WORKLIST ENTRIES (1):
GLHYDLASE14A View alignment View Structure Bacterial beta-amylase signature
Type of fingerprint: COMPOUND with 5 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; PR00842 GLHYDLASE14B; PR00847 HYALURONDASE; PR00848 SPERMPH20
INTERPRO; IPR000125
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-amylases.
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]. Sequence alignments allow us to relate
features of the bacterial beta-amylases to the soybean structure.
GLHYDLASE14A is a 5-element fingerprint that provides a signature for
the bacterial beta-amylases. The fingerprint was derived from an initial
alignment of 4 sequences: the motifs were drawn from conserved sections
spanning virtually the full alignment length, focusing on those regions
that characterise the bacterial beta-amylases but distinguish them from
the rest of the beta-amylase family - motif 1 spans helices 5 and 6, beta-
strand 6 and the N-terminus of strand 7; motif 2 includes the C-terminal
half of helix 12; and motif 3 includes helix 13. Two iterations on OWL30.0
were required to reach convergence, at which point a true set comprising 6
sequences was identified. A single partial match was also found, AB000264,
a fragment from Bacillus firmus that lacks the portion of sequence bearing
motif 5.
An update on SPTR37_9f identified a true set of 4 sequences.
SUMMARY INFORMATION
4 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
5| 4 4 4 4 4
4| 0 0 0 0 0
3| 0 0 0 0 0
2| 0 0 0 0 0
--+--------------------------
| 1 2 3 4 5
True positives..
AMYB_BACCI AMYB_PAEPO AMYB_THETU AMYB_BACCE
PROTEIN TITLES
AMYB_BACCI BETA-AMYLASE PRECURSOR (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALT
AMYB_PAEPO BETA/ALPHA-AMYLASE PRECURSOR [INCLUDES: BETA-AMYLASE (EC 3.2
AMYB_THETU BETA-AMYLASE, THERMOPHILIC PRECURSOR (EC 3.2.1.2) (1,4-ALPHA
AMYB_BACCE BETA-AMYLASE PRECURSOR (EC 3.2.1.2) (1,4-ALPHA-D-GLUCAN MALT
SCAN HISTORY
OWL30_0 2 75 NSINGLE
SPTR37_9f 2 6 NSINGLE
INITIAL MOTIF SETS
GLHYDLASE14A1 Length of motif = 20 Motif number = 1
Bacterial beta-amylase motif I - 1
PCODE ST INT
WSKGSADEMQFKDESGYVNN AMYB_BACCI 136 136
SSKGSADEMQFKDESGYANS AMYB_BACPO 135 135
WTKDTQDNMQYKDEAGNWDN AMYB_THETU 132 132
WNQKSDDSLYFKSETGTVNK AMYB_BACCE 138 138
GLHYDLASE14A2 Length of motif = 16 Motif number = 2
Bacterial beta-amylase motif II - 1
PCODE ST INT
TAMTTKYGSLDKINAA AMYB_BACCI 232 76
TAMNDKYGSLDKINAA AMYB_BACPO 231 76
NAMKSKYGTIAAVNSA AMYB_THETU 228 76
LWVLNKYGSLNEVNKA AMYB_BACCE 235 77
GLHYDLASE14A3 Length of motif = 18 Motif number = 3
Bacterial beta-amylase motif III - 1
PCODE ST INT
WGTNLTSMSQISPPTDSD AMYB_BACCI 248 0
WGTKLTSLSQINPPTDGD AMYB_BACPO 247 0
WGTSLTDFSQISPPTDGD AMYB_THETU 244 0
WGTKLISELAILPPSDGE AMYB_BACCE 251 0
GLHYDLASE14A4 Length of motif = 22 Motif number = 4
Bacterial beta-amylase motif IV - 1
PCODE ST INT
TRFGYNGFTLLRINNIVNSDGS AMYB_BACCI 413 147
TKFGYHGFTLLRINNLVNNDGS AMYB_BACPO 412 147
TGYNFSGFTLLRLSNIVNSDGS AMYB_THETU 412 150
FNYNFSGFTLLRYQDVMYNNSL AMYB_BACCE 416 147
GLHYDLASE14A5 Length of motif = 14 Motif number = 5
Bacterial beta-amylase motif V - 1
PCODE ST INT
PGVKMPDSEISGYA AMYB_BACCI 490 55
PGVKMQDAEISGYA AMYB_BACPO 487 53
GPASCPNYPTWTIT AMYB_THETU 490 56
DSHSNDWRGNVVLP AMYB_BACCE 489 51
FINAL MOTIF SETS
GLHYDLASE14A1 Length of motif = 20 Motif number = 1
Bacterial beta-amylase motif I - 2
PCODE ST INT
WSKGSADEMQFKDESGYVNN AMYB_BACCI 136 136
SSKGSADEMQFKDESGYANS AMYB_PAEPO 135 135
WTKDTQDNMQYKDEAGNWDN AMYB_THETU 132 132
WNQKSDDSLYFKSETGTVNK AMYB_BACCE 138 138
GLHYDLASE14A2 Length of motif = 16 Motif number = 2
Bacterial beta-amylase motif II - 2
PCODE ST INT
TAMTTKYGSLDKINAA AMYB_BACCI 232 76
TAMNDKYGSLDKINAA AMYB_PAEPO 231 76
NAMKSKYGTIAAVNSA AMYB_THETU 228 76
LWVLNKYGSLNEVNKA AMYB_BACCE 235 77
GLHYDLASE14A3 Length of motif = 18 Motif number = 3
Bacterial beta-amylase motif III - 2
PCODE ST INT
WGTNLTSMSQISPPTDSD AMYB_BACCI 248 0
WGTKLTSLSQINPPTDGD AMYB_PAEPO 247 0
WGTSLTDFSQISPPTDGD AMYB_THETU 244 0
WGTKLISELAILPPSDGE AMYB_BACCE 251 0
GLHYDLASE14A4 Length of motif = 22 Motif number = 4
Bacterial beta-amylase motif IV - 2
PCODE ST INT
TRFGYNGFTLLRINNIVNSDGS AMYB_BACCI 413 147
TKFGYHGFTLLRINNLVNNDGS AMYB_PAEPO 412 147
TGYNFSGFTLLRLSNIVNSDGS AMYB_THETU 412 150
FNYNFSGFTLLRYQDVMYNNSL AMYB_BACCE 416 147
GLHYDLASE14A5 Length of motif = 14 Motif number = 5
Bacterial beta-amylase motif V - 2
PCODE ST INT
PGVKMPDSEISGYA AMYB_BACCI 490 55
PGVKMQDAEISGYA AMYB_PAEPO 487 53
GPASCPNYPTWTIT AMYB_THETU 490 56
DSHSNDWRGNVVLP AMYB_BACCE 489 51
User query: Display/Full Code "GLHYDLASE14A"