Reviewed, UniProtKB/Swiss-Prot P06278 (AMY_BACLI)

Names and origin

Protein names

Recommended name:
    Alpha-amylase
    EC=3.2.1.1
Alternative name(s):
    1,4-alpha-D-glucan glucanohydrolase
    BLA

Gene names

Name:	amyS
Synonyms:	amyL

Organism

Bacillus licheniformis

Taxonomic identifier

1402 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	512 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)

Catalytic activity	Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in oligosaccharides and polysaccharides.
Cofactor	Binds 3 calcium ions per subunit. Binds 1 sodium ion per subunit.
Subunit structure	Monomer.
Biotechnological use	Used in the food industry for high temperature liquefaction of starch-containing mashes and in the detergent industry to remove starch. Sold under the name Termamyl by Novozymes.
Sequence similarities	Belongs to the glycosyl hydrolase 13 family.
Biophysicochemical properties	pH dependence: Active up to pH 11. Temperature dependence: Active up to 100 degrees Celsius.

Ontologies

Keywords
Biological process	Carbohydrate metabolism
Domain	Signal
Ligand	Calcium Metal-binding
Molecular function	Glycosidase Hydrolase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	carbohydrate metabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	alpha-amylase activity Inferred from electronic annotation. Source: EC calcium ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 29

29

Ref.8

Chain

30 – 512

483

Alpha-amylase

PRO_0000001332

Sites

Active site

260

1

Nucleophile

Active site

290

1

Proton donor

Active site

357

1

By similarity

Metal binding

133

1

Calcium 1

Metal binding

190

1

Calcium 2

Metal binding

190

1

Sodium

Metal binding

210

1

Calcium 2; via carbonyl oxygen

Metal binding

212

1

Calcium 2

Metal binding

212

1

Sodium

Metal binding

223

1

Calcium 1

Metal binding

223

1

Sodium

Metal binding

229

1

Calcium 1

Metal binding

229

1

Sodium

Metal binding

231

1

Calcium 2

Metal binding

233

1

Calcium 2

Metal binding

264

1

Calcium 1; via carbonyl oxygen

Metal binding

329

1

Calcium 3; via carbonyl oxygen

Metal binding

436

1

Calcium 3

Metal binding

459

1

Calcium 3

Experimental info

Mutagenesis

64

1

H → X: No effect on thermostability. Ref.10

Mutagenesis

150

1

D → X: Decrease in thermostability. Ref.12

Mutagenesis

155

1

N → X: Decrease in thermostability. Ref.12

Mutagenesis

162

1

H → I or V: Increase in thermostability. Ref.10

Mutagenesis

162

1

H → P: Great decrease in thermostability. Ref.10

Mutagenesis

162

1

H → V: Great increase in thermostability; when associated with F-219; V-238; S-293 and Y-294. Ref.10

Mutagenesis

175

1

R → X: No effect on thermostability. Ref.12

Mutagenesis

193

1

D → A, C, E, H or R: Loss of activity. Ref.12

Mutagenesis

201

1

N → H or K: Increase in thermostability. Ref.12

Mutagenesis

201

1

N → R: Great increase in thermostability. Ref.12

Mutagenesis

207

1

Q → X: No effect on thermostability. Ref.12

Mutagenesis

217

1

N → P: Great increase in thermostability. Ref.12

Mutagenesis

219

1

N → A, E, Q, P or S: Great decrease in thermostability. Ref.12

Mutagenesis

219

1

N → F: Great increase in thermostability. Great increase in thermostability; when associated with V-162; V-238; S-293 and Y-294. Ref.12

Mutagenesis

219

1

N → L: Increase in thermostability. Ref.12

Mutagenesis

221

1

N → X: Great decrease in thermostability. Ref.12

Mutagenesis

229

1

D → X: Great decrease in thermostability. Ref.12

Mutagenesis

233

1

D → X: Great decrease in thermostability. Ref.12

Mutagenesis

238

1

A → V: Increase in thermostability. Great increase in thermostability; when associated with V-162; F-219; S-293 and Y-294. Ref.11

Mutagenesis

276

1

H → X: No effect on thermostability. Ref.10

Mutagenesis

292

1

W → L: Decrease in activity; when associated with Y-315. Ref.14

Mutagenesis

293

1

Q → S: Increase in thermostability; when associated with Y-294. Great increase in thermostability; when associated with V-162; F-219; V-238 and Y-294. Ref.13

Mutagenesis

294

1

N → Y: Increase in thermostability; when associated with S-293. Great increase in thermostability; when associated with V-162; F-219; V-238 and S-293. Ref.13

Mutagenesis

298

1

A → H, K, L, Q or R: Loss of activity. Ref.12

Mutagenesis

300

1

E → X: No effect on thermostability. Ref.12

Mutagenesis

315

1

V → F: Decrease in activity. Ref.14

Mutagenesis

315

1

V → Y: Increase in activity. Decrease in activity; when associated with W-292. Ref.14

Mutagenesis

322

1

H → X: No effect on thermostability. Ref.10

Mutagenesis

359

1

Q → X: No effect on thermostability. Ref.12

Mutagenesis

365

1

E → H: Loss of activity. Ref.12

Mutagenesis

435

1

H → X: No effect on thermostability. Ref.10

Mutagenesis

479

1

H → X: No effect on thermostability. Ref.10

Sequence conflict

4

1

Q → H Ref.4

Sequence conflict

13

1

T → P Ref.3

Sequence conflict

13

1

T → P Ref.4

Sequence conflict

33

1

N → I in AAA22232. Ref.6

Sequence conflict

38

1

Q → Y AA sequence Ref.8

Sequence conflict

48

1

G → R Ref.4

Sequence conflict

62 – 64

3

AEH → VED Ref.4

Sequence conflict

68 – 69

2

AV → VA Ref.4

Sequence conflict

72

1

P → S Ref.4

Sequence conflict

81

1

A → D Ref.3

Sequence conflict

81

1

A → D Ref.4

Sequence conflict

105 – 117

13

Missing Ref.4

Sequence conflict

117

1

K → N in AAO26743. Ref.3

Sequence conflict

158

1

I → T in AAO26743. Ref.3

Sequence conflict

162

1

H → Q in AAO26743. Ref.3

Sequence conflict

163

1

R → L in AAA22240. Ref.2

Sequence conflict

171

1

H → Q in AAO26743. Ref.3

Sequence conflict

218

1

E → V in AAO26743. Ref.3

Sequence conflict

237 – 238

2

VA → AT in AAO26743. Ref.3

Sequence conflict

339

1

S → G Ref.2

Sequence conflict

339

1

S → G Ref.3

Sequence conflict

347

1

L → V in AAO26743. Ref.3

Sequence conflict

349

1

A → S in AAA22240. Ref.2

Sequence conflict

385

1

S → A in AAO26743. Ref.3

Sequence conflict

390

1

V → I in AAO26743. Ref.3

Sequence conflict

401

1

D → A in AAO26743. Ref.3

Sequence conflict

421

1

K → I in AAO26743. Ref.3

Sequence conflict

464

1

A → T in AAO26743. Ref.3

Sequence conflict

487 – 488

2

EP → DS in AAO26743. Ref.3

Sequence conflict

493

1

S → A in AAO26743. Ref.3

Secondary structure

1

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512

Helix Strand Turn

Details...

Beta strand

36 – 38

3

Helix

50 – 56

7

Helix

58 – 63

6

Beta strand

68 – 70

3

Beta strand

101 – 103

3

Helix

109 – 121

13

Beta strand

125 – 130

6

Beta strand

133 – 135

3

Beta strand

139 – 149

11

Beta strand

151 – 153

3

Beta strand

162 – 170

9

Turn

173 – 177

5

Helix

186 – 188

3

Beta strand

189 – 193

5

Turn

196 – 199

4

Beta strand

204 – 206

3

Turn

207 – 209

3

Beta strand

213 – 215

3

Helix

223 – 226

4

Beta strand

228 – 230

3

Helix

235 – 252

18

Beta strand

256 – 259

4

Helix

262 – 264

3

Helix

267 – 281

15

Beta strand

286 – 289

4

Helix

296 – 305

10

Turn

306 – 308

3

Beta strand

310 – 313

4

Helix

315 – 326

12

Turn

327 – 329

3

Helix

333 – 337

5

Beta strand

338 – 340

3

Helix

341 – 344

4

Helix

346 – 348

3

Beta strand

349 – 353

5

Turn

356 – 358

3

Turn

370 – 372

3

Helix

373 – 382

10

Beta strand

383 – 391

9

Helix

392 – 396

5

Helix

410 – 422

13

Beta strand

428 – 431

4

Beta strand

434 – 442

9

Beta strand

453 – 461

9

Beta strand

463 – 468

6

Helix

471 – 473

3

Beta strand

477 – 480

4

Beta strand

495 – 501

7

Beta strand

506 – 510

5

Sequences

	Sequence		Length	Mass (Da)
	P06278-1 [UniParc]. Last modified January 1, 1988. Version 1. Checksum: D8BB77759CD4C482	FASTA	512	58,549
	10 20 30 40 50 60 MKQQKRLYAR LLTLLFALIF LLPHSAAAAA NLNGTLMQYF EWYMPNDGQH WKRLQNDSAY 70 80 90 100 110 120 LAEHGITAVW IPPAYKGTSQ ADVGYGAYDL YDLGEFHQKG TVRTKYGTKG ELQSAIKSLH 130 140 150 160 170 180 SRDINVYGDV VINHKGGADA TEDVTAVEVD PADRNRVISG EHRIKAWTHF HFPGRGSTYS 190 200 210 220 230 240 DFKWHWYHFD GTDWDESRKL NRIYKFQGKA WDWEVSNENG NYDYLMYADI DYDHPDVAAE 250 260 270 280 290 300 IKRWGTWYAN ELQLDGFRLD AVKHIKFSFL RDWVNHVREK TGKEMFTVAE YWQNDLGALE 310 320 330 340 350 360 NYLNKTNFNH SVFDVPLHYQ FHAASTQGGG YDMRKLLNST VVSKHPLKAV TFVDNHDTQP 370 380 390 400 410 420 GQSLESTVQT WFKPLAYAFI LTRESGYPQV FYGDMYGTKG DSQREIPALK HKIEPILKAR 430 440 450 460 470 480 KQYAYGAQHD YFDHHDIVGW TREGDSSVAN SGLAALITDG PGGAKRMYVG RQNAGETWHD 490 500 510 ITGNRSEPVV INSEGWGEFH VNGGSVSIYV QR

References

[1]	"Complete nucleotide sequence of a gene coding for heat- and pH-stable alpha-amylase of Bacillus licheniformis: comparison of the amino acid sequences of three bacterial liquefying alpha-amylases deduced from the DNA sequences." Yuuki T., Nomura T., Tezuka H., Tsuboi A., Yamagata H., Tsukagoshi N., Udaka S. J. Biochem. 98:1147-1156(1985) [PubMed: 2418011] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 27811 / CCRC 10494 / FERM P-1038.
[2]	"Structural genes encoding the thermophilic alpha-amylases of Bacillus stearothermophilus and Bacillus licheniformis." Gray G.L., Mainzer S.E., Rey M.W., Lamsa M.H., Kindle K.L., Carmona C., Requadt C. J. Bacteriol. 166:635-643(1986) [PubMed: 3009417] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Expression and secretion of an alpha-amylase gene from a native strain of Bacillus licheniformis in Escherichia coli by T7 promoter and putative signal peptide of the gene." Shahhoseini M., Ziaee A.A., Ghaemi N. J. Appl. Microbiol. 95:1250-1254(2003) [PubMed: 14632998] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Isolation and the 5'-end nucleotide sequence of Bacillus licheniformis alpha-amylase gene." Sibakov M., Palva I. Eur. J. Biochem. 145:567-572(1984) [PubMed: 6334606] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-121. Strain: ATCC 14580 / DSM 13 / IFO 12200 / NCIB 9375 / NCTC 10341.
[5]	"Nucleotide sequence of the 5' region of the Bacillus licheniformis alpha-amylase gene: comparison with the B. amyloliquefaciens gene." Stephens M.A., Ortlepp S.A., Ollington J.F., McConnell D.J. J. Bacteriol. 158:369-372(1984) [PubMed: 6609154] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-104.
[6]	"In vivo genetic engineering: homologous recombination as a tool for plasmid construction." Jorgensen L., Hansen C.K., Poulsen G.B., Diderichsen B. Gene 96:37-41(1990) [PubMed: 2265757] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-33.
[7]	"Bacillus licheniformis alpha-amylase gene, amyL, is subject to promoter-independent catabolite repression in Bacillus subtilis." Laoide B.M., Chambliss G.H., McConnell D.J. J. Bacteriol. 171:2435-2442(1989) [PubMed: 2540150] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-29.
[8]	"N-terminal amino acid sequence of Bacillus licheniformis alpha-amylase: comparison with Bacillus amyloliquefaciens and Bacillus subtilis enzymes." Kuhn H., Fietzek P.P., Lampen J.O. J. Bacteriol. 149:372-373(1982) [PubMed: 6172418] [Abstract] Cited for: PROTEIN SEQUENCE OF 30-47.
[9]	"Action pattern and subsite mapping of Bacillus licheniformis alpha-amylase (BLA) with modified maltooligosaccharide substrates." Kandra L., Gyemant G., Remenyik J., Hovanszki G., Liptak A. FEBS Lett. 518:79-82(2002) [PubMed: 11997021] [Abstract] Cited for: MAPPING OF SUBSTRATE-BINDING SITE.
[10]	"Use of amber suppressors to investigate the thermostability of Bacillus licheniformis alpha-amylase. Amino acid replacements at 6 histidine residues reveal a critical position at His-133." Declerck N., Joyet P., Gaillardin C., Masson J.-M. J. Biol. Chem. 265:15481-15488(1990) [PubMed: 2394736] [Abstract] Cited for: MUTAGENESIS OF HIS-64; HIS-162; HIS-276; HIS-322; HIS-435 AND HIS-479. Strain: ATCC 6598 / NRS 745.
[11]	"Hyperthermostable mutants of Bacillus licheniformis alpha-amylase: multiple amino acid replacements and molecular modelling." Declerck N., Joyet P., Trosset J.Y., Garnier J., Gaillardin C. Protein Eng. 8:1029-1037(1995) [PubMed: 8771184] [Abstract] Cited for: MUTAGENESIS OF ALA-238. Strain: ATCC 6598 / NRS 745.
[12]	"Probing structural determinants specifying high thermostability in Bacillus licheniformis alpha-amylase." Declerck N., Machius M., Wiegand G., Huber R., Gaillardin C. J. Mol. Biol. 301:1041-1057(2000) [PubMed: 10966804] [Abstract] Cited for: MUTAGENESIS OF ASP-150; ASN-155; ARG-175; ASP-193; ASN-201; GLN-207; ASN-217; ASN-219; ASN-221; ASP-229; ASP-233; ALA-298; GLU-300; GLN-359 AND GLU-365. Strain: ATCC 6598 / NRS 745.
[13]	"Hyperthermostabilization of Bacillus licheniformis alpha-amylase and modulation of its stability over a 50 degrees C temperature range." Declerck N., Machius M., Joyet P., Wiegand G., Huber R., Gaillardin C. Protein Eng. 16:287-293(2003) [PubMed: 12736372] [Abstract] Cited for: MUTAGENESIS OF GLN-293 AND ASN-294. Strain: ATCC 6598 / NRS 745.
[14]	"Alpha-amylase from Bacillus licheniformis mutants near to the catalytic site: effects on hydrolytic and transglycosylation activity." Rivera M.H., Lopez-Munguia A., Soberon X., Saab-Rincon G. Protein Eng. 16:505-514(2003) [PubMed: 12915728] [Abstract] Cited for: MUTAGENESIS OF TRP-292 AND VAL-315. Strain: ATCC 27811 / CCRC 10494 / FERM P-1038.
[15]	"Crystal structure of calcium-depleted Bacillus licheniformis alpha-amylase at 2.2-A resolution." Machius M., Wiegand G., Huber R. J. Mol. Biol. 246:545-559(1995) [PubMed: 7877175] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS). Strain: ATCC 27811 / CCRC 10494 / FERM P-1038.
[16]	"Activation of Bacillus licheniformis alpha-amylase through a disorder-->order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad." Machius M., Declerck N., Huber R., Wiegand G. Structure 6:281-292(1998) [PubMed: 9551551] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[17]	"Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes." Brzozowski A.M., Lawson D.M., Turkenburg J.P., Bisgaard-Frantzen H., Svendsen A., Borchert T.V., Dauter Z., Wilson K.S., Davies G.J. Biochemistry 39:9099-9107(2000) [PubMed: 10924103] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 330-512.
[18]	"Kinetic stabilization of Bacillus licheniformis alpha-amylase through introduction of hydrophobic residues at the surface." Machius M., Declerck N., Huber R., Wiegand G. J. Biol. Chem. 278:11546-11553(2003) [PubMed: 12540849] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANT VAL-162/PHE-219/VAL-238/SER-293/TYR-294. Strain: ATCC 6598 / NRS 745.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X03236 Genomic DNA. Translation: CAA26981.1.
M38570 Genomic DNA. Translation: AAA22226.1.
M13256 Genomic DNA. Translation: AAA22240.1.
AF438149 Genomic DNA. Translation: AAO26743.1.
K01984 Genomic DNA. Translation: AAA22193.1.
M62637 Genomic DNA. Translation: AAA22232.1.
M26412 Genomic DNA. Translation: AAA22237.1.

PIR

ALBSL. A91997.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BLI	X-ray	1.90	A	30-512	[»]
1BPL	X-ray	2.20	A	30-218	[»]
			B	219-512	[»]
1E3X	X-ray	1.90	A	-	[»]
1E3Z	X-ray	1.93	A	-	[»]
1E40	X-ray	2.20	A	-	[»]
1E43	X-ray	1.70	A	-	[»]
1OB0	X-ray	1.83	A	30-512	[»]
1VJS	X-ray	1.70	A	30-512	[»]

ModBase

Search...

Protein family/group databases

CAZy

GH13. Glycoside Hydrolase Family 13.

Enzyme and pathway databases

BRENDA

3.2.1.1. 1017.

Family and domain databases

InterPro

IPR013776. A-amylase_thermo.
IPR006047. Glyco_hydro_13_cat.
IPR006589. Glyco_hydro_13_sub_cat.
IPR013781. Glyco_hydro_sg_catalytic.
[Graphical view]

Gene3D

G3DSA:3.20.20.80. Glyco_hydro_cat. 1 hit.

Pfam

PF00128. Alpha-amylase. 1 hit.
[Graphical view]

PIRSF

PIRSF001021. Alph-amls_thrmst. 1 hit.

SMART

SM00642. Aamy. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

AMY_BACLI

Accession

Primary (citable) accession number: P06278
Secondary accession number(s): Q45283, Q84I71

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	January 1, 1988
Last modified:	June 16, 2009
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)