Q06625 (GDE_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glycogen debranching enzyme

Alternative name(s):
Glycogen debrancher

Including the following 2 domains:

1. 4-alpha-glucanotransferase
   EC=2.4.1.25
   Alternative name(s):
   Oligo-1,4-1,4-glucantransferase
2. Amylo-alpha-1,6-glucosidase
   Short name=Amylo-1,6-glucosidase
   EC=3.2.1.33
   Alternative name(s):
   Dextrin 6-alpha-D-glucosidase

Gene names

Name:	GDB1
Ordered Locus Names:	YPR184W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	1536 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Multifunctional enzyme acting as 1,4-alpha-D-glucan:1,4-alpha-D-glucan 4-alpha-D-glycosyltransferase and amylo-1,6-glucosidase in glycogen degradation. Ref.4 Ref.8
Catalytic activity	Transfers a segment of a (1->4)-alpha-D-glucan to a new position in an acceptor, which may be glucose or a (1->4)-alpha-D-glucan. Hydrolysis of (1->6)-alpha-D-glucosidic branch linkages in glycogen phosphorylase limit dextrin.
Enzyme regulation	Activity is inhibited by IGD1. Ref.8
Subunit structure	Interacts with IGD1. Ref.8
Subcellular location	Mitochondrion. Cytoplasm Ref.5.
Miscellaneous	Present with 125 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the glycogen debranching enzyme family.

Ontologies

Keywords
Biological process	Glycogen biosynthesis
Cellular component	Cytoplasm Mitochondrion
Molecular function	Glycosidase Glycosyltransferase Hydrolase Transferase
PTM	Phosphoprotein
Technical term	Complete proteome Direct protein sequencing Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological_process	glycogen biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW glycogen catabolic process Inferred from mutant phenotype Ref.4. Source: SGD
Cellular_component	mitochondrion Inferred from direct assay PubMed 14576278PubMed 16823961. Source: SGD nucleus Inferred from Biological aspect of Ancestor. Source: RefGenome
Molecular_function	4-alpha-glucanotransferase activity Inferred from direct assay Ref.4. Source: SGD amylo-alpha-1,6-glucosidase activity Inferred from direct assay Ref.4. Source: SGD cation binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1536	1536	Glycogen debranching enzyme		PRO_0000087452
Regions
	Region	1 – ?		4-alpha-glucanotransferase
	Region	? – 1536		Amylo-1,6-glucosidase
Sites
	Active site	535	1	By similarity
	Active site	538	1	By similarity
	Active site	670	1	By similarity
Amino acid modifications
	Modified residue	45	1	Phosphothreonine Ref.7
Experimental info
	Sequence conflict	368	1	R → K in BAA34996. Ref.1
	Sequence conflict	536	1	N → Y in BAA34996. Ref.1
	Sequence conflict	774	1	D → N in BAA34996. Ref.1
	Sequence conflict	1180	1	R → K in BAA34996. Ref.1
	Sequence conflict	1289	1	K → N in BAA34996. Ref.1
	Sequence conflict	1489	1	F → S in BAA34996. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q06625 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 167270B2EE15EDF9	FASTA	1,536	174,972
	10 20 30 40 50 60 MNRSLLLRLS DTGEPITSCS YGKGVLTLPP IPLPKDAPKD QPLYTVKLLV SAGSPVARDG 70 80 90 100 110 120 LVWTNCPPDH NTPFKRDKFY KKIIHSSFHE DDCIDLNVYA PGSYCFYLSF RNDNEKLETT 130 140 150 160 170 180 RKYYFVALPM LYINDQFLPL NSIALQSVVS KWLGSDWEPI LSKIAAKNYN MVHFTPLQER 190 200 210 220 230 240 GESNSPYSIY DQLQFDQEHF KSPEDVKNLV EHIHRDLNML SLTDIVFNHT ANNSPWLVEH 250 260 270 280 290 300 PEAGYNHITA PHLISAIELD QELLNFSRNL KSWGYPTELK NIEDLFKIMD GIKVHVLGSL 310 320 330 340 350 360 KLWEYYAVNV QTALRDIKAH WNDESNESYS FPENIKDISS DFVKLASFVK DNVTEPNFGT 370 380 390 400 410 420 LGERNSNRIN VPKFIQLLKL INDGGSDDSE SSLATAQNIL NEVNLPLYRE YDDDVSEILE 430 440 450 460 470 480 QLFNRIKYLR LDDGGPKQGP VTVDVPLTEP YFTRFKGKDG TDYALANNGW IWNGNPLVDF 490 500 510 520 530 540 ASQNSRAYLR REVIVWGDCV KLRYGKSPED SPYLWERMSK YIEMNAKIFD GFRIDNCHST 550 560 570 580 590 600 PIHVGEYFLD LARKYNPNLY VVAELFSGSE TLDCLFVERL GISSLIREAM QAWSEEELSR 610 620 630 640 650 660 LVHKHGGRPI GSYKFVPMDD FSYPADINLN EEHCFNDSND NSIRCVSEIM IPKILTATPP 670 680 690 700 710 720 HALFMDCTHD NETPFEKRTV EDTLPNAALV ALCSSAIGSV YGYDEIFPHL LNLVTEKRHY 730 740 750 760 770 780 DISTPTGSPS IGITKVKATL NSIRTSIGEK AYDIEDSEMH VHHQGQYITF HRMDVKSGKG 790 800 810 820 830 840 WYLIARMKFS DNDDPNETLP PVVLNQSTCS LRFSYALERV GDEIPNDDKF IKGIPTKLKE 850 860 870 880 890 900 LEGFDISYDD SKKISTIKLP NEFPQGSIAI FETQQNGVDE SLDHFIRSGA LKATSSLTLE 910 920 930 940 950 960 SINSVLYRSE PEEYDVSAGE GGAYIIPNFG KPVYCGLQGW VSVLRKIVFY NDLAHPLSAN 970 980 990 1000 1010 1020 LRNGHWALDY TISRLNYYSD EAGINEVQNW LRSRFDRVKK LPSYLVPSYF ALIIGILYGC 1030 1040 1050 1060 1070 1080 CRLKAIQLMS RNIGKSTLFV QSLSMTSIQM VSRMKSTSIL PGENVPSMAA GLPHFSVNYM 1090 1100 1110 1120 1130 1140 RCWGRDVFIS LRGMLLTTGR FDEAKAHILA FAKTLKHGLI PNLLDAGRNP RYNARDAAWF 1150 1160 1170 1180 1190 1200 FLQAVQDYVY IVPDGEKILQ EQVTRRFPLD DTYIPVDDPR AFSYSSTLEE IIYEILSRHA 1210 1220 1230 1240 1250 1260 KGIKFREANA GPNLDRVMTD KGFNVEIHVD WSTGLIHGGS QYNCGTWMDK MGESEKAGSV 1270 1280 1290 1300 1310 1320 GIPGTPRDGA AIEINGLLKS ALRFVIELKN KGLFKFSDVE TQDGGRIDFT EWNQLLQDNF 1330 1340 1350 1360 1370 1380 EKRYYVPEDP SQDADYDVSA KLGVNRRGIY RDLYKSGKPY EDYQLRPNFA IAMTVAPELF 1390 1400 1410 1420 1430 1440 VPEHAIKAIT IADEVLRGPV GMRTLDPSDY NYRPYYNNGE DSDDFATSKG RNYHQGPEWV 1450 1460 1470 1480 1490 1500 WLYGYFLRAF HHFHFKTSPR CQNAAKEKPS SYLYQQLYYR LKGHRKWIFE SVWAGLTELT 1510 1520 1530 NKDGEVCNDS SPTQAWSSAC LLDLFYDLWD AYEDDS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"High expression of glycogen-debranching enzyme in Escherichia coli and its competent purification method." Nakayama A., Yamamoto K., Tabata S. Protein Expr. Purif. 19:298-303(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 208-216; 302-311; 351-358; 1296-1305 AND 1356-1365. Strain: ATCC 56960 / D-346.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI." Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M. , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J. Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"The Saccharomyces cerevisiae YPR184w gene encodes the glycogen debranching enzyme." Teste M.A., Enjalbert B., Parrou J.L., Francois J.M. FEMS Microbiol. Lett. 193:105-110(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[5]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[6]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]	"Profiling phosphoproteins of yeast mitochondria reveals a role of phosphorylation in assembly of the ATP synthase." Reinders J., Wagner K., Zahedi R.P., Stojanovski D., Eyrich B., van der Laan M., Rehling P., Sickmann A., Pfanner N., Meisinger C. Mol. Cell. Proteomics 6:1896-1906(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-45, MASS SPECTROMETRY. Strain: ATCC 76625 / YPH499.
[8]	"The Saccharomyces cerevisiae fermentation stress response protein Igd1p/Yfr017p regulates glycogen levels by inhibiting the glycogen debranching enzyme." Walkey C.J., Luo Z., Borchers C.H., Measday V., van Vuuren H.J. FEMS Yeast Res. 11:499-508(2011) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH IGD1, ENZYME REGULATION, FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AB018078 Genomic DNA. Translation: BAA34996.1. U25842 Genomic DNA. Translation: AAB68117.1. BK006949 Genomic DNA. Translation: DAA11600.1.
PIR	S59841.
RefSeq	NP_015510.1. NM_001184281.1.
3D structure databases
ProteinModelPortal	Q06625.
SMR	Q06625. Positions 158-237.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2578N.
IntAct	Q06625. 8 interactions.
MINT	MINT-532857.
STRING	4932.YPR184W.
Protein family/group databases
CAZy	GH13. Glycoside Hydrolase Family 13.
Proteomic databases
PaxDb	Q06625.
PeptideAtlas	Q06625.
PRIDE	Q06625.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YPR184W; YPR184W; YPR184W.
GeneID	856314.
KEGG	sce:YPR184W.
Organism-specific databases
CYGD	YPR184w.
SGD	S000006388. GDB1.
Phylogenomic databases
eggNOG	COG3408.
GeneTree	ENSGT00390000012596.
HOGENOM	HOG000212981.
KO	K01196.
OMA	WKQMSSF.
OrthoDB	EOG4V1B7W.
Enzyme and pathway databases
BioCyc	MetaCyc:MONOMER-13683.
Gene expression databases
Genevestigator	Q06625.
GermOnline	YPR184W. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	3.20.20.80. 3 hits.
InterPro	IPR008928. 6-hairpin_glycosidase-like. IPR010401. GDE_C. IPR006047. Glyco_hydro_13_cat_dom. IPR013781. Glyco_hydro_catalytic_dom. IPR006421. Glycogen_debranch_met. IPR017853. Glycoside_hydrolase_SF. [Graphical view]
PANTHER	PTHR10569. PTHR10569. 1 hit.
Pfam	PF00128. Alpha-amylase. 1 hit. PF06202. GDE_C. 1 hit. [Graphical view]
SUPFAM	SSF51445. Glyco_hydro_cat. 1 hit. SSF48208. Glyco_trans_6hp. 1 hit.
TIGRFAMs	TIGR01531. glyc_debranch. 1 hit.
ProtoNet	Search...
Other
NextBio	981694.

Entry information

Entry name

GDE_YEAST

Accession

Primary (citable) accession number: Q06625
Secondary accession number(s): D6W4I4, O93808

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 2005
Last sequence update:	November 1, 1996
Last modified:	April 3, 2013
This is version 105 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program