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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF SOYBEAN BETA-AMYLASE DETERMINED AT 3.0 ANGSTROMS RESOLUTION: PRELIMINARY CHAIN TRACING OF THE COMPLEX WITH ALPHA-CYCLODEXTRIN
 
Authors :  B. Mikami, E. J. Hehre, M. Sato, Y. Katsube, M. Hirose, Y. Morita, J. C. Sacchettini
Date :  18 Feb 93  (Deposition) - 31 Oct 93  (Release) - 07 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase(O-Glycosyl) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Mikami, E. J. Hehre, M. Sato, Y. Katsube, M. Hirose, Y. Morita, J. C. Sacchettini
The 2. 0-A Resolution Structure Of Soybean Beta-Amylase Complexed With Alpha-Cyclodextrin.
Biochemistry V. 32 6836 1993
PubMed-ID: 8334116
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-AMYLASE
    Chains: A
    EC Number: 3.2.1.2
    Engineered: YES
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2GLC6Ligand/IonALPHA-D-GLUCOSE
3SO41Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:384 , GLC A:497 , GLC A:501 , HOH A:756BINDING SITE FOR RESIDUE GLC A 496
02AC2SOFTWAREALA A:382 , LEU A:383 , LEU A:419 , GLC A:496 , GLC A:498 , HOH A:757BINDING SITE FOR RESIDUE GLC A 497
03AC3SOFTWAREALA A:382 , GLC A:497 , GLC A:499BINDING SITE FOR RESIDUE GLC A 498
04AC4SOFTWAREPHE A:200 , HIS A:300 , MET A:346 , GLC A:498 , GLC A:500 , HOH A:686BINDING SITE FOR RESIDUE GLC A 499
05AC5SOFTWARELEU A:383 , GLC A:499 , GLC A:501BINDING SITE FOR RESIDUE GLC A 500
06AC6SOFTWAREGLC A:496 , GLC A:500BINDING SITE FOR RESIDUE GLC A 501
07AC7SOFTWAREHIS A:146 , ARG A:326 , ARG A:372 , HOH A:627 , HOH A:822BINDING SITE FOR RESIDUE SO4 A 1
08AC8SOFTWARECYS A:95 , GLY A:96 , HOH A:606 , HOH A:811BINDING SITE FOR RESIDUE BME A 502
09AC9SOFTWAREARG A:162 , GLY A:287 , CYS A:288BINDING SITE FOR RESIDUE BME A 503
10BC1SOFTWARECYS A:343 , LEU A:344 , GLU A:345 , MET A:346 , PRO A:359 , VAL A:363BINDING SITE FOR RESIDUE BME A 504
11BC2SOFTWAREGLN A:445 , ASP A:446 , TYR A:447 , CYS A:448 , LYS A:453 , HOH A:595BINDING SITE FOR RESIDUE BME A 505
12S1AUTHORLEU A:383 , PRO A:384RESIDUES BINDING GLC A 496
13S2AUTHORALA A:382 , LEU A:383RESIDUES BINDING GLC A 497
14S3AUTHORTRP A:301 , ALA A:382RESIDUES BINDING GLC A 498
15S4AUTHORTRP A:198 , PHE A:200 , HIS A:300 , TRP A:301 , MET A:346 , LEU A:383RESIDUES BINDING GLC A 499
16S5AUTHORLEU A:383RESIDUES BINDING GLC A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BTC)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:200 -Pro A:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BTC)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_AMYLASE_1PS00506 Beta-amylase active site 1.AMYB_SOYBN94-102  1A:93-101
2BETA_AMYLASE_2PS00679 Beta-amylase active site 2.AMYB_SOYBN183-193  1A:182-192

(-) Exons   (0, 0)

(no "Exon" information available for 1BTC)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:491
 aligned with AMYB_SOYBN | P10538 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:491
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495 
           AMYB_SOYBN     6 SNMLLNYVPVYVMLPLGVVNVDNVFEDPDGLKEQLLQLRAAGVDGVMVDVWWGIIELKGPKQYDWRAYRSLFQLVQECGLTLQAIMSFHQCGGNVGDIVNIPIPQWVLDIGESNHDIFYTNRSGTRNKEYLTVGVDNEPIFHGRTAIEIYSDYMKSFRENMSDFLESGLIIDIEVGLGPAGELRYPSYPQSQGWEFPRIGEFQCYDKYLKADFKAAVARAGHPEWELPDDAGKYNDVPESTGFFKSNGTYVTEKGKFFLTWYSNKLLNHGDQILDEANKAFLGCKVKLAIKVSGIHWWYKVENHAAELTAGYYNLNDRDGYRPIARMLSRHHAILNFTCLEMRDSEQPSDAKSGPQELVQQVLSGGWREDIRVAGENALPRYDATAYNQIILNAKPQGVNNNGPPKLSMFGVTYLRLSDDLLQKSNFNIFKKFVLKMHADQDYCANPQKYNHAITPLKPSAPKIPIEVLLEATKPTLPFPWLPETDMKVDG 496
               SCOP domains d1btca_ A: beta-Amylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1btcA00 A:5-495 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh..eeeeeeee...........hhhhhhhhhhhhhh...eeeeeeehhhh..........hhhhhhhhhhhh...eeeeeee...e.........e...hhhhhhhhh.....eee..eeee..................hhhhhhhhhhhhhhh.hhhhh.....eeeeee.............................hhhhhhhhhhhhhh.................................hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee............hhhhh...........hhhhhhhhhh..eeeeeee...............hhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhh...............eeeee.......hhhhhhhhhhhhhhhh........hhh...............hhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------BETA_AMYL--------------------------------------------------------------------------------BETA_AMYLAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1btc A   5 SNMLLNYVPVYVMLPLGVVNVDNVFEDPDGLKEQLLQLRAAGVDGVMVDVWWGIIELKGPKQYDWRAYRSLFQLVQECGLTLQAIMSFHQCGGNVGDIVNIPIPQWVLDIGESNHDIFYTNRSGTRNKEYLTVGVDNEPIFHGRTAIEIYSDYMKSFRENMSDFLESGLIIDIEVGLGPAGELRYPSYPQSQGWEFPRIGEFQCYDKYLKADFKAAVARAGHPEWELPDDAGKYNDVPESTGFFKSNGTYVTEKGKFFLTWYSNKLLNHGDQILDEANKAFLGCKVKLAIKVSGIHWWYKVENHAAELTAGYYNLNDRDGYRPIARMLSRHHAILNFTCLEMRDSEQPSDAKSGPQELVQQVLSGGWREDIRVAGENALPRYDATAYNQIILNAKPQGVNNNGPPKLSMFGVTYLRLSDDLLQKSNFNIFKKFVLKMHADQDYCANPQKYNHAITPLKPSAPKIPIEVLLEATKPTLPFPWLPETDMKVDG 495
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BTC)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMYB_SOYBN | P10538)
molecular function
    GO:0016161    beta-amylase activity    Catalysis of the reaction: (1,4-alpha-D-glucosyl)(n+1) + H2O = (1,4-alpha-D-glucosyl)(n-1) + alpha-maltose. This reaction is the hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AMYB_SOYBN | P10538: 1bfn 1bya 1byb 1byc 1byd 1q6c 1q6d 1q6e 1q6f 1q6g 1uko 1ukp 1v3h 1v3i 1wdp 1wdq 1wdr 1wds

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BTC)