DR SMART; SM00642; Aamy; 1.
DR SMART; SM00810; Alpha-amyl_C2; 1.
DR SUPFAM; SSF51445; SSF51445; 1.
PE 1: Evidence at protein level;
KW Carbohydrate metabolism; Chloroplast; Disulfide bond; Glycosidase;
KW Hydrolase; Metal-binding; Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..55
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 56..887
FT /note="Alpha-amylase 3, chloroplastic"
FT /id="PRO_0000418863"
FT ACT_SITE 666
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P04063"
FT ACT_SITE 691
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P04063"
FT BINDING 545..546
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P04063"
FT BINDING 664..669
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P04063"
FT BINDING 693
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 695
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P04063"
FT BINDING 712
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 754
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 760..762
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P04063"
FT BINDING 773
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 779
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 857
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 884
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT SITE 774
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT DISULFID 499..587
FT /evidence="ECO:0000269|PubMed:24089528"
FT MUTAGEN 285
FT /note="C->S: Reduced activity under reducing conditions and
FT no activity under oxidizing conditions."
FT /evidence="ECO:0000269|PubMed:24089528"
FT MUTAGEN 363
FT /note="C->S: Increased activity under reducing conditions,
FT but no activity under oxidizing conditions."
FT /evidence="ECO:0000269|PubMed:24089528"
FT MUTAGEN 499
FT /note="C->S: Loss of activity under reducing or oxidizing
FT conditions."
FT /evidence="ECO:0000269|PubMed:24089528"
FT MUTAGEN 587
FT /note="C->S: Low activity under reducing conditions, but
FT retains activity under oxidizing conditions."
FT /evidence="ECO:0000269|PubMed:24089528"
FT MUTAGEN 652
FT /note="C->S: Reduced activity under reducing conditions and
FT no activity under oxidizing conditions."
FT /evidence="ECO:0000269|PubMed:24089528"
FT MUTAGEN 666
FT /note="D->N: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:24089528"
SQ SEQUENCE 887 AA; 99842 MW; 8EA417384B1AEB69 CRC64;
MSTVPIESLL HHSYLRHNSK VNRGNRSFIP ISLNLRSHFT SNKLLHSIGK SVGVSSMNKS
PVAIRATSSD TAVVETAQSD DVIFKEIFPV QRIEKAEGKI YVRLKEVKEK NWELSVGCSI
PGKWILHWGV SYVGDTGSEW DQPPEDMRPP GSIAIKDYAI ETPLKKLSEG DSFFEVAINL
NLESSVAALN FVLKDEETGA WYQHKGRDFK VPLVDDVPDN GNLIGAKKGF GALGQLSNIP
LKQDKSSAET DSIEERKGLQ EFYEEMPISK RVADDNSVSV TARKCPETSK NIVSIETDLP
GDVTVHWGVC KNGTKKWEIP SEPYPEETSL FKNKALRTRL QRKDDGNGSF GLFSLDGKLE
GLCFVLKLNE NTWLNYRGED FYVPFLTSSS SPVETEAAQV SKPKRKTDKE VSASGFTKEI
ITEIRNLAID ISSHKNQKTN VKEVQENILQ EIEKLAAEAY SIFRSTTPAF SEEGVLEAEA
DKPDIKISSG TGSGFEILCQ GFNWESNKSG RWYLELQEKA DELASLGFTV LWLPPPTESV
SPEGYMPKDL YNLNSRYGTI DELKDTVKKF HKVGIKVLGD AVLNHRCAHF KNQNGVWNLF
GGRLNWDDRA VVADDPHFQG RGNKSSGDNF HAAPNIDHSQ DFVRKDIKEW LCWMMEEVGY
DGWRLDFVRG FWGGYVKDYM DASKPYFAVG EYWDSLSYTY GEMDYNQDAH RQRIVDWINA
TSGAAGAFDV TTKGILHTAL QKCEYWRLSD PKGKPPGVVG WWPSRAVTFI ENHDTGSTQG
HWRFPEGKEM QGYAYILTHP GTPAVFFDHI FSDYHSEIAA LLSLRNRQKL HCRSEVNIDK
SERDVYAAII DEKVAMKIGP GHYEPPNGSQ NWSVAVEGRD YKVWETS
