Q9M0S5 (ISOA3_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Isoamylase 3, chloroplastic
Short name=AtISA3
EC=3.2.1.68

Gene names

Name:	ISA3
Ordered Locus Names:	At4g09020
ORF Names:	F23J3.50

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	764 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in starch catabolism. ISA3 removes different branches than ISA1-ISA2, namely short chains that prevent amylopectin crystallization. May be the debranching enzyme required to assist beta-amylases for starch degradation in leaves at night. Ref.6 Ref.8 Ref.9
Catalytic activity	Hydrolysis of (1->6)-alpha-D-glucosidic branch linkages in glycogen, amylopectin and their beta-limit dextrins.
Pathway	Glycan degradation; starch degradation.
Subcellular location	Plastid › chloroplast. Note: Localizes to granule-like structures inside the chloroplast. Ref.6 Ref.7
Disruption phenotype	Strong increase of the starch level in leaves at the end of both day and night periods, but no modification in water-soluble polysaccharides content. No alteration of the amylase-to-amylopectin ratio. Ref.5 Ref.6
Miscellaneous	Double mutant shows that ISA3 and PU1 have redundant function for starch degradation.
Sequence similarities	Belongs to the glycosyl hydrolase 13 family.
Sequence caution	The sequence CAB78026.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Carbohydrate metabolism
Cellular component	Chloroplast Plastid
Domain	Transit peptide
Molecular function	Glycosidase Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	starch catabolic process Inferred from mutant phenotype Ref.9PubMed 19776162. Source: TAIR
Cellular_component	chloroplast starch grain Inferred from direct assay Ref.6. Source: TAIR chloroplast stroma Inferred from direct assay PubMed 16207701PubMed 18633119PubMed 20061580. Source: TAIR
Molecular_function	cation binding Inferred from electronic annotation. Source: InterPro isoamylase activity Inferred from direct assay Ref.9. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 70	70	Chloroplast Potential
	Chain	71 – 764	694	Isoamylase 3, chloroplastic		PRO_0000379529
Sites
	Active site	428	1	Nucleophile By similarity
	Active site	465	1	Proton donor By similarity
	Site	538	1	Transition state stabilizer By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q9M0S5 [UniParc]. Last modified July 7, 2009. Version 2. Checksum: EE9F163AE7F5E052	FASTA	764	86,322
	10 20 30 40 50 60 MLTSPSSSST YDPFSSNFSP SLTNAFSSSF TIPMGLKLSR RVTRARIFSR KIKDRSTLKV 70 80 90 100 110 120 TCRRAHERVV EEEASTMTET KLFKVSSGEV SPLGVSQVDK GINFALFSQN ATSVTLCLSL 130 140 150 160 170 180 SQSGKDDTDD DGMIELVLDP SVNKTGDTWH ICVEDLPLNN VLYGYRVDGP GEWQQGHRFD 190 200 210 220 230 240 RSILLLDPYA KLVKGHSSFG DSSQKFAQFY GTYDFESSPF DWGDDYKFPN IPEKDLVIYE 250 260 270 280 290 300 MNVRAFTADE SSGMDPAIGG SYLGFIEKIP HLQDLGINAV ELLPVFEFDE LELQRRSNPR 310 320 330 340 350 360 DHMVNTWGYS TVNFFAPMSR YASGEGDPIK ASKEFKEMVK ALHSAGIEVI LDVVYNHTNE 370 380 390 400 410 420 ADDKYPYTTS FRGIDNKVYY MLDPNNQLLN FSGCGNTLNC NHPVVMELIL DSLRHWVTEY 430 440 450 460 470 480 HVDGFRFDLA SVLCRATDGS PLSAPPLIRA IAKDSVLSRC KIIAEPWDCG GLYLVGKFPN 490 500 510 520 530 540 WDRWAEWNGM YRDDVRRFIK GDSGMKGSFA TRVSGSSDLY QVNQRKPYHG VNFVIAHDGF 550 560 570 580 590 600 TLRDLVSYNF KHNEANGEGG NDGCNDNHSW NCGFEGETGD AHIKSLRTRQ MKNFHLALMI 610 620 630 640 650 660 SQGTPMMLMG DEYGHTRYGN NNSYGHDTSL NNFQWKELDA KKQNHFRFFS EVIKFRHSHH 670 680 690 700 710 720 VLKHENFLTQ GEITWHEDNW DNSESKFLAF TLHDGIGGRD IYVAFNAHDY FVKALIPQPP 730 740 750 760 PGKQWFRVAD TNLESPDDFV REGVAGVADT YNVAPFSSIL LQSK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana." Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B. , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R. Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[2]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[3]	"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.
[4]	"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 (JUL-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"Mutants of Arabidopsis lacking a chloroplastic isoamylase accumulate phytoglycogen and an abnormal form of amylopectin." Wattebled F., Dong Y., Dumez S., Delvalle D., Planchot V., Berbezy P., Vyas D., Colonna P., Chatterjee M., Ball S., D'Hulst C. Plant Physiol. 138:184-195(2005) [PubMed] [Europe PMC] [Abstract] Cited for: DISRUPTION PHENOTYPE.
[6]	"Evidence for distinct mechanisms of starch granule breakdown in plants." Delatte T., Umhang M., Trevisan M., Eicke S., Thorneycroft D., Smith S.M., Zeeman S.C. J. Biol. Chem. 281:12050-12059(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
[7]	"Sorting signals, N-terminal modifications and abundance of the chloroplast proteome." Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O., Sun Q., van Wijk K.J. PLoS ONE 3:E1994-E1994(2008) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[8]	"Starch granule biosynthesis in Arabidopsis is abolished by removal of all debranching enzymes but restored by the subsequent removal of an endoamylase." Streb S., Delatte T., Umhang M., Eicke S., Schorderet M., Reinhardt D., Zeeman S.C. Plant Cell 20:3448-3466(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Further evidence for the mandatory nature of polysaccharide debranching for the aggregation of semicrystalline starch and for overlapping functions of debranching enzymes in Arabidopsis leaves." Wattebled F., Planchot V., Dong Y., Szydlowski N., Pontoire B., Devin A., Ball S., D'Hulst C. Plant Physiol. 148:1309-1323(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AL161513 Genomic DNA. Translation: CAB78026.1. Sequence problems. CP002687 Genomic DNA. Translation: AEE82713.1. AY091058 mRNA. Translation: AAM13879.1. AY133739 mRNA. Translation: AAM91673.1. AK227049 mRNA. Translation: BAE99109.1.
IPI	IPI00519580.
PIR	B85091.
RefSeq	NP_192641.2. NM_116971.5.
UniGene	At.33717.
3D structure databases
HSSP	HSSP built from PDB template 1BF2 based on UniProtKB P10342.
ProteinModelPortal	Q9M0S5.
SMR	Q9M0S5. Positions 88-672.
ModBase	Search...
Protein family/group databases
CAZy	CBM48. Carbohydrate-Binding Module Family 48. GH13. Glycoside Hydrolase Family 13.
Proteomic databases
PaxDb	Q9M0S5.
PRIDE	Q9M0S5.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT4G09020.1; AT4G09020.1; AT4G09020.
GeneID	826481.
KEGG	ath:AT4G09020.
Organism-specific databases
TAIR	At4g09020.
Phylogenomic databases
eggNOG	COG1523.
HOGENOM	HOG000239197.
InParanoid	Q8RWW6.
KO	K02438.
OMA	VPTVWPG.
PhylomeDB	Q9M0S5.
ProtClustDB	CLSN2915032.
Enzyme and pathway databases
BioCyc	ARA:AT4G09020-MONOMER. MetaCyc:AT4G09020-MONOMER.
UniPathway	UPA00153.
Gene expression databases
Genevestigator	Q9M0S5.
Family and domain databases
Gene3D	2.60.40.10. 1 hit. 2.60.40.1180. 1 hit. 3.20.20.80. 1 hit.
InterPro	IPR015902. Glyco_hydro_13. IPR013780. Glyco_hydro_13_b. IPR006047. Glyco_hydro_13_cat_dom. IPR004193. Glyco_hydro_13_N. IPR013781. Glyco_hydro_catalytic_dom. IPR017853. Glycoside_hydrolase_SF. IPR013783. Ig-like_fold. IPR014756. Ig_E-set. [Graphical view]
PANTHER	PTHR10357. PTHR10357. 1 hit.
Pfam	PF00128. Alpha-amylase. 1 hit. PF02922. CBM_48. 1 hit. [Graphical view]
SUPFAM	SSF51445. Glyco_hydro_cat. 1 hit. SSF81296. Ig_E-set. 1 hit.
ProtoNet	Search...

Entry information

Entry name

ISOA3_ARATH

Accession

Primary (citable) accession number: Q9M0S5
Secondary accession number(s): Q8RWW6

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 7, 2009
Last sequence update:	July 7, 2009
Last modified:	May 1, 2013
This is version 76 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program