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(-) Description

Title :  CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS
 
Authors :  B. Mikami, M. Degano, E. J. Hehre, J. C. Sacchettini
Date :  25 Jan 94  (Deposition) - 31 Jul 94  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase(O-Glycosyl) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Mikami, M. Degano, E. J. Hehre, J. C. Sacchettini
Crystal Structures Of Soybean Beta-Amylase Reacted With Beta-Maltose And Maltal: Active Site Components And Their Apparent Roles In Catalysis.
Biochemistry V. 33 7779 1994
PubMed-ID: 8011643  |  Reference-DOI: 10.1021/BI00191A005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-AMYLASE
    ChainsA
    EC Number3.2.1.2
    EngineeredYES
    Organism CommonSOYBEAN
    Organism ScientificGLYCINE MAX
    Organism Taxid3847

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GLC4Ligand/IonALPHA-D-GLUCOSE
2SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:20 , ASP A:53 , TRP A:55 , HIS A:93 , ASP A:101 , ARG A:420 , GLC A:497 , HOH A:501 , HOH A:589 , HOH A:680 , HOH A:849BINDING SITE FOR RESIDUE GLC A 496
2AC2SOFTWAREMET A:17 , ALA A:184 , GLU A:186 , LYS A:295 , THR A:342 , GLU A:380 , ALA A:382 , GLC A:496 , GLC A:498 , HOH A:500 , HOH A:501 , HOH A:866BINDING SITE FOR RESIDUE GLC A 497
3AC3SOFTWAREGLU A:186 , ARG A:188 , TYR A:192 , SER A:297 , GLY A:298 , THR A:342 , CYS A:343 , GLC A:497 , GLC A:499 , HOH A:868BINDING SITE FOR RESIDUE GLC A 498
4AC4SOFTWAREVAL A:99 , HIS A:300 , TRP A:301 , MET A:346 , GLC A:498 , HOH A:503 , HOH A:504BINDING SITE FOR RESIDUE GLC A 499
5AC5SOFTWAREHIS A:146 , ARG A:326 , ARG A:372 , LYS A:478BINDING SITE FOR RESIDUE SO4 A 860

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BYB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1BYB)

(-) 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 d1byba_ A: beta-Amylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1bybA00 A:5-495 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeee...........hhhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhh...eeeeeee.................hhhhhhhhh................................hhhhhhhhhhhhhhhhhhhhh.....eeeeee.............................hhhhhhhhhhhhhh.................................hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee............hhhhh...........hhhhhhhhhh..eeeeeee...............hhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhh...............eeeee.......hhhhhhhhhhhhhhhh..........................hhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------BETA_AMYL--------------------------------------------------------------------------------BETA_AMYLAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1byb 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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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 | P105381bfn 1btc 1bya 1byc 1byd 1q6c 1q6d 1q6e 1q6f 1q6g 1uko 1ukp 1v3h 1v3i 1wdp 1wdq 1wdr 1wds

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