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(-) Description

Title :  SEVENFOLD MUTANT OF BARLEY BETA-AMYLASE
 
Authors :  B. Mikami, H. J. Yoon, N. Yoshigi
Date :  25 Nov 98  (Deposition) - 02 Dec 98  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase(O-Glycosyl) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Mikami, H. J. Yoon, N. Yoshigi
The Crystal Structure Of The Sevenfold Mutant Of Barley Beta-Amylase With Increased Thermostability At 2. 5 A Resolution.
J. Mol. Biol. V. 285 1235 1999
PubMed-ID: 9918723  |  Reference-DOI: 10.1006/JMBI.1998.2379
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (BETA-AMYLASE)
    Chains: A
    EC Number: 3.2.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PB927
    Expression System Taxid: 562
    Expression System Variant: JM 109
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
    Variant: CV. HARUNA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2GLC1Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:15 , ASP A:51 , TRP A:53 , ILE A:87 , HIS A:91 , ASN A:96 , ASP A:99 , ALA A:182 , ARG A:418 , BGC A:551 , HOH A:658 , HOH A:684 , HOH A:728BINDING SITE FOR RESIDUE GLC A 550
2AC2SOFTWAREVAL A:97 , ALA A:182 , GLU A:184 , LYS A:293 , THR A:340 , GLU A:378 , ALA A:380 , GLC A:550 , HOH A:684BINDING SITE FOR RESIDUE BGC A 551
3AC3SOFTWAREGLN A:192 , PHE A:198 , HIS A:298 , HOH A:718BINDING SITE FOR RESIDUE BGC A 552

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B1Y)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:198 -Pro A:199
2Leu A:417 -Arg A:418
3Gln A:472 -Pro A:473

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B1Y)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_AMYLASE_1PS00506 Beta-amylase active site 1.AMYB_HORVU91-99  1A:91-99
2BETA_AMYLASE_2PS00679 Beta-amylase active site 2.AMYB_HORVU180-190  1A:180-190

(-) Exons   (0, 0)

(no "Exon" information available for 1B1Y)

(-) 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:500
 aligned with AMYB_HORVU | P16098 from UniProtKB/Swiss-Prot  Length:535

    Alignment length:500
                                    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       504
           AMYB_HORVU     5 VKGNYVQVYVMLPLDAVSVNNRFEKGDELRAQLRKLVEAGVDGVMVDVWWGLVEGKGPKAYDWSAYKQLFELVQKAGLKLQAIMSFHQCGGNVGDAVNIPIPQWVRDVGTRDPDIFYTDGHGTRNIEYLTLGVDNQPLFHGRSAVQMYADYMTSFRENMKDFLDAGVIVDIEVGLGPAGEMRYPSYPQSHGWSFPGIGEFICYDKYLQADFKAAAAAVGHPEWEFPNDVGQYNDTPERTQFFRDNGTYLSEKGRFFLAWYSNNLIKHGDRILDEANKVFLGYKVQLAIKISGIHWWYKVPSHAAELTAGYYNLHDRDGYRTIARMLKRHRASINFTCAEMRDLEQSSQAMSAPEELVQQVLSAGWREGLNVACENALPRYDPTAYNTILRNARPHGINQSGPPEHKLFGFTYLRLSNQLVEGQNYVNFKTFVDRMHANLPRDPYVDPMAPLPRSGPEISIEMILQAAQPKLQPFPFQEHTDLPVGPTGGMGGQAEGPTCG 504
               SCOP domains d1b1ya_ A: beta-Amylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1b1yA00 A:5-504 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh..eeeee.............hhhhhhhhhhhhhh....eeeeeee...hhhh.......hhhhhhhhhhhhh..eeeeeee.................hhhhhhhhh.hhheee.....eeeeee.hhh..........hhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhh........hhh..............hhhhhhhhhhhhh..................hhh........hhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee............hhhhhh...........hhhhhhh.....eeee......hhh........hhhhhhhhhhhhhh....eee........hhhhhhhhhhh................eeee.........hhhhhhhhhhhhhhh.......................hhhhhhh.................................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------BETA_AMYL--------------------------------------------------------------------------------BETA_AMYLAS-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b1y A   5 MKGNYVQVYVMLPLDAVSVNNRFEKGDELRAQLRKLVEAGVDGVMVDVWWGLVEGKGPKAYDWSAYKQLFELVQKAGLKLQAIMSFHQCGGNVGDAVNIPIPQWVRDVGTRDPDIFYTDGHGTRNIEYLTLGVDNQPLFHGRSAVQMYADYMTSFRENMKDFLDAGVIVDIEVGLGPAGELRYPSYPQSHGWSFPGIGEFICYDKYLQADFKAAAAAVGHPEWEFPNDAGQYNDTPERTQFFRDNGTYLSEKGRFFLAWYSNNLIKHGDRILDEANKVFLGYKVQLAIKIAGVHWWYKVPSHAAELTAGYYNLHDRDGYRTIARMLKRHRASINFTCAEMRDSEQPPDAMSAPEELVQQVLSAGWREGLNVSCENALPRYDPTAYNTILRNARPHGINQSGPPEHKLFGFTYLRLSNQLVEGQNYVNFKTFVDRMHANLPRDPYVDPMAPLPRSGPEISIEMILQAAQPKIQPFPFQEHTDLPVGPTGGMGGQAEGPTCG 504
                                    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       504
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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
(-)
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 1B1Y)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMYB_HORVU | P16098)
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.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
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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  AMYB_HORVU | P16098
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMYB_HORVU | P16098: 2xff 2xfr 2xfy 2xg9 2xgb 2xgi

(-) Related Entries Specified in the PDB File

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