AGAL_ORYSJ
ID AGAL_ORYSJ Reviewed; 417 AA.
AC Q9FXT4; F4MGX5; Q0IWR2; Q84UX2;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=Alpha-galactosidase {ECO:0000303|PubMed:12423882};
DE EC=3.2.1.22 {ECO:0000269|PubMed:12423882};
DE AltName: Full=Alpha-D-galactoside galactohydrolase {ECO:0000305};
DE AltName: Full=Melibiase {ECO:0000305};
DE Flags: Precursor;
GN OrderedLocusNames=Os10g0493600 {ECO:0000312|EMBL:BAT11449.1},
GN LOC_Os10g35110 {ECO:0000312|EMBL:AAP54412.1};
GN ORFNames=OSJNBa0041P03 {ECO:0000312|EMBL:AAM92832.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 56-95, FUNCTION, CATALYTIC
RP ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVITY REGULATION.
RC STRAIN=cv. Nipponbare; TISSUE=Callus;
RX PubMed=12423882; DOI=10.1016/s0031-9422(02)00368-0;
RA Kim W.-D., Kobayashi O., Kaneko S., Sakakibara Y., Park G.-G., Kusakabe I.,
RA Tanaka H., Kobayashi H.;
RT "Alpha-galactosidase from cultured rice (Oryza sativa L. var. Nipponbare)
RT cells.";
RL Phytochemistry 61:621-630(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12791992; DOI=10.1126/science.1083523;
RA Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT "In-depth view of structure, activity, and evolution of rice chromosome
RT 10.";
RL Science 300:1566-1569(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 101-284.
RC STRAIN=cv. Tainung 67; TISSUE=Leaf;
RA Lee R.H., Chen S.C.G.;
RL Submitted (MAR-2000) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF 56-417 IN COMPLEX WITH
RP ALPHA-D-GALACTOSE, ACTIVE SITES, AND DISULFIDE BONDS.
RX PubMed=12657636; DOI=10.1074/jbc.m302292200;
RA Fujimoto Z., Kaneko S., Momma M., Kobayashi H., Mizuno H.;
RT "Crystal structure of rice alpha-galactosidase complexed with D-
RT galactose.";
RL J. Biol. Chem. 278:20313-20318(2003).
CC -!- FUNCTION: Hydrolyzes melibiose, raffinose and stachyose in the
CC following decreasing order of reactivity: raffinose, melibiose,
CC stachyose (PubMed:12423882). Acts on both the terminal alpha-galactosyl
CC residue and the side-chain alpha-galactosyl residue of the
CC galactomanno-oligosaccharides (PubMed:12423882).
CC {ECO:0000269|PubMed:12423882}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of terminal, non-reducing alpha-D-galactose
CC residues in alpha-D-galactosides, including galactose
CC oligosaccharides, galactomannans and galactolipids.; EC=3.2.1.22;
CC Evidence={ECO:0000269|PubMed:12423882};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + melibiose = D-galactose + D-glucose;
CC Xref=Rhea:RHEA:28663, ChEBI:CHEBI:4139, ChEBI:CHEBI:4167,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:28053;
CC Evidence={ECO:0000269|PubMed:12423882};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:28664;
CC Evidence={ECO:0000269|PubMed:12423882};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + raffinose = D-galactose + sucrose; Xref=Rhea:RHEA:70275,
CC ChEBI:CHEBI:4139, ChEBI:CHEBI:15377, ChEBI:CHEBI:16634,
CC ChEBI:CHEBI:17992; Evidence={ECO:0000269|PubMed:12423882};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:70276;
CC Evidence={ECO:0000269|PubMed:12423882};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + stachyose = D-galactose + raffinose;
CC Xref=Rhea:RHEA:70279, ChEBI:CHEBI:4139, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:16634, ChEBI:CHEBI:17164;
CC Evidence={ECO:0000269|PubMed:12423882};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:70280;
CC Evidence={ECO:0000269|PubMed:12423882};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=alpha-D-Gal-(1->6)-beta-D-Man-(1->4)-beta-D-Man-(1->4)-D-Man +
CC H2O = beta-D-Man-(1->4)-beta-D-Man-(1->4)-D-Man + D-galactose;
CC Xref=Rhea:RHEA:70339, ChEBI:CHEBI:4139, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:62785, ChEBI:CHEBI:189418;
CC Evidence={ECO:0000269|PubMed:12423882};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:70340;
CC Evidence={ECO:0000269|PubMed:12423882};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=beta-D-Man-(1->4)-[alpha-D-Gal-(1->6)]-beta-D-Man-(1->4)-beta-
CC D-Man-(1->4)-D-Man + H2O = beta-D-Man-(1->4)-beta-D-Man-(1->4)-beta-
CC D-Man-(1->4)-D-Man + D-galactose; Xref=Rhea:RHEA:70351,
CC ChEBI:CHEBI:4139, ChEBI:CHEBI:15377, ChEBI:CHEBI:62973,
CC ChEBI:CHEBI:189417; Evidence={ECO:0000269|PubMed:12423882};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:70352;
CC Evidence={ECO:0000269|PubMed:12423882};
CC -!- ACTIVITY REGULATION: 1 mM Hg(2+) and Ag(2+) decrease activity by 98%
CC and 96%, respectively. 1 mM Para-chloromercuribenzoic acid (PCMB)
CC completely inhibits enzymatic activity. {ECO:0000269|PubMed:12423882}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 5.0. Slowly inactivated above pH 8.0 and below pH 3.
CC {ECO:0000269|PubMed:12423882};
CC Temperature dependence:
CC Optimum temperature is 45 degrees Celsius with p-nitrophenyl-alpha-D-
CC galactopyranoside as substrate. {ECO:0000269|PubMed:12423882};
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 27 family. {ECO:0000305}.
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DR EMBL; AB039671; BAB12570.1; -; mRNA.
DR EMBL; AC068950; AAM92832.1; -; Genomic_DNA.
DR EMBL; DP000086; AAP54412.1; -; Genomic_DNA.
DR EMBL; DP000086; ABB47819.1; -; Genomic_DNA.
DR EMBL; AP008216; BAF26853.2; -; Genomic_DNA.
DR EMBL; AP014966; BAT11449.1; -; Genomic_DNA.
DR EMBL; AF251064; AAO85428.1; -; mRNA.
DR RefSeq; XP_015613565.1; XM_015758079.1.
DR RefSeq; XP_015613566.1; XM_015758080.1.
DR PDB; 1UAS; X-ray; 1.50 A; A=56-417.
DR PDBsum; 1UAS; -.
DR AlphaFoldDB; Q9FXT4; -.
DR SMR; Q9FXT4; -.
DR IntAct; Q9FXT4; 9.
DR STRING; 4530.OS10T0493600-01; -.
DR ChEMBL; CHEMBL4537; -.
DR CAZy; GH27; Glycoside Hydrolase Family 27.
DR PaxDb; Q9FXT4; -.
DR PRIDE; Q9FXT4; -.
DR EnsemblPlants; Os10t0493600-01; Os10t0493600-01; Os10g0493600.
DR GeneID; 4348988; -.
DR Gramene; Os10t0493600-01; Os10t0493600-01; Os10g0493600.
DR KEGG; osa:4348988; -.
DR eggNOG; KOG2366; Eukaryota.
DR InParanoid; Q9FXT4; -.
DR OMA; DDLWDRW; -.
DR OrthoDB; 964130at2759; -.
DR BRENDA; 3.2.1.22; 4460.
DR EvolutionaryTrace; Q9FXT4; -.
DR Proteomes; UP000000763; Chromosome 10.
DR Proteomes; UP000059680; Chromosome 10.
DR ExpressionAtlas; Q9FXT4; baseline and differential.
DR Genevisible; Q9FXT4; OS.
DR GO; GO:0048046; C:apoplast; IEA:EnsemblPlants.
DR GO; GO:0009505; C:plant-type cell wall; IBA:GO_Central.
DR GO; GO:0052692; F:raffinose alpha-galactosidase activity; IEA:UniProtKB-EC.
DR GO; GO:0044275; P:cellular carbohydrate catabolic process; IEA:UniProt.
DR GO; GO:0009965; P:leaf morphogenesis; IEA:EnsemblPlants.
DR GO; GO:0009911; P:positive regulation of flower development; IEA:EnsemblPlants.
DR GO; GO:0009620; P:response to fungus; IEA:EnsemblPlants.
DR CDD; cd14792; GH27; 1.
DR Gene3D; 2.60.40.1180; -; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR002241; Glyco_hydro_27.
DR InterPro; IPR000111; Glyco_hydro_27/36_CS.
DR InterPro; IPR013780; Glyco_hydro_b.
DR InterPro; IPR017853; Glycoside_hydrolase_SF.
DR InterPro; IPR041233; Melibiase_C.
DR PANTHER; PTHR11452; PTHR11452; 1.
DR Pfam; PF16499; Melibiase_2; 1.
DR Pfam; PF17801; Melibiase_C; 1.
DR PRINTS; PR00740; GLHYDRLASE27.
DR SUPFAM; SSF51445; SSF51445; 1.
DR PROSITE; PS00512; ALPHA_GALACTOSIDASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Disulfide bond; Glycosidase;
KW Hydrolase; Reference proteome; Signal.
FT SIGNAL 1..55
FT /evidence="ECO:0000269|PubMed:12423882"
FT CHAIN 56..417
FT /note="Alpha-galactosidase"
FT /id="PRO_0000001000"
FT ACT_SITE 185
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:12657636"
FT ACT_SITE 240
FT /note="Proton donor"
FT /evidence="ECO:0000269|PubMed:12657636"
FT BINDING 71
FT /ligand="alpha-D-galactose"
FT /ligand_id="ChEBI:CHEBI:28061"
FT /evidence="ECO:0000269|PubMed:12657636"
FT BINDING 106
FT /ligand="alpha-D-galactose"
FT /ligand_id="ChEBI:CHEBI:28061"
FT /evidence="ECO:0000269|PubMed:12657636"
FT BINDING 107
FT /ligand="alpha-D-galactose"
FT /ligand_id="ChEBI:CHEBI:28061"
FT /evidence="ECO:0000269|PubMed:12657636"
FT BINDING 156
FT /ligand="alpha-D-galactose"
FT /ligand_id="ChEBI:CHEBI:28061"
FT /evidence="ECO:0000269|PubMed:12657636"
FT BINDING 183
FT /ligand="alpha-D-galactose"
FT /ligand_id="ChEBI:CHEBI:28061"
FT /evidence="ECO:0000269|PubMed:12657636"
FT BINDING 185
FT /ligand="alpha-D-galactose"
FT /ligand_id="ChEBI:CHEBI:28061"
FT /evidence="ECO:0000269|PubMed:12657636"
FT BINDING 219
FT /ligand="alpha-D-galactose"
FT /ligand_id="ChEBI:CHEBI:28061"
FT /evidence="ECO:0000269|PubMed:12657636"
FT BINDING 236
FT /ligand="alpha-D-galactose"
FT /ligand_id="ChEBI:CHEBI:28061"
FT /evidence="ECO:0000269|PubMed:12657636"
FT BINDING 240
FT /ligand="alpha-D-galactose"
FT /ligand_id="ChEBI:CHEBI:28061"
FT /evidence="ECO:0000269|PubMed:12657636"
FT DISULFID 76..108
FT /evidence="ECO:0000269|PubMed:12657636"
FT DISULFID 156..187
FT /evidence="ECO:0000269|PubMed:12657636"
FT STRAND 66..70
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 71..74
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 80..92
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 95..98
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 102..104
FT /evidence="ECO:0007829|PDB:1UAS"
FT TURN 124..126
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 131..140
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 144..154
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 158..161
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 167..177
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 181..185
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 194..208
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 212..218
FT /evidence="ECO:0007829|PDB:1UAS"
FT TURN 219..222
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 224..226
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 228..230
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 233..236
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 245..256
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 257..261
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 266..269
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 277..280
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 282..294
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 299..301
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 310..316
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 319..325
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 334..339
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 342..348
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 354..360
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 362..364
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 366..371
FT /evidence="ECO:0007829|PDB:1UAS"
FT HELIX 372..374
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 382..387
FT /evidence="ECO:0007829|PDB:1UAS"
FT TURN 388..391
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 392..404
FT /evidence="ECO:0007829|PDB:1UAS"
FT STRAND 409..416
FT /evidence="ECO:0007829|PDB:1UAS"
SQ SEQUENCE 417 AA; 45821 MW; 5F7B16326C042BF5 CRC64;
MARASSSSSP PSPRLLLLLL VAVAATLLPE AAALGNFTAE SRGARWRSRR ARRRAFENGL
GRTPQMGWNS WNHFYCGINE QIIRETADAL VNTGLAKLGY QYVNIDDCWA EYSRDSQGNF
VPNRQTFPSG IKALADYVHA KGLKLGIYSD AGSQTCSNKM PGSLDHEEQD VKTFASWGVD
YLKYDNCNDA GRSVMERYTR MSNAMKTYGK NIFFSLCEWG KENPATWAGR MGNSWRTTGD
IADNWGSMTS RADENDQWAA YAGPGGWNDP DMLEVGNGGM SEAEYRSHFS IWALAKAPLL
IGCDVRSMSQ QTKNILSNSE VIAVNQDSLG VQGKKVQSDN GLEVWAGPLS NNRKAVVLWN
RQSYQATITA HWSNIGLAGS VAVTARDLWA HSSFAAQGQI SASVAPHDCK MYVLTPN
