WORKLIST ENTRIES (1):
GLHYDLASE14B View alignment View Structure Plant beta-amylase signature
Type of fingerprint: COMPOUND with 7 elements
Links:
PRINTS; PR00131 GLHYDRLASE1; PR00132 GLHYDRLASE2; PR00133 GLHYDRLASE3
PRINTS; PR00732 GLHYDRLASE4; PR00733 GLHYDRLASE6; PR00734 GLHYDRLASE7
PRINTS; PR00735 GLHYDRLASE8; PR00134 GLHYDRLASE10; PR00911 GLHYDRLASE11
PRINTS; PR00736 GLHYDRLASE15; PR00737 GLHYDRLASE16; PR00738 GLHYDRLASE20
PRINTS; PR00739 GLHYDRLASE26; PR00740 GLHYDRLASE27; PR00741 GLHYDRLASE29
PRINTS; PR00843 GLHYDRLASE30; PR00742 GLHYDRLASE35; PR00743 GLHYDRLASE36
PRINTS; PR00744 GLHYDRLASE37; PR00745 GLHYDRLASE39; PR00746 GLHYDRLASE41
PRINTS; PR00747 GLHYDRLASE47; PR00844 GLHYDRLASE48; PR00845 GLHYDRLASE52
PRINTS; PR00846 GLHYDRLASE56; PR00849 GLHYDRLASE58; PR00850 GLHYDRLASE59
PRINTS; PR00748 MELIBIASE; PR00137 LYSOZYME; PR00684 T4LYSOZYME
PRINTS; PR00749 LYSOZYMEG; PR00110 ALPHAAMYLASE; PR00750 BETAAMYLASE
PRINTS; PR00841 GLHYDLASE14A; PR00847 HYALURONDASE; PR00848 SPERMPH20
INTERPRO; IPR001371
PDB; 1BTC 3Dinfo
SCOP; 1BTC
CATH; 1BTC
Creation date 11-MAR-1998; UPDATE 07-JUN-1999
1. HENRISSAT, B.
A classification of glycosyl hydrolases based on amino acid sequence
similarities.
BIOCHEM.J. 280 309-316 (1991).
2. HENRISSAT, B. AND BAIROCH, A.
New families in the classification of glycosyl hydrolases based on amino
acid sequence similarities.
BIOCHEM.J. 293 781-788 (1993).
3. HENRISSAT, B. AND BAIROCH, A.
Updating the sequence-based classification of glycosyl hydrolases.
BIOCHEM.J. 316 695-696 (1996).
4. EL HASSOUNI, M., HENRISSAT, B., CHIPPAUX, M. AND BARRAS, F.
Nucleotide sequences of the Arb genes, which control beta-glucosidase
utilisation in Erwinia chrysanthemi - Comparison with the Escherichia
coli Bgl operon and evidence for a new beta-glycohydrolase family
including enzymes from eubacteria, archaebacteria and humans.
J.BACTERIOL. 174 765-777 (1992).
5. VIKSONIELSEN, A., CHRISTENSEN, T.M., BOJKO, M. AND MARCUSSEN, J.
Purification and characterization of beta-amylase from leaves of potato
(Solanum tuberosum).
PHYSIOLOGIA PLANTARUM 99 190-196 (1997).
6. MIKAMI, B., SATO, M., SHIBATA, T., HIROSE, M., AIBARA, S., KATSUBE, Y.
AND MORITA, Y.
Three-dimensional structure of soybean beta-amylase determined at 3.0 A
resolution: preliminary chain tracing of the complex with alpha-cyclodextrin.
J.BIOCHEM. 112 541-546 (1992).
O-Glycosyl hydrolases (EC 3.2.1.-) are a widespread group of enzymes that
hydrolyse the glycosidic bond between two or more carbohydrates, or between
a carbohydrate and a non-carbohydrate moiety. A classification system for
glycosyl hydrolases, based on sequence similarity, has led to the definition
of up to 60 different families [1-4] (http://expasy.hcuge.ch/cgi-bin/lists?
glycosid.txt). Family 14 (EC 3.2.1.2) encompasses the beta-amylase enzymes.
Beta-amylases, which are found in plants and bacteria, hydrolyse 1,4-alpha-
glucosidic linkages in starch-type polysaccharide substrates, removing
successive maltose units from the non-reducing ends of the chains [5]. In
potato plants, the enzyme has been found to work optimally at 40 degrees C,
becoming unstable above this temperature [5]. On the basis of sequence
comparisons, plant and bacterial beta-amylases can be readily distinguished
from each other.
The 3D structure of a complex of soybean beta-amylase with an inhibitor
(alpha-cyclodextrin) has been determined to 3.0A resolution by X-ray
diffraction [6]. The enzyme folds into large and small domains: the large
domain has a (beta alpha)8 super-secondary structural core, while the smaller
is formed from two long loops extending from the beta-3 and beta-4 strands
of the (beta alpha)8 fold [6]. The interface of the two domains, together
with shorter loops from the (beta alpha)8 core, form a deep cleft, in which
the inhibitor binds [6]. Two maltose molecules also bind in the cleft,
one sharing a binding site with alpha-cyclodextrin, and the other sitting
more deeply in the cleft [6].
GLHYDLASE14B is a 7-element fingerprint that provides a signature for
plant beta-amylases. The fingerprint was derived from an initial
alignment of 5 sequences: the motifs were drawn from conserved regions
spanning the C-terminal half of the alignment, focusing on those regions
that characterise the plant beta-amylases but distinguish them from the rest
of the beta-amylase family - motif 1 includes beta-strand 8; motif 2 spans
helix 17; motif 3 spans the C-terminus of helix 20 and strand 11; motif 4
includes the N-terminus of helix 21; motif 6 spans the C-terminus of strand
12, helix 22 and the N-terminus of helix 23; motif 7 encodes the remainder
of helix 23. Two iterations on OWL30.0 were required to reach convergence,
at which point a true set comprising 15 sequences was identified. Two partial
matches were also found: AMYB_SECCE is a fragment from Secale cereale that
lacks the portion of sequence bearing motif 1; and AF012345 is a fragment
from Hordeum vulgare that matches motifs 2-5.
An update on SPTR37_9f identified a true set of 13 sequences.
SUMMARY INFORMATION
13 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
7| 13 13 13 13 13 13 13
6| 0 0 0 0 0 0 0
5| 0 0 0 0 0 0 0
4| 0 0 0 0 0 0 0
3| 0 0 0 0 0 0 0
2| 0 0 0 0 0 0 0
--+------------------------------------
| 1 2 3 4 5 6 7
True positives..
Q42795 Q42989 Q42990 AMYB_SOYBN
AMYB_WHEAT AMYB_VIGUN Q08335 AMYB_MEDSA
AMYB_TRIRP AMYB_IPOBA AMYB_MAIZE AMYB_HORVU
AMYB_ARATH
PROTEIN TITLES
Q42795 BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
Q42989 BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
Q42990 BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
AMYB_SOYBN BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
AMYB_WHEAT BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
AMYB_VIGUN BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
Q08335 BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
AMYB_MEDSA BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
AMYB_TRIRP BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
AMYB_IPOBA BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
AMYB_MAIZE BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
AMYB_HORVU BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
AMYB_ARATH BETA-AMYLASE (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
SCAN HISTORY
OWL30_3 2 75 NSINGLE
SPTR37_9f 2 14 NSINGLE
INITIAL MOTIF SETS
GLHYDLASE14B1 Length of motif = 10 Motif number = 1
Plant beta-amylase motif I - 1
PCODE ST INT
GVIVDIEVGL AMYB_ARATH 175 175
GVIVDIEVGL AMYB_HORVU 170 170
GVVVDIEVGL AMYB_MAIZE 170 170
GDIVDIEVGC AMYB_IPOBA 173 173
GLIIDIEVGL AMYB_SOYBN 172 172
GLHYDLASE14B2 Length of motif = 11 Motif number = 2
Plant beta-amylase motif II - 1
PCODE ST INT
IARMLSKHYGI AMYB_ARATH 331 146
IARMLKRHRAS AMYB_HORVU 326 146
IAHMLTRHRAS AMYB_MAIZE 326 146
IARMLARHHAT AMYB_IPOBA 330 147
IARMLSRHHAI AMYB_SOYBN 328 146
GLHYDLASE14B3 Length of motif = 10 Motif number = 3
Plant beta-amylase motif III - 1
PCODE ST INT
AWKEGIEVAG AMYB_ARATH 373 31
GWREGLNVAC AMYB_HORVU 368 31
GWREGLNLAC AMYB_MAIZE 368 31
GWKEYIDVAG AMYB_IPOBA 372 31
GWREDIRVAG AMYB_SOYBN 370 31
GLHYDLASE14B4 Length of motif = 10 Motif number = 4
Plant beta-amylase motif IV - 1
PCODE ST INT
ETYGAKGYNQ AMYB_ARATH 387 4
PRYDPTAYNT AMYB_HORVU 382 4
NRYDATAYNT AMYB_MAIZE 382 4
PRYDATAYNQ AMYB_IPOBA 386 4
PRYDATAYNQ AMYB_SOYBN 384 4
GLHYDLASE14B5 Length of motif = 17 Motif number = 5
Plant beta-amylase motif V - 1
PCODE ST INT
RPNGVNPNGKPKLRMYG AMYB_ARATH 402 5
RPHGINQSGPPEHKLFG AMYB_HORVU 397 5
RPQGINKNGPPEHKLHG AMYB_MAIZE 397 5
RPNGVNLNGPPKLKMSG AMYB_IPOBA 401 5
KPQGVNNNGPPKLSMFG AMYB_SOYBN 399 5
GLHYDLASE14B6 Length of motif = 15 Motif number = 6
Plant beta-amylase motif VI - 1
PCODE ST INT
TYLRLSDTVFQENNF AMYB_ARATH 420 1
TYLRLSNQLVEGQNY AMYB_HORVU 415 1
TYLRVSDELFQEQNY AMYB_MAIZE 415 1
TYLRLSDDLLQTDNF AMYB_IPOBA 419 1
TYLRLSDDLLQKSNF AMYB_SOYBN 417 1
GLHYDLASE14B7 Length of motif = 15 Motif number = 7
Plant beta-amylase motif VII - 1
PCODE ST INT
ELFKKLVRKMHADQD AMYB_ARATH 435 0
VNFKTFVDRMHANLP AMYB_HORVU 430 0
TTFKTFVRRMHANLD AMYB_MAIZE 430 0
ELFKKFVKKMHADLD AMYB_IPOBA 434 0
NIFKKFVLKMHADQD AMYB_SOYBN 432 0
FINAL MOTIF SETS
GLHYDLASE14B1 Length of motif = 10 Motif number = 1
Plant beta-amylase motif I - 2
PCODE ST INT
GLIIDIEVGL Q42795 173 173
GVIVDIEVGL Q42989 170 170
GVIVDIEVGL Q42990 170 170
GLIIDIEVGL AMYB_SOYBN 172 172
GTIVDIEVGL AMYB_WHEAT 170 170
EVIIDIEVGL AMYB_VIGUN 173 173
GTIVDIEVGL Q08335 170 170
EVIIDIEVGL AMYB_MEDSA 173 173
ELIIDIEVGL AMYB_TRIRP 173 173
GDIVDIEVGC AMYB_IPOBA 173 173
GVVVDIEVGL AMYB_MAIZE 170 170
GVIVDIEVGL AMYB_HORVU 170 170
GVIVDIEVGL AMYB_ARATH 175 175
GLHYDLASE14B2 Length of motif = 11 Motif number = 2
Plant beta-amylase motif II - 2
PCODE ST INT
IARMLSRHHAI Q42795 329 146
IARMLTRHRAC Q42989 326 146
IARMLTRHRAC Q42990 326 146
IARMLSRHHAI AMYB_SOYBN 328 146
IARMLTRHHAS AMYB_WHEAT 326 146
IAKMVSRHHAS AMYB_VIGUN 329 146
IARMLTRHHAS Q08335 326 146
IAKIVSRHHAI AMYB_MEDSA 329 146
IAKMVSRHHGI AMYB_TRIRP 329 146
IARMLARHHAT AMYB_IPOBA 330 147
IAHMLTRHRAS AMYB_MAIZE 326 146
IARMLKRHRAS AMYB_HORVU 326 146
IARMLSKHYGI AMYB_ARATH 331 146
GLHYDLASE14B3 Length of motif = 10 Motif number = 3
Plant beta-amylase motif III - 2
PCODE ST INT
GWREDIRVAG Q42795 371 31
GWREGLHVAC Q42989 368 31
GWREGLHVAC Q42990 368 31
GWREDIRVAG AMYB_SOYBN 370 31
GWREGLHVAC AMYB_WHEAT 368 31
GWRENIEVAG AMYB_VIGUN 371 31
GWREGLHVAC Q08335 368 31
GWRENIEVAG AMYB_MEDSA 371 31
GWRENIEVAG AMYB_TRIRP 371 31
GWKEYIDVAG AMYB_IPOBA 372 31
GWREGLNLAC AMYB_MAIZE 368 31
GWREGLNVAC AMYB_HORVU 368 31
AWKEGIEVAG AMYB_ARATH 373 31
GLHYDLASE14B4 Length of motif = 10 Motif number = 4
Plant beta-amylase motif IV - 2
PCODE ST INT
PRYDATAYNQ Q42795 385 4
GRYDATAYNT Q42989 382 4
GRYDATAYNT Q42990 382 4
PRYDATAYNQ AMYB_SOYBN 384 4
GRYDATAYNT AMYB_WHEAT 382 4
SRYDATAYNQ AMYB_VIGUN 385 4
GRYDATAYNT Q08335 382 4
SRYDATAYNQ AMYB_MEDSA 385 4
SRYDATAYNQ AMYB_TRIRP 385 4
PRYDATAYNQ AMYB_IPOBA 386 4
NRYDATAYNT AMYB_MAIZE 382 4
PRYDPTAYNT AMYB_HORVU 382 4
ETYGAKGYNQ AMYB_ARATH 387 4
GLHYDLASE14B5 Length of motif = 17 Motif number = 5
Plant beta-amylase motif V - 2
PCODE ST INT
RPQGVNNNGPPKLSMFG Q42795 400 5
RPHGINKNGPPEHKLFG Q42989 397 5
RPHGINKNGPPEYKLFG Q42990 397 5
KPQGVNNNGPPKLSMFG AMYB_SOYBN 399 5
RPKGINKNGPPEHKLFG AMYB_WHEAT 397 5
RPQGVNKDGPPKHRMYG AMYB_VIGUN 400 5
RPKGINENGPPQHKLYG Q08335 397 5
RPQGVNKDGPPKLRMYG AMYB_MEDSA 400 5
RPQGVNKDGPPKLRMYG AMYB_TRIRP 400 5
RPNGVNLNGPPKLKMSG AMYB_IPOBA 401 5
RPQGINKNGPPEHKLHG AMYB_MAIZE 397 5
RPHGINQSGPPEHKLFG AMYB_HORVU 397 5
RPNGVNPNGKPKLRMYG AMYB_ARATH 402 5
GLHYDLASE14B6 Length of motif = 15 Motif number = 6
Plant beta-amylase motif VI - 2
PCODE ST INT
TYLRLSDDLLQKSNF Q42795 418 1
TYLRLSDELLEGQNY Q42989 415 1
TYLRLSDELLEGQNY Q42990 415 1
TYLRLSDDLLQKSNF AMYB_SOYBN 417 1
TYLRLSNELLEGQNY AMYB_WHEAT 415 1
TYLRLSDELLQQSNF AMYB_VIGUN 418 1
TYLRLSNELQEGQNY Q08335 415 1
TYLRLSDDLMQQSNF AMYB_MEDSA 418 1
TYLRLSDDLLQESNF AMYB_TRIRP 418 1
TYLRLSDDLLQTDNF AMYB_IPOBA 419 1
TYLRVSDELFQEQNY AMYB_MAIZE 415 1
TYLRLSNQLVEGQNY AMYB_HORVU 415 1
TYLRLSDTVFQENNF AMYB_ARATH 420 1
GLHYDLASE14B7 Length of motif = 15 Motif number = 7
Plant beta-amylase motif VII - 2
PCODE ST INT
NIFKKFVLKMHADQD Q42795 433 0
STFKTFVKRMHANLV Q42989 430 0
STFKTFVKRMHANLV Q42990 430 0
NIFKKFVLKMHADQD AMYB_SOYBN 432 0
ATFQTFVEKMHANLG AMYB_WHEAT 430 0
DIFKKFVVKMHADQD AMYB_VIGUN 433 0
ATFQTFVEKMHANLG Q08335 430 0
DIFKKFVVKMHADQD AMYB_MEDSA 433 0
EIFKKFVVKMHADQS AMYB_TRIRP 433 0
ELFKKFVKKMHADLD AMYB_IPOBA 434 0
TTFKTFVRRMHANLD AMYB_MAIZE 430 0
VNFKTFVDRMHANLP AMYB_HORVU 430 0
ELFKKLVRKMHADQD AMYB_ARATH 435 0
User query: Display/Full Code "GLHYDLASE14B"