ISOA3_ARATH
ID ISOA3_ARATH Reviewed; 764 AA.
AC Q9M0S5; Q8RWW6;
DT 07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 07-JUL-2009, sequence version 2.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Isoamylase 3, chloroplastic;
DE Short=AtISA3;
DE EC=3.2.1.68;
DE Flags: Precursor;
GN Name=ISA3; OrderedLocusNames=At4g09020; ORFNames=F23J3.50;
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP DISRUPTION PHENOTYPE.
RX PubMed=15849301; DOI=10.1104/pp.105.059295;
RA Wattebled F., Dong Y., Dumez S., Delvalle D., Planchot V., Berbezy P.,
RA Vyas D., Colonna P., Chatterjee M., Ball S., D'Hulst C.;
RT "Mutants of Arabidopsis lacking a chloroplastic isoamylase accumulate
RT phytoglycogen and an abnormal form of amylopectin.";
RL Plant Physiol. 138:184-195(2005).
RN [6]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=16495218; DOI=10.1074/jbc.m513661200;
RA Delatte T., Umhang M., Trevisan M., Eicke S., Thorneycroft D., Smith S.M.,
RA Zeeman S.C.;
RT "Evidence for distinct mechanisms of starch granule breakdown in plants.";
RL J. Biol. Chem. 281:12050-12059(2006).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=18431481; DOI=10.1371/journal.pone.0001994;
RA Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O., Sun Q.,
RA van Wijk K.J.;
RT "Sorting signals, N-terminal modifications and abundance of the chloroplast
RT proteome.";
RL PLoS ONE 3:E1994-E1994(2008).
RN [8]
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 [9]
RP FUNCTION.
RX PubMed=18815382; DOI=10.1104/pp.108.129379;
RA Wattebled F., Planchot V., Dong Y., Szydlowski N., Pontoire B., Devin A.,
RA Ball S., D'Hulst C.;
RT "Further evidence for the mandatory nature of polysaccharide debranching
RT for the aggregation of semicrystalline starch and for overlapping functions
RT of debranching enzymes in Arabidopsis leaves.";
RL Plant Physiol. 148:1309-1323(2008).
CC -!- FUNCTION: Involved in starch catabolism. ISA3 removes different
CC branches than ISA1-ISA2, namely short chains that prevent amylopectin
CC crystallization. May be the debranching enzyme required to assist beta-
CC amylases for starch degradation in leaves at night.
CC {ECO:0000269|PubMed:16495218, ECO:0000269|PubMed:18815382,
CC ECO:0000269|PubMed:19074683}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of (1->6)-alpha-D-glucosidic branch linkages in
CC glycogen, amylopectin and their beta-limit dextrins.; EC=3.2.1.68;
CC -!- PATHWAY: Glycan degradation; starch degradation.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:16495218, ECO:0000269|PubMed:18431481}.
CC Note=Localizes to granule-like structures inside the chloroplast.
CC -!- DISRUPTION PHENOTYPE: Strong increase of the starch level in leaves at
CC the end of both day and night periods, but no modification in water-
CC soluble polysaccharides content. No alteration of the amylase-to-
CC amylopectin ratio. {ECO:0000269|PubMed:15849301,
CC ECO:0000269|PubMed:16495218}.
CC -!- MISCELLANEOUS: Double mutant shows that ISA3 and PU1 have redundant
CC function for starch degradation.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 13 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB78026.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL161513; CAB78026.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE82713.1; -; Genomic_DNA.
DR EMBL; AY091058; AAM13879.1; -; mRNA.
DR EMBL; AY133739; AAM91673.1; -; mRNA.
DR EMBL; AK227049; BAE99109.1; -; mRNA.
DR PIR; B85091; B85091.
DR RefSeq; NP_192641.2; NM_116971.6.
DR AlphaFoldDB; Q9M0S5; -.
DR SMR; Q9M0S5; -.
DR STRING; 3702.AT4G09020.1; -.
DR CAZy; CBM48; Carbohydrate-Binding Module Family 48.
DR CAZy; GH13; Glycoside Hydrolase Family 13.
DR iPTMnet; Q9M0S5; -.
DR MetOSite; Q9M0S5; -.
DR PaxDb; Q9M0S5; -.
DR PRIDE; Q9M0S5; -.
DR ProteomicsDB; 228859; -.
DR EnsemblPlants; AT4G09020.1; AT4G09020.1; AT4G09020.
DR GeneID; 826481; -.
DR Gramene; AT4G09020.1; AT4G09020.1; AT4G09020.
DR KEGG; ath:AT4G09020; -.
DR Araport; AT4G09020; -.
DR TAIR; locus:2122343; AT4G09020.
DR eggNOG; KOG0470; Eukaryota.
DR HOGENOM; CLU_011725_1_1_1; -.
DR InParanoid; Q9M0S5; -.
DR OMA; SEPWDCG; -.
DR OrthoDB; 533388at2759; -.
DR PhylomeDB; Q9M0S5; -.
DR BioCyc; ARA:AT4G09020-MON; -.
DR BioCyc; MetaCyc:AT4G09020-MON; -.
DR BRENDA; 3.2.1.68; 399.
DR UniPathway; UPA00153; -.
DR PRO; PR:Q9M0S5; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9M0S5; baseline and differential.
DR Genevisible; Q9M0S5; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009569; C:chloroplast starch grain; IDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0019156; F:isoamylase activity; IDA:TAIR.
DR GO; GO:0005983; P:starch catabolic process; IMP:TAIR.
DR CDD; cd02856; E_set_GDE_Isoamylase_N; 1.
DR Gene3D; 2.60.40.10; -; 1.
DR Gene3D; 2.60.40.1180; -; 1.
DR InterPro; IPR044505; GlgX_Isoamylase_N_E_set.
DR InterPro; IPR006047; Glyco_hydro_13_cat_dom.
DR InterPro; IPR004193; Glyco_hydro_13_N.
DR InterPro; IPR013780; Glyco_hydro_b.
DR InterPro; IPR017853; Glycoside_hydrolase_SF.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR014756; Ig_E-set.
DR Pfam; PF00128; Alpha-amylase; 1.
DR Pfam; PF02922; CBM_48; 1.
DR SMART; SM00642; Aamy; 1.
DR SUPFAM; SSF51445; SSF51445; 1.
DR SUPFAM; SSF81296; SSF81296; 1.
PE 1: Evidence at protein level;
KW Carbohydrate metabolism; Chloroplast; Glycosidase; Hydrolase; Plastid;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..70
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 71..764
FT /note="Isoamylase 3, chloroplastic"
FT /id="PRO_0000379529"
FT ACT_SITE 428
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P04746"
FT ACT_SITE 465
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P04746"
FT SITE 538
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P04746"
SQ SEQUENCE 764 AA; 86322 MW; EE9F163AE7F5E052 CRC64;
MLTSPSSSST YDPFSSNFSP SLTNAFSSSF TIPMGLKLSR RVTRARIFSR KIKDRSTLKV
TCRRAHERVV EEEASTMTET KLFKVSSGEV SPLGVSQVDK GINFALFSQN ATSVTLCLSL
SQSGKDDTDD DGMIELVLDP SVNKTGDTWH ICVEDLPLNN VLYGYRVDGP GEWQQGHRFD
RSILLLDPYA KLVKGHSSFG DSSQKFAQFY GTYDFESSPF DWGDDYKFPN IPEKDLVIYE
MNVRAFTADE SSGMDPAIGG SYLGFIEKIP HLQDLGINAV ELLPVFEFDE LELQRRSNPR
DHMVNTWGYS TVNFFAPMSR YASGEGDPIK ASKEFKEMVK ALHSAGIEVI LDVVYNHTNE
ADDKYPYTTS FRGIDNKVYY MLDPNNQLLN FSGCGNTLNC NHPVVMELIL DSLRHWVTEY
HVDGFRFDLA SVLCRATDGS PLSAPPLIRA IAKDSVLSRC KIIAEPWDCG GLYLVGKFPN
WDRWAEWNGM YRDDVRRFIK GDSGMKGSFA TRVSGSSDLY QVNQRKPYHG VNFVIAHDGF
TLRDLVSYNF KHNEANGEGG NDGCNDNHSW NCGFEGETGD AHIKSLRTRQ MKNFHLALMI
SQGTPMMLMG DEYGHTRYGN NNSYGHDTSL NNFQWKELDA KKQNHFRFFS EVIKFRHSHH
VLKHENFLTQ GEITWHEDNW DNSESKFLAF TLHDGIGGRD IYVAFNAHDY FVKALIPQPP
PGKQWFRVAD TNLESPDDFV REGVAGVADT YNVAPFSSIL LQSK
