EzCatDB: D00165

DB codeD00165
RLCP classification1.30.36000.3
CATH domainDomain 13.20.20.80Catalytic domain
Domain 22.60.40.1180
E.C.3.2.1.1
CSA1amy

CATH domainRelated DB codes (homologues)
2.60.40.1180M00113,T00307,D00176,D00664,D00665,D00863,D00864,M00112,M00193,M00314,T00057,T00062,T00067
3.20.20.80S00202,S00210,S00748,S00906,S00907,S00911,S00912,S00915,M00134,M00160,D00479,S00204,S00205,S00206,S00207,S00203,S00208,S00209,S00211,S00213,S00214,M00113,T00307,D00166,D00169,D00176,D00501,D00502,D00503,D00844,D00861,D00864,M00026,M00112,M00193,M00346,T00057,T00062,T00063,T00066,T00067

Enzyme Name
Swiss-protKEGG

P04063P00691P56271P0C1B3P29957P56634P00690P04745P04746
Protein nameAlpha-amylase type B isozymeAlpha-amylaseAcid alpha-amylaseAlpha-amylase A type-1/2Alpha-amylaseAlpha-amylasePancreatic alpha-amylaseAlpha-amylase 1Pancreatic alpha-amylasealpha-amylase
glycogenase
alpha amylase, alpha-amylase
endoamylase
Taka-amylase A
1,4-alpha-D-glucan glucanohydrolase
SynonymsEC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
AMY2-2
High pI alpha-amylase
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
EC 3.2.1.1
Taka-amylase A
TAA
1,4-alpha-D-glucan glucanohydrolase
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
PA
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase 1
Salivary alpha-amylase
PA
EC 3.2.1.1
1,4-alpha-D-glucan glucanohydrolase

KEGG pathways
MAP codePathways
MAP00500Starch and sucrose metabolism

Swiss-prot:Accession NumberP04063P00691P56271P0C1B3P29957P56634P00690P04745P04746
Entry nameAMY2_HORVUAMY_BACSUAMYA_ASPNGAMYA1_ASPORAMY_PSEHAAMY_TENMOAMYP_PIGAMY1_HUMANAMYP_HUMAN
ActivityEndohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.
SubunitMonomer.Monomer.Monomer.Monomer.Monomer.Monomer.
Monomer.Monomer.
Subcellular location
Secreted.



Secreted, extracellular space.Secreted.Secreted, extracellular space.
CofactorBinds 3 calcium ions per subunit.Binds 2 calcium ions per subunit.Binds 2 calcium ions per subunit. Calcium is inhibitory at high concentrations.Binds 2 calcium ions per subunit. Calcium is inhibitory at high concentrations.Binds 1 calcium ion per subunit.,Binds 1 chloride ion per subunit.Binds 1 calcium ion per subunit.,Binds 1 chloride ion per subunit.Binds 1 calcium ion per subunit.,Binds 1 chloride ion per subunit.Binds 1 calcium ion per subunit.,Binds 1 chloride ion per subunit.Binds 1 calcium ion per subunit.,Binds 1 chloride ion per subunit.


CofactorsSubstratesProductsintermediates
KEGG-idC00076C00115C00369C00001C00369C00721
CompoundCalciumChlorideStarchH2OStarchDextrin
Typedivalent metal (Ca2+, Mg2+)halidepolysaccharideH2Opolysaccharidepolysaccharide
1amyA01Bound:3x_CAUnboundUnbound
UnboundUnboundUnbound
1avaA01Bound:3x_CAUnboundUnbound
UnboundUnboundUnbound
1avaB01Bound:3x_CAUnboundUnbound
UnboundUnboundUnbound
1bg9A01Bound:3x_CAUnboundUnbound
UnboundUnboundTransition-state-analogue:DAF-GLC
1bagA01Bound:3x_CAUnboundBound:GLC-GLC-GLC-GLC-GLC
UnboundUnboundUnbound
2aaaA01Bound:_CAUnboundUnbound
UnboundUnboundUnbound
2taaA01Bound:_CAUnboundUnbound
UnboundUnboundUnbound
6taaA01Bound:2x_CAUnboundUnbound
UnboundUnboundUnbound
7taaA01Bound:_CAUnboundUnbound
UnboundUnboundTransition-state-analogue:ABC
1aqhA01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1aqmA01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1b0iA01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1clvA01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1jaeA01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1tmqA01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1viwA01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1bvnP01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1dhkA01Bound:2x_CABound:_CLUnbound
UnboundUnboundUnbound
1jfhA01Bound:_CABound:_CLUnbound
Analogue:MA2-MA3Analogue:MAN-MA1Unbound
1oseA01Bound:_CABound:_CLUnbound
UnboundUnboundTransition-state-analogue:AC1-GLC-AC1-GLC
1pifA01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1pigA01Bound:_CABound:_CLUnbound
UnboundUnboundTransition-state-analogue:AGL-GLC-HMC-AGL-GLC-GLC
1ppiA01Bound:_CABound:_CLUnbound
UnboundUnboundTransition-state-analogue:GLC-GLC-DAF-GLC
1smdA01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1bsiA01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1cpuA01Bound:_CABound:_CLUnbound
UnboundUnboundTransition-state-analogue:GLC-GLC-HMC-AGL-GLC
1hnyA01Bound:_CABound:_CLUnbound
UnboundUnboundUnbound
1amyA02UnboundUnboundUnbound
UnboundUnboundUnbound
1avaA02UnboundUnboundUnbound
UnboundUnboundUnbound
1avaB02UnboundUnboundUnbound
UnboundUnboundUnbound
1bg9A02UnboundUnboundUnbound
UnboundUnboundUnbound
1bagA02UnboundUnboundUnbound
UnboundUnboundUnbound
2aaaA02UnboundUnboundUnbound
UnboundUnboundUnbound
2taaA02UnboundUnboundUnbound
UnboundUnboundUnbound
6taaA02UnboundUnboundUnbound
UnboundUnboundUnbound
7taaA02UnboundUnboundUnbound
UnboundUnboundUnbound
1aqhA02UnboundUnboundUnbound
UnboundUnboundUnbound
1aqmA02UnboundUnboundUnbound
UnboundUnboundUnbound
1b0iA02UnboundUnboundUnbound
UnboundUnboundUnbound
1clvA02UnboundUnboundUnbound
UnboundUnboundUnbound
1jaeA02UnboundUnboundUnbound
UnboundUnboundUnbound
1tmqA02UnboundUnboundUnbound
UnboundUnboundUnbound
1viwA02UnboundUnboundUnbound
UnboundUnboundUnbound
1bvnP02UnboundUnboundUnbound
UnboundUnboundUnbound
1dhkA02UnboundUnboundUnbound
UnboundUnboundUnbound
1jfhA02UnboundUnboundUnbound
UnboundUnboundUnbound
1oseA02UnboundUnboundUnbound
UnboundUnboundUnbound
1pifA02UnboundUnboundUnbound
UnboundUnboundUnbound
1pigA02UnboundUnboundUnbound
UnboundUnboundUnbound
1ppiA02UnboundUnboundUnbound
UnboundUnboundUnbound
1smdA02UnboundUnboundUnbound
UnboundUnboundUnbound
1bsiA02UnboundUnboundUnbound
UnboundUnboundUnbound
1cpuA02UnboundUnboundUnbound
UnboundUnboundUnbound
1hnyA02UnboundUnboundUnbound
UnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P04063, P00691, P56271, P10529, P29957, P29957, P56634, P00690, P04745, P04746
pdbCatalytic residuesCofactor-binding residuesModified residuescomment
1amyA01ASP 179;GLU 204;ASP 289
ASN  91;PHE 143;ASP 148;ASP 142(Calcium binding);GLU 108;THR 111;ASP 113;ASP 117(2nd calcium);ASP 127;ASP 138;ALA 141;ALA 146(3rd calcium)


1avaA01ASP 179;GLU 204;ASP 289
ASN  91;PHE 143;ASP 148;ASP 142(Calcium binding);GLU 108;THR 111;ASP 113;ASP 117(2nd calcium);ASP 127;ASP 138;ALA 141;ALA 146(3rd calcium)


1avaB01ASP 179;GLU 204;ASP 289
ASN  91;PHE 143;ASP 148;ASP 142(Calcium binding);GLU 108;THR 111;ASP 113;ASP 117(2nd calcium);ASP 127;ASP 138;ALA 141;ALA 146(3rd calcium)


1bg9A01ASP 179;GLU 204;ASP 289
ASN  91;ASP 142;PHE 143;ASP 148(Calcium binding);GLU 108;THR 111;ASP 113;ASP 117(2nd calcium);ASP 127;ASP 138;ALA 141;ALA 146(3rd calcium)


1bagA01ASP 176;       ;ASP 269
ASN 101;THR 137;ASP 146;HIS 180(Calcium binding);GLY 169;ASP 171(2nd calcium)

mutant E208Q
2aaaA01ASP 206;GLU 230;ASP 297
ASP 121;GLU 162;ASP 175;GLU 210(Calcium binding);ASP 206;GLU 230(Inhibitory calcium binding)


2taaA01ASP 206;GLU 230;ASP 297
ASN 121;GLU 162;ASP 175;HIS 210(Calcium binding);ASP 206;GLU 230(Inhibitory calcium binding)


6taaA01ASP 206;GLU 230;ASP 297
ASN 121;GLU 162;ASP 175;HIS 210(Calcium binding);ASP 206;GLU 230(Inhibitory calcium binding)


7taaA01ASP 206;GLU 230;ASP 297
ASN 121;GLU 162;ASP 175;HIS 210(Calcium binding);ASP 206;GLU 230(Inhibitory calcium binding)


1aqhA01ASP 174;GLU 200;ASP 264
ASN  88;GLN 135;ASP 144;HIS 178(Calcium binding);ARG 172;ASN 262;LYS 300(Chloride binding)


1aqmA01ASP 174;GLU 200;ASP 264
ASN  88;GLN 135;ASP 144;HIS 178(Calcium binding);ARG 172;ASN 262;LYS 300(Chloride binding)


1b0iA01ASP 174;GLU 200;ASP 264
ASN  88;GLN 135;ASP 144;HIS 178(Calcium binding);ARG 172;ASN 262;LYS 300(Chloride binding)


1clvA01ASP 185;GLU 222;ASP 287
ASN  98;ARG 146;ASP 155;HIS 189(Calcium binding);ARG 183;ASN 285;ARG 321(Chloride binding)


1jaeA01ASP 185;GLU 222;ASP 287
ASN  98;ARG 146;ASP 155;HIS 189(Calcium binding);ARG 183;ASN 285;ARG 321(Chloride binding)


1tmqA01ASP 185;GLU 222;ASP 287
ASN  98;ARG 146;ASP 155;HIS 189(Calcium binding);ARG 183;ASN 285;ARG 321(Chloride binding)


1viwA01ASP 185;GLU 222;ASP 287
ASN  98;ARG 146;ASP 155;HIS 189(Calcium binding);ARG 183;ASN 285;ARG 321(Chloride binding)


1bvnP01ASP 197;GLU 233;ASP 300
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)


1dhkA01ASP 197;GLU 233;ASP 300
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)


1jfhA01ASP 197;GLU 233;ASP 300
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)


1oseA01ASP 197;GLU 233;ASP 300
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)


1pifA01ASP 197;GLU 233;ASP 300
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)


1pigA01ASP 197;GLU 233;ASP 300
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)


1ppiA01ASP 197;GLU 233;ASP 300
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)


1smdA01ASP 197;GLU 233;ASP 300
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
ASN 350(Deamidation)

1bsiA01ASP 197;GLU 233;ASP 300
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)


1cpuA01ASP 197;GLU 233;ASP 300
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)


1hnyA01ASP 197;GLU 233;ASP 300
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)


1amyA02



1avaA02



1avaB02



1bg9A02



1bagA02



2aaaA02



2taaA02



6taaA02



7taaA02



1aqhA02



1aqmA02



1b0iA02



1clvA02



1jaeA02



1tmqA02



1viwA02



1bvnP02



1dhkA02



1jfhA02



1oseA02



1pifA02



1pigA02



1ppiA02



1smdA02

ASN 412;ASN 459(Deamidation)

1bsiA02



1cpuA02



1hnyA02




References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.699-700
[9]Fig. 1, Fig. 2, p.215, p.219-2203
[18]Fig. 6, p.207-2083
[22]Fig. 2, p.298-3015
[23]p.6292-6293
[27]p.1580-1582
[37]Scheme 24
[38]Fig. 2, p.10843-108454
[43]Fig. 1, p.201-2032
[44]p.403-404
[45]p.211-214
[46]p.620-622
[47]p.565-568
[61]Fig. 2, p.4785-478910
[62]Fig. 5, p.261-2642
[69]Fig. 2, Fig. 8A, p.77074
[70]Fig. 2, p.4-58
[77]Fig. 3, p.4277-42788
[78]Scheme 1, p.4500-450210
[79]Fig. 34

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (5 ANGSTROMS)
JournalActa Crystallogr B
Year1980
Volume36
Pages416-21
AuthorsPayan F, Haser R, Pierrot M, Frey M, Astier JP, Abadie B, Duee B, Buisson G
TitleThe three-dimensional structure of [alpha]-amylase from porcine pancreas at 5 A resolution - the active-site location.
Related Swiss-protP00690
[2]
CommentsX-RAY CRYSTALLOGRAPHY (3 ANGSTROMS)
PubMed ID6156152
JournalJ Biochem (Tokyo)
Year1980
Volume87
Pages1555-8
AuthorsMatsuura Y, Kusunoki M, Harada W, Tanaka N, Iga Y, Yasuoka N, Toda H, Narita K, Kakudo M
TitleMolecular structure of taka-amylase A. I. Backbone chain folding at 3 A resolution.
Related Swiss-protP10529
[3]
PubMed ID6611158
JournalBiochem Biophys Res Commun
Year1984
Volume122
Pages75-81
AuthorsProdanov E, Seigner C, Marchis-Mouren G
TitleSubsite profile of the active center of porcine pancreatic alpha-amylase. Kinetic studies using maltooligosaccharides as substrates.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (3 ANGSTROMS)
PubMed ID6609921
JournalJ Biochem (Tokyo)
Year1984
Volume95
Pages697-702
AuthorsMatsuura Y, Kusunoki M, Harada W, Kakudo M
TitleStructure and possible catalytic residues of Taka-amylase A.
Related PDB2taa
Related Swiss-protP10529
[5]
PubMed ID3872211
JournalEur J Biochem
Year1985
Volume148
Pages161-8
AuthorsSeigner C, Prodanov E, Marchis-Mouren G
TitleOn porcine pancreatic alpha-amylase action: kinetic evidence for the binding of two maltooligosaccharide molecules (maltose, maltotriose and o-nitrophenylmaltoside) by inhibition studies. Correlation with the five-subsite energy profile.
[6]
PubMed ID3496084
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Year1987
Volume242
Pages681-7
AuthorsReddy MK, Heda GD, Reddy JK
TitlePurification and characterization of alpha-amylase from rat pancreatic acinar carcinoma. Comparison with pancreatic alpha-amylase.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS)
PubMed ID3502087
JournalEMBO J
Year1987
Volume6
Pages3909-16
AuthorsBuisson G, Duee E, Haser R, Payan F
TitleThree dimensional structure of porcine pancreatic alpha-amylase at 2.9 A resolution. Role of calcium in structure and activity.
Related Swiss-protP00690
[8]
PubMed ID3267138
JournalJ Protein Chem
Year1988
Volume7
Pages399-415
AuthorsMacGregor EA
TitleAlpha-amylase structure and activity.
[9]
PubMed ID2784982
JournalBiochim Biophys Acta
Year1989
Volume995
Pages214-20
AuthorsTao BY, Reilly PJ, Robyt JF
TitleDetection of a covalent intermediate in the mechanism of action of porcine pancreatic alpha-amylase by using 13C nuclear magnetic resonance.
[10]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS)
PubMed ID2207069
JournalBiochemistry
Year1990
Volume29
Pages6244-9
AuthorsBoel E, Brady L, Brzozowski AM, Derewenda Z, Dodson GG, Jensen VJ, Petersen SB, Swift H, Thim L, Woldike HF
TitleCalcium binding in alpha-amylases: an X-ray diffraction study at 2.1-A resolution of two enzymes from Aspergillus.
Related PDB2aaa
Related Swiss-protP56271
[11]
PubMed ID2143471
JournalEur J Biochem
Year1990
Volume191
Pages287-95
AuthorsHayashi M, Tsuru A, Mitsui T, Takahashi N, Hanzawa H, Arata Y, Akazawa T
TitleStructure and biosynthesis of the xylose-containing carbohydrate moiety of rice alpha-amylase.
[12]
CommentsX-ray crystallography
PubMed ID1930835
JournalActa Crystallogr B
Year1991
Volume47
Pages535-44
AuthorsSwift HJ, Brady L, Derewenda ZS, Dodson EJ, Dodson GG, Turkenburg JP, Wilkinson AJ
TitleStructure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method.
Related PDB6taa
[13]
PubMed ID1806988
JournalScand J Clin Lab Invest
Year1991
Volume51
Pages735-8
AuthorsHuguet J, Fuentes-Arderiu X
TitleBiological variation in the catalytic concentration of pancreatic alpha-amylase and triacylglycerol lipase in serum.
[14]
PubMed ID1606147
JournalBiochemistry
Year1992
Volume31
Pages5232-6
AuthorsMatsui I, Ishikawa K, Miyairi S, Fukui S, Honda K
TitleAlteration of bond-cleavage pattern in the hydrolysis catalyzed by Saccharomycopsis alpha-amylase altered by site-directed mutagenesis.
[15]
PubMed ID1576155
JournalBiochim Biophys Acta
Year1992
Volume1120
Pages281-8
AuthorsTakase K, Matsumoto T, Mizuno H, Yamane K
TitleSite-directed mutagenesis of active site residues in Bacillus subtilis alpha-amylase.
[16]
PubMed ID1369074
JournalBiosci Biotechnol Biochem
Year1992
Volume56
Pages1792-6
AuthorsKawaguchi T, Nagae H, Murao S, Arai M
TitlePurification and some properties of a Haim-sensitive alpha-amylase from newly isolated Bacillus sp. No. 195.
[17]
PubMed ID1377974
JournalBiosci Biotechnol Biochem
Year1992
Volume56
Pages207-10
AuthorsNagashima T, Tada S, Kitamoto K, Gomi K, Kumagai C, Toda H
TitleSite-directed mutagenesis of catalytic active-site residues of Taka-amylase A.
[18]
PubMed ID1569044
JournalJ Biochem (Tokyo)
Year1992
Volume111
Pages204-9
AuthorsIsoda Y, Shimizu Y, Hashimoto A, Fujiwara H, Nitta Y, Kagemoto A
TitleMechanism of hydrolyses of phenyl alpha-maltosides catalyzed by taka-amylase A.
[19]
PubMed ID8421303
JournalJ Mol Biol
Year1993
Volume229
Pages235-8
AuthorsChang C, Kim KK, Hwang KY, Choi MU, Suh SW
TitleCrystallization and preliminary X-ray crystallographic analysis of alpha-amylase from Bacillus subtilis.
[20]
PubMed ID8263932
JournalJ Mol Biol
Year1993
Volume234
Pages1282-3
AuthorsMizuno H, Morimoto Y, Tsukihara T, Matsumoto T, Takase K
TitleCrystallization and preliminary X-ray studies of wild type and catalytic-site mutant alpha-amylase from Bacillus subtilis.
[21]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), AND REVISIONS
PubMed ID8515451
JournalJ Mol Biol
Year1993
Volume231
Pages785-99
AuthorsQian M, Haser R, Payan F
TitleStructure and molecular model refinement of pig pancreatic alpha-amylase at 2.1 A resolution.
Related Swiss-protP00690
[22]
PubMed ID7945374
JournalBiochem Biophys Res Commun
Year1994
Volume204
Pages297-302
AuthorsMazur AK, Haser R, Payan F
TitleThe catalytic mechanism of alpha-amylases based upon enzyme crystal structures and model building calculations.
[23]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
PubMed ID8193143
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Year1994
Volume33
Pages6284-94
AuthorsQian M, Haser R, Buisson G, Duee E, Payan F
TitleThe active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-A resolution.
Related PDB1ppi
Related Swiss-protP00690
[24]
PubMed ID7822101
JournalInt J Pept Protein Res
Year1994
Volume44
Pages245-52
AuthorsHansen G, Heese O, Hohne WE, Hofemeister B
Titlealpha-Amylases from Thermoactinomyces vulgaris: characteristics, primary structure and structure prediction.
[25]
PubMed ID8206864
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Year1994
Volume115
Pages179-81
AuthorsMiyazaki T, Morimoto T, Fukuyama K, Matsubara H
TitleCrystallization and preliminary X-ray diffraction studies of the alpha-amylase inhibitor coded 0.19 from wheat kernel.
[26]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS)
PubMed ID8196040
JournalJ Mol Biol
Year1994
Volume239
Pages104-21
AuthorsKadziola A, Abe J, Svensson B, Haser R
TitleCrystal and molecular structure of barley alpha-amylase.
Related PDB1amy
Related Swiss-protP04063
[27]
PubMed ID8107092
JournalJ Mol Biol
Year1994
Volume235
Pages1560-84
AuthorsLarson SB, Greenwood A, Cascio D, Day J, McPherson A
TitleRefined molecular structure of pig pancreatic alpha-amylase at 2.1 A resolution.
[28]
PubMed ID8107117
JournalJ Mol Biol
Year1994
Volume236
Pages368-71
AuthorsVallee F, Kadziola A, Bourne Y, Abe J, Svensson B, Haser R
TitleCharacterization, crystallization and preliminary X-ray crystallographic analysis of the complex between barley alpha-amylase and the bifunctional alpha-amylase/subtilisin inhibitor from barley seeds.
[29]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF COMPLEX WITH INHIBITOR
PubMed ID7897663
JournalJ Mol Biol
Year1995
Volume247
Pages99-110
AuthorsWiegand G, Epp O, Huber R
TitleThe crystal structure of porcine pancreatic alpha-amylase in complex with the microbial inhibitor Tendamistat.
Related PDB1bvn
Related Swiss-protP00690
[30]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS)
PubMed ID8528071
JournalProtein Sci
Year1995
Volume4
Pages1730-42
AuthorsBrayer GD, Luo Y, Withers SG
TitleThe structure of human pancreatic alpha-amylase at 1.8 A resolution and comparisons with related enzymes.
Related PDB1hny
Related Swiss-protP04746
[31]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS)
JournalActa Crystallogr D Biol Crystallogr
Year1996
Volume52
Pages435-46
AuthorsRamasubbu N, Paloth V, Luo Y, Brayer GD, Levine MJ
TitleStructure of Human Salivary [alpha]-Amylase at 1.6 A Resolution: Implications for its Role in the Oral Cavity.
Related PDB1smd
Related Swiss-protP04745
[32]
PubMed ID8862470
JournalClin Chim Acta
Year1996
Volume251
Pages145-62
AuthorsGubern G, Canalias F, Gella FJ, Colinet E, Profilis C, Calam DH, Ceriotti F, Dufaux J, Hadjivassiliou AG, Lessinger JM, Lorentz K, Vassault A
TitleProduction and certification of an enzyme reference material for pancreatic alpha-amylase (CRM 476).
[33]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), AND REVISIONS
PubMed ID8681972
JournalEur J Biochem
Year1996
Volume238
Pages561-9
AuthorsGilles C, Astier JP, Marchis-Mouren G, Cambillau C, Payan F
TitleCrystal structure of pig pancreatic alpha-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose.
Related PDB1ose
Related Swiss-protP00690
[34]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS)
PubMed ID8757803
JournalJ Mol Biol
Year1996
Volume260
Pages409-21
AuthorsMachius M, Vertesy L, Huber R, Wiegand G
TitleCarbohydrate and protein-based inhibitors of porcine pancreatic alpha-amylase: structure analysis and comparison of their binding characteristics.
Related PDB1pif,1pig
Related Swiss-protP00690
[35]
PubMed ID8897615
JournalProtein Sci
Year1996
Volume5
Pages2128-9
AuthorsAghajari N, Feller G, Gerday C, Haser R
TitleCrystallization and preliminary X-ray diffraction studies of alpha-amylase from the antarctic psychrophile Alteromonas haloplanctis A23.
[36]
CommentsX-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF COMPLEX WITH INHIBITOR
PubMed ID8994970
JournalStructure
Year1996
Volume4
Pages1441-52
AuthorsBompard-Gilles C, Rousseau P, Rouge P, Payan F
TitleSubstrate mimicry in the active center of a mammalian alpha-amylase: structural analysis of an enzyme-inhibitor complex.
Related PDB1dhk
Related Swiss-protP00690
[37]
PubMed ID8636115
JournalJ Biol Chem
Year1996
Volume271
Pages6889-94
AuthorsMcCarter JD, Withers SG
TitleUnequivocal identification of Asp-214 as the catalytic nucleophile of Saccharomyces cerevisiae alpha-glucosidase using 5-fluoro glycosyl fluorides.
[38]
CommentsX-RAY CRYSTALLOGRAPHY (1.98 ANGSTROMS)
PubMed ID9283074
JournalBiochemistry
Year1997
Volume36
Pages10837-45
AuthorsBrzozowski AM, Davies GJ
TitleStructure of the Aspergillus oryzae alpha-amylase complexed with the inhibitor acarbose at 2.0 A resolution.
Related PDB7taa
Related Swiss-protP10529
[39]
PubMed ID9434115
JournalBiochim Biophys Acta
Year1997
Volume1343
Pages243-50
AuthorsMatsumoto T, Makimoto S, Taniguchi Y
TitleEffect of pressure on the mechanism of hydrolysis of maltotetraose, maltopentaose, and maltohexose catalyzed by porcine pancreatic alpha-amylase.
[40]
PubMed ID9199514
JournalFEBS Lett
Year1997
Volume409
Pages109-14
AuthorsStrobl S, Gomis-Ruth FX, Maskos K, Frank G, Huber R, Glockshuber R
TitleThe alpha-amylase from the yellow meal worm: complete primary structure, crystallization and preliminary X-ray analysis.
[41]
PubMed ID9278396
JournalJ Biol Chem
Year1997
Volume272
Pages22456-63
AuthorsMatsui I, Svensson B
TitleImproved activity and modulated action pattern obtained by random mutagenesis at the fourth beta-alpha loop involved in substrate binding to the catalytic (beta/alpha)8-barrel domain of barley alpha-amylase 1.
[42]
CommentsX-RAY CRYSTALLOGRAPHY (2.03 ANGSTROMS)
PubMed ID9385631
JournalProtein Sci
Year1997
Volume6
Pages2285-96
AuthorsQian M, Spinelli S, Driguez H, Payan F
TitleStructure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution.
Related PDB1jfh
Related Swiss-protP00690
[43]
PubMed ID9649747
JournalBiochem Soc Trans
Year1998
Volume26
Pages198-204
AuthorsGottschalk TE, Fierobe HP, Mirgorodskaya E, Clarke AJ, Tull D, Sigurskjold BW, Christensen T, Payre N, Frandsen TP, Juge N, McGuire KA, Cottaz S, Roepstorff P, Driguez H, Williamson G, Svensson B
TitleStructure, function and protein engineering of starch-degrading enzymes.
[44]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 42-466
PubMed ID9514750
JournalJ Mol Biol
Year1998
Volume277
Pages393-407
AuthorsFujimoto Z, Takase K, Doui N, Momma M, Matsumoto T, Mizuno H
TitleCrystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose.
Related PDB1bag
Related Swiss-protP00691
[45]
CommentsX-ray crystallography
PubMed ID9571044
JournalJ Mol Biol
Year1998
Volume278
Pages205-17
AuthorsKadziola A, Sogaard M, Svensson B, Haser R
TitleMolecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis.
Related PDB1bg9
[46]
CommentsX-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS)
PubMed ID9600843
JournalJ Mol Biol
Year1998
Volume278
Pages617-28
AuthorsStrobl S, Maskos K, Betz M, Wiegand G, Huber R, Gomis-Ruth FX, Glockshuber R
TitleCrystal structure of yellow meal worm alpha-amylase at 1.64 A resolution.
Related PDB1jae
Related Swiss-protP56634
[47]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 25-477
PubMed ID9541387
JournalProtein Sci
Year1998
Volume7
Pages564-72
AuthorsAghajari N, Feller G, Gerday C, Haser R
TitleCrystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor.
Related PDB1aqh,1aqm
Related Swiss-protP29957
[48]
CommentsX-ray crystallography
PubMed ID9862804
JournalStructure
Year1998
Volume6
Pages1503-16
AuthorsAghajari N, Feller G, Gerday C, Haser R
TitleStructures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.
Related PDB1b0i
[49]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
PubMed ID9687373
JournalStructure
Year1998
Volume6
Pages911-21
AuthorsStrobl S, Maskos K, Wiegand G, Huber R, Gomis-Ruth FX, Glockshuber R
TitleA novel strategy for inhibition of alpha-amylases: yellow meal worm alpha-amylase in complex with the Ragi bifunctional inhibitor at 2.5 A resolution.
Related PDB1tmq
Related Swiss-protP56634
[50]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF COMPLEX WITH BASI
PubMed ID9634702
JournalStructure
Year1998
Volume6
Pages649-59
AuthorsVallee F, Kadziola A, Bourne Y, Juy M, Rodenburg KW, Svensson B, Haser R
TitleBarley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution.
Related PDB1ava
Related Swiss-protP04063
[51]
CommentsX-ray crystallography
PubMed ID10089450
JournalActa Crystallogr D Biol Crystallogr
Year1999
Volume55
Pages360-2
AuthorsNahoum V, Farisei F, Le-Berre-Anton V, Egloff MP, Rouge P, Poerio E, Payan F
TitleA plant-seed inhibitor of two classes of alpha-amylases: X-ray analysis of Tenebrio molitor larvae alpha-amylase in complex with the bean Phaseolus vulgaris inhibitor.
Related PDB1viw
[52]
PubMed ID10547530
JournalBiopolymers
Year1999
Volume50
Pages751-62
AuthorsAndre G, Buleon A, Haser R, Tran V
TitleAmylose chain behavior in an interacting context. III. Complete occupancy of the AMY2 barley alpha-amylase cleft and comparison with biochemical data.
[53]
Medline ID99198742
PubMed ID10100643
JournalFEBS Lett
Year1999
Volume446
Pages203-6
AuthorsYoung NM, Thibault P, Watson DC, Chrispeels MJ
TitlePost-translational processing of two alpha-amylase inhibitors and an arcelin from the common bean, Phaseolus vulgaris.
[54]
PubMed ID10650713
JournalIndian J Biochem Biophys
Year1999
Volume36
Pages150-7
AuthorsDey S, Agarwal SO
TitleCharacterization of a thermostable alpha-amylase from a thermophilic Streptomyces megasporus strain SD12.
[55]
PubMed ID10222200
JournalJ Mol Biol
Year1999
Volume287
Pages907-21
AuthorsKamitori S, Kondo S, Okuyama K, Yokota T, Shimura Y, Tonozuka T, Sakano Y
TitleCrystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution.
[56]
PubMed ID10556241
JournalProtein Eng
Year1999
Volume12
Pages819-24
AuthorsHasegawa K, Kubota M, Matsuura Y
TitleRoles of catalytic residues in alpha-amylases as evidenced by the structures of the product-complexed mutants of a maltotetraose-forming amylase.
[57]
CommentsX-ray crystallography
PubMed ID10091666
JournalProtein Sci
Year1999
Volume8
Pages635-43
AuthorsRydberg EH, Sidhu G, Vo HC, Hewitt J, Cote HC, Wang Y, Numao S, MacGillivray RT, Overall CM, Brayer GD, Withers SG
TitleCloning, mutagenesis, and structural analysis of human pancreatic alpha-amylase expressed in Pichia pastoris.
Related PDB1bsi
[58]
CommentsX-ray crystallography
PubMed ID10508777
JournalStructure Fold Des
Year1999
Volume7
Pages1079-88
AuthorsPereira PJ, Lozanov V, Patthy A, Huber R, Bode W, Pongor S, Strobl S
TitleSpecific inhibition of insect alpha-amylases: yellow meal worm alpha-amylase in complex with the amaranth alpha-amylase inhibitor at 2.0 A resolution.
Related PDB1clv
[59]
PubMed ID10657258
JournalBiochem J
Year2000
Volume346 Pt 1
Pages201-8
AuthorsNahoum V, Roux G, Anton V, Rouge P, Puigserver A, Bischoff H, Henrissat B, Payan F
TitleCrystal structures of human pancreatic alpha-amylase in complex with carbohydrate and proteinaceous inhibitors.
[60]
PubMed ID10947962
JournalBiochem J
Year2000
Volume350 Pt 2
Pages477-84
AuthorsSumitani J, Tottori T, Kawaguchi T, Arai M
TitleNew type of starch-binding domain: the direct repeat motif in the C-terminal region of Bacillus sp. no. 195 alpha-amylase contributes to starch binding and raw starch degrading.
[61]
CommentsX-ray crystallography
PubMed ID10769135
JournalBiochemistry
Year2000
Volume39
Pages4778-91
AuthorsBrayer GD, Sidhu G, Maurus R, Rydberg EH, Braun C, Wang Y, Nguyen NT, Overall CM, Withers SG
TitleSubsite mapping of the human pancreatic alpha-amylase active site through structural, kinetic, and mutagenesis techniques.
Related PDB1cpu
[62]
PubMed ID11150610
JournalBiochim Biophys Acta
Year2000
Volume1543
Pages253-74
AuthorsNielsen JE, Borchert TV
TitleProtein engineering of bacterial alpha-amylases.
[63]
PubMed ID10969023
JournalBiophys J
Year2000
Volume79
Pages1629-36
AuthorsFitter J, Heberle J
TitleStructural equilibrium fluctuations in mesophilic and thermophilic alpha-amylase.
[64]
PubMed ID11210138
JournalBiosci Biotechnol Biochem
Year2000
Volume64
Pages2692-5
AuthorsIchikawa K, Tonozuka T, Yokota T, Shimura Y, Sakano Y
TitleAnalysis of catalytic residues of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) by site-directed mutagenesis.
[65]
PubMed ID10925206
JournalGene
Year2000
Volume253
Pages95-105
AuthorsD'Amico S, Gerday C, Feller G
TitleStructural similarities and evolutionary relationships in chloride-dependent alpha-amylases.
[66]
PubMed ID11307950
JournalJ Protein Chem
Year2000
Volume19
Pages663-9
AuthorsTibbot BK, Wong DW, Robertson GH
TitleA functional raw starch-binding domain of barley alpha-amylase expressed in Escherichia coli.
[67]
PubMed ID10775658
JournalProtein Eng
Year2000
Volume13
Pages167-77
AuthorsDa Silva MC, de Sa MF, Chrispeels MJ, Togawa RC, Neshich G
TitleAnalysis of structural and physico-chemical parameters involved in the specificity of binding between alpha-amylases and their inhibitors.
[68]
PubMed ID11669621
JournalBiochemistry
Year2001
Volume40
Pages12844-54
AuthorsGottschalk TE, Tull D, Aghajari N, Haser R, Svensson B
TitleSpecificity modulation of barley alpha-amylase through biased random mutagenesis involving a conserved tripeptide in beta --> alpha loop 7 of the catalytic (beta/alpha)(8)-barrel domain.
[69]
PubMed ID11412124
JournalBiochemistry
Year2001
Volume40
Pages7700-9
AuthorsQian M, Nahoum V, Bonicel J, Bischoff H, Henrissat B, Payan F
TitleEnzyme-catalyzed condensation reaction in a mammalian alpha-amylase. High-resolution structural analysis of an enzyme-inhibitor complex.
[70]
PubMed ID11257505
JournalBiochim Biophys Acta
Year2001
Volume1546
Pages1-20
AuthorsMacGregor EA, Janecek S, Svensson B
TitleRelationship of sequence and structure to specificity in the alpha-amylase family of enzymes.
[71]
PubMed ID11342250
JournalBiochim Biophys Acta
Year2001
Volume1525
Pages29-36
AuthorsSlaughter SL, Ellis PR, Butterworth PJ
TitleAn investigation of the action of porcine pancreatic alpha-amylase on native and gelatinised starches.
[72]
PubMed ID11527532
JournalCarbohydr Res
Year2001
Volume334
Pages309-13
AuthorsOhtaki A, Kondo S, Shimura Y, Tonozuka T, Sakano Y, Kamitori S
TitleRole of Phe286 in the recognition mechanism of cyclomaltooligosaccharides (cyclodextrins) by Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structures of the mutant TVAIIs, F286A and F286Y, and kinetic analyses of the Phe286-replaced mutant TVAIIs.
[73]
PubMed ID11508823
JournalGen Physiol Biophys
Year2001
Volume20
Pages7-32
AuthorsHorvathova V, Janecek S, Sturdik E
TitleAmylolytic enzymes: molecular aspects of their properties.
[74]
PubMed ID11226882
JournalJ Biochem (Tokyo)
Year2001
Volume129
Pages423-8
AuthorsKondo S, Ohtaki A, Tonozuka T, Sakano Y, Kamitori S
TitleStudies on the hydrolyzing mechanism for cyclodextrins of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structure of the mutant E354A complexed with beta-cyclodextrin, and kinetic analyses on cyclodextrins.
[75]
PubMed ID11522925
JournalProtein Eng
Year2001
Volume14
Pages505-12
AuthorsNielsen JE, Borchert TV, Vriend G
TitleThe determinants of alpha-amylase pH-activity profiles.
[76]
PubMed ID12115056
JournalArch Microbiol
Year2002
Volume178
Pages115-23
AuthorsLo HF, Lin LL, Chiang WY, Chie MC, Hsu WH, Chang CT
TitleDeletion analysis of the C-terminal region of the alpha-amylase of Bacillus sp. strain TS-23.
[77]
PubMed ID11914073
JournalBiochemistry
Year2002
Volume41
Pages4273-80
AuthorsAghajari N, Roth M, Haser R
TitleCrystallographic evidence of a transglycosylation reaction: ternary complexes of a psychrophilic alpha-amylase.
[78]
PubMed ID11914097
JournalBiochemistry
Year2002
Volume41
Pages4492-502
AuthorsRydberg EH, Li C, Maurus R, Overall CM, Brayer GD, Withers SG
TitleMechanistic analyses of catalysis in human pancreatic alpha-amylase: detailed kinetic and structural studies of mutants of three conserved carboxylic acids.
[79]
PubMed ID12423336
JournalEur J Biochem
Year2002
Volume269
Pages5377-90
AuthorsMori H, Bak-Jensen KS, Svensson B
TitleBarley alpha-amylase Met53 situated at the high-affinity subsite -2 belongs to a substrate binding motif in the beta-->alpha loop 2 of the catalytic (beta/alpha)8-barrel and is critical for activity and substrate specificity.
[80]
PubMed ID12379350
JournalJ Immunol Methods
Year2002
Volume269
Pages29-37
AuthorsGoncalves O, Dintinger T, Blanchard D, Tellier C
TitleFunctional mimicry between anti-Tendamistat antibodies and alpha-amylase.
[81]
PubMed ID12051850
JournalJ Mol Biol
Year2002
Volume318
Pages443-53
AuthorsKamitori S, Abe A, Ohtaki A, Kaji A, Tonozuka T, Sakano Y
TitleCrystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution.
[82]
PubMed ID12578360
JournalBiochemistry
Year2003
Volume42
Pages1478-87
AuthorsNielsen PK, Bonsager BC, Berland CR, Sigurskjold BW, Svensson B
TitleKinetics and energetics of the binding between barley alpha-amylase/subtilisin inhibitor and barley alpha-amylase 2 analyzed by surface plasmon resonance and isothermal titration calorimetry.
[83]
PubMed ID12581203
JournalEur J Biochem
Year2003
Volume270
Pages635-45
AuthorsJanecek S, Svensson B, MacGregor EA
TitleRelation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain.

comments
The enzyme belongs to the glycosyl hydrolase family-13.
The polysaccharide substrate/product data contained in the PDB data are described from the non-reducing end to the reducing end.
The Swiss-prot data are corresponding to the PDB data as follows:
AMY2_HORVU;P04063: 1amy, 1ava, 1bg9
AMY_BACSU;P00691 : 1bag
AMYA_ASPNG;P56271: 2aaa
AMYA_ASPOR;P10529: 2taa, 6taa, 7taa
AMY_ALTHA;P29957 : 1aqh, 1aqm, 1b0i
AMY_TENMO;P56634 : 1clv, 1jae, 1tmq, 1viw
AMYP_PIG;P00690 : 1bvn, 1dhk, 1jfh, 1ose, 1pif, 1pig, 1ppi
AMYS_HUMAN;P04745: 1smd
AMYP_HUMAN;P04746: 1bsi, 1cpu, 1hny
Binding modes of calcium and chloride ions are various among the alpha-amylase enzymes. However, the first calcium ion binding sites can be superimposed, except for those from barley (Swiss-prot; P04063). The enzyme from barley has got the distinct binding sites for three calcium ions. Although the calcium ions are necessary for the catalytic activities, they are not involved in catalysis, and may stabilize the enzyme structures. On the other hand, in chloride-dependent alpha-amlyases, the chloride ion seems to be involved in catalysis, by raising the pKa of the catalytic glutamic acid by its electrostatic effect (see [47]).
A variety of catalytic mechanisms has been proposed. In the proposed mechanisms, three acidic residues at the active site (Asp at beta-4, Glu at beta-5 and Asp at beta-7 of (alpha/beta)8 barrel structure) seemed to be involved in catalysis.
Paper [22] proposed a ring-opening mechanism, in which opening of glucose ring is induced by a nucleophilic attack by a catalytic water. However, this mechanism is more complicated and unlikely than any other proposed ones, as no experimental evidence has been reported so far.
On the other hand, a single displacement mechanism and a double displacement mechanism have been proposed and discussed. In both the mechanisms, an oxocarbenium ion seems to be formed either as a long-lived intermediate, or as a transition state.
Papers ([4], [23], [27], [44] & [46]) proposed and supported a single displacement mechanism, in which a catalytic water would hydrolyze the glycosidic bond of the substrate directly, assisted by the acid-base catalysis. In this mechanism, the Glu resiue at the C-terminal end of beta-5 acts as a general acid, protonating the leaving oxygen atom(O4). This protonation results in the formation of oxocarbenium ion intermediate (dissociative mechanism). Next, the general base activates the catalytic water, which would make a nucleophilic attack on the C1 atom of the intermediate.
On the other hand, the other papers ([9], [18], [37], [38], [43], [45], [47], [61], [62], [69], [70], [77] & [78]) supported a double displacement mechanism, in which a covalent enzyme-glycosyl intermediate would be formed prior to the hydrolysis by a catalytic water. Moreover, the papers, [18], [45], [47], [70] & [77], mentioned that protonation to the glycosidic oxygen (O4) by a general base, the Glu residue at beta-5, would occur, forming an oxocarbenium ion-like transtion state, prior to the nucleophilic attack by the Asp residue at beta-4 (suggesting a dissociative mechanism instead of an associative mechanism). After the formation of the covalent intermediate, Glu at beta-5 acts as a general base to activate a water molecule. The activated water makes a nucleophilic attack on the intermediate to complete the reaction.
Considering that the anomeric configuration of the glycosidic bond is retatined, the double displacement mechanism is more compelling than the single displacement mechanism. Moreover, the papers, [9] & [37], reproted that the experimental identification of the enzyme-glycosyl intermediate could be carried out. Taken together, the double displacement mechanism seems to be supported. In this reaction mechanism, the third acidic residue, Asp at beta-7, seems to stabilize the half-chair conformation during the transition state, and raise the pKa of the catalytic acid, Glu at beta-5. However, to acts as a modulator for Glu at beta-5, Asp at beta-7 is a bit too distant.

createdupdated
2003-11-042009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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