Q8GTR4 (PULA1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pullulanase 1, chloroplastic
Short name=AtPU1
EC=3.2.1.142

Alternative name(s):
Protein LIMIT DEXTRINASE
Short name=AtLDA

Gene names

Name:	PU1
Synonyms:	LDA
Ordered Locus Names:	At5g04360
ORF Names:	T19N18.90

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	965 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 degradation and also probably in the trimming of pre-amylopectin chains during starch synthesis. Ref.5 Ref.7 Ref.8
Catalytic activity	Hydrolysis of (1->6)-alpha-D-glucosidic linkages in alpha- and beta-limit dextrins of amylopectin and glycogen, and in amylopectin and pullulan.
Pathway	Glycan biosynthesis; starch biosynthesis. Glycan degradation; starch degradation.
Subcellular location	Plastid › chloroplast stroma Ref.5 Ref.6.
Disruption phenotype	No effect on the starch level in leaves and slight increase of water-soluble polysaccharides. No alteration of the amylase-to-amylopectin ratio. ISA3 is able to fully compensate for the loss of PU1. Ref.4
Miscellaneous	Double mutant shows that PU1 and ISA3 have redundant function for starch degradation. The involvement of PU1 in amylopectin synthesis is infered from the phenotype of double mutant in PU1 and ISA2.
Sequence similarities	Belongs to the glycosyl hydrolase 13 family.

Ontologies

Keywords
Biological process	Carbohydrate metabolism Starch biosynthesis
Cellular component	Chloroplast Plastid
Domain	Transit peptide
Molecular function	Glycosidase Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	starch biosynthetic process Inferred from mutant phenotype Ref.8. Source: TAIR starch catabolic process Inferred from mutant phenotype Ref.8PubMed 19776162. Source: TAIR
Cellular_component	chloroplast stroma Inferred from direct assay PubMed 20061580. Source: TAIR
Molecular_function	cation binding Inferred from electronic annotation. Source: InterPro limit dextrinase activity Inferred from direct assay Ref.4. Source: TAIR pullulanase activity Inferred from direct assay Ref.8. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 62	62	Chloroplast Potential
	Chain	63 – 965	903	Pullulanase 1, chloroplastic		PRO_0000379530
Regions
	Compositional bias	62 – 68	7	Poly-Ser
Sites
	Active site	552	1	Nucleophile By similarity
	Active site	589	1	Proton donor By similarity
	Site	721	1	Transition state stabilizer By similarity
Experimental info
	Sequence conflict	859	1	Q → K in AAO00771. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Q8GTR4 [UniParc]. Last modified May 3, 2011. Version 2. Checksum: 27074C8B5D71BDAC	FASTA	965	107,067
	10 20 30 40 50 60 MALTLTPTSS VHLLSSISVA RPRIFAADFN LRSRWRRRRP VTSISNFRLR LPSKTSLHCL 70 80 90 100 110 120 CSSSSASSPM SLEVSSPNSQ FLDCLIYSRA YWVTQGVIAW NVDVGEGSCY FYASKSAGLS 130 140 150 160 170 180 FSEDGIDGYD LRIKLEAESG SLPADVIEKF PHIRNYKSFK VPKDLDIRDL VKSQLAVVCF 190 200 210 220 230 240 DAEGRLIQGT GLQLPGVLDE LFSYDGPLGA HFTPEGVSLH LWAPTAQAVS VCIYKNPLDK 250 260 270 280 290 300 SPMEICPLKE ANGVWSTEGA CSWGGCYYVY KVSVYHPSTM KLETCYANDP YARGLSADGR 310 320 330 340 350 360 KTFLVNLDSD DLKPEGWDNL ADKKPCLRSF SDISIYELHV RDFSANDETV EPENRGGYLA 370 380 390 400 410 420 FTSKDSAGVK HLQKLVDAGL THLHLLPTFQ FGDVDDEKEN WKSVDTSLLE GLRPDSTEAQ 430 440 450 460 470 480 ARITEIQNDD GYNWGYNPVL WGVPKGSYAS DPTGPCRIIE FRKMVQALNC TGLNVVLDVV 490 500 510 520 530 540 YNHLHASGPH DKESVLDKIV PGYYLRRNSD GFIENSTCVN NTASEHYMVD RLIRDDLLNW 550 560 570 580 590 600 VVNYKVDGFR FDLMGHIMKA TIVNAKSAIG SLRKETDGVD GSRIYLYGEG WNFGEVAENG 610 620 630 640 650 660 RGINASQFNL GGTGIGSFND RIRDATLGGS PFGHPLQQGF ITGLLLQPNA HDHGSEATQE 670 680 690 700 710 720 LMLSTAKNHI QTGMAANLKD YMLTNHEGKE VKGSEVLMHD ATPVAYASLP TETINYVSAH 730 740 750 760 770 780 DNETLFDIIS LKTPMEISVD ERCRINHLAS SMIALSQGIP FFHAGDEILR SKSLDRDSYN 790 800 810 820 830 840 SGDWFNRLDF SYSSNNWGVG LPPKGKNEHN WPLIKPRLQD PSFKPKSSHI VATLHNFLDL 850 860 870 880 890 900 LRIRYSSPLF RLDTARAIQE RVRFHNTGPS SIPGAIVMSI EDGHRGIPSV SQIDPIYSLI 910 920 930 940 950 960 VVIFNARPSE FSYPSPALKD RKLELHPVQV MSADEIVKKS VYDSFSGGFT VPARTTTVFV ESRNG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana." Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K. , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F. Nature 408:823-826(2000) [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]	"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.
[5]	"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.
[6]	"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].
[7]	"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.
[8]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP002688 Genomic DNA. Translation: AED90732.1. BT002411 mRNA. Translation: AAO00771.1.
IPI	IPI00530984.
RefSeq	NP_196056.2. NM_120518.4.
UniGene	At.26109.
3D structure databases
ProteinModelPortal	Q8GTR4.
SMR	Q8GTR4. Positions 88-963.
ModBase	Search...
Protein-protein interaction databases
STRING	3702.AT5G04360.1-P.
Protein family/group databases
CAZy	CBM48. Carbohydrate-Binding Module Family 48. GH13. Glycoside Hydrolase Family 13.
Proteomic databases
PaxDb	Q8GTR4.
PRIDE	Q8GTR4.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT5G04360.1; AT5G04360.1; AT5G04360.
GeneID	830315.
KEGG	ath:AT5G04360.
Organism-specific databases
TAIR	At5g04360.
Phylogenomic databases
eggNOG	COG1523.
HOGENOM	HOG000251916.
InParanoid	Q8GTR4.
OMA	ERCRINH.
Enzyme and pathway databases
UniPathway	UPA00152. UPA00153.
Gene expression databases
Genevestigator	Q8GTR4.
Family and domain databases
Gene3D	2.60.40.10. 1 hit. 3.20.20.80. 3 hits.
InterPro	IPR015902. Glyco_hydro_13. 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. IPR011839. Pullul_strch. IPR024561. Pullul_strch_C. [Graphical view]
PANTHER	PTHR10357. PTHR10357. 1 hit.
Pfam	PF00128. Alpha-amylase. 1 hit. PF02922. CBM_48. 1 hit. PF11852. DUF3372. 1 hit. [Graphical view]
SUPFAM	SSF51445. Glyco_hydro_cat. 1 hit. SSF81296. Ig_E-set. 1 hit.
TIGRFAMs	TIGR02103. pullul_strch. 1 hit.
ProtoNet	Search...

Entry information

Entry name

PULA1_ARATH

Accession

Primary (citable) accession number: Q8GTR4

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 7, 2009
Last sequence update:	May 3, 2011
Last modified:	May 1, 2013
This is version 66 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program