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(-) Description

Title :  CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE AT ATOMIC RESOLUTION
 
Authors :  M. Rejzek, C. E. M. Stevenson, A. M. Southard, D. Stanley, K. Denyer, A. M M. J. Naldrett, D. M. Lawson, R. A. Field
Date :  28 May 10  (Deposition) - 01 Dec 10  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.97
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Carbohydrate Metabolism, Glycosyl Hydrolase Family 14, Starch Degradation, Germination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Rejzek, C. E. M. Stevenson, A. M. Southard, D. Stanley, K. Denyer, A. M. Smith, M. J. Naldrett, D. M. Lawson, R. A. Field
Chemical Genetics And Cereal Starch Metabolism: Structural Basis Of The Non-Covalent And Covalent Inhibition Of Barley Beta-Amylase.
Mol. Biosyst. V. 7 718 2011
PubMed-ID: 21085740  |  Reference-DOI: 10.1039/C0MB00204F

(-) Compounds

Molecule 1 - BETA-AMYLASE
    Chains: A
    EC Number: 3.2.1.2
    Organism Common: BARLEY
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
    Other Details: PROTEIN PURCHASED FROM MEGAZYME
    Synonym: 1,4-ALPHA-D-GLUCAN MALTOHYDROLASE
    Tissue: GRAIN ENDOSPERM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:127 , ASN A:129 , PRO A:188 , PRO A:191 , TYR A:236 , HOH A:2492 , HOH A:2943BINDING SITE FOR RESIDUE EDO A1490
2AC2SOFTWAREGLN A:212 , PHE A:215 , GLU A:228 , PHE A:229 , HOH A:2945 , HOH A:2947 , HOH A:2948BINDING SITE FOR RESIDUE EDO A1491

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XFR)

(-) 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 2XFR)

(-) 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 2XFR)

(-) 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:487
 aligned with AMYB_HORVU | P16098 from UniProtKB/Swiss-Prot  Length:535

    Alignment length:487
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       
           AMYB_HORVU     3 VNVKGNYVQVYVMLPLDAVSVNNRFEKGDELRAQLRKLVEAGVDGVMVDVWWGLVEGKGPKAYDWSAYKQLFELVQKAGLKLQAIMSFHQCGGNVGDAVNIPIPQWVRDVGTRDPDIFYTDGHGTRNIEYLTLGVDNQPLFHGRSAVQMYADYMTSFRENMKDFLDAGVIVDIEVGLGPAGEMRYPSYPQSHGWSFPGIGEFICYDKYLQADFKAAAAAVGHPEWEFPNDVGQYNDTPERTQFFRDNGTYLSEKGRFFLAWYSNNLIKHGDRILDEANKVFLGYKVQLAIKISGIHWWYKVPSHAAELTAGYYNLHDRDGYRTIARMLKRHRASINFTCAEMRDLEQSSQAMSAPEELVQQVLSAGWREGLNVACENALPRYDPTAYNTILRNARPHGINQSGPPEHKLFGFTYLRLSNQLVEGQNYVNFKTFVDRMHANLPRDPYVDPMAPLPRSGPEISIEMILQAAQPKLQPFPFQEHTDLPVG 489
               SCOP domains d2xfra_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeeee.............hhhhhhhhhhhhhhh...eeeeeeehhhhh........hhhhhhhhhhhhhh..eeeeeee................hhhhhhhhhhh...eee.....eeeeee.hhhh........hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhh.......................hhhhhhhhhhhhhhh................hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee............hhhhhhhh.........hhhhhhhhhh...eeee.....hhhhhhhhhh.hhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhh...............eeee........hhhhhhhhhhhhhhhh......................hhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------BETA_AMYL--------------------------------------------------------------------------------BETA_AMYLAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xfr A   3 VNVKGNYVQVYVMLPLDAVSVNNRFEKGDELRAQLRKLVEAGVDGVMVDVWWGLVEGKGPKAYDWSAYKQLFELVQKAGLKLQAIMSFHQCGGNVGDAVNIPIPQWVRDVGTRDPDIFYTDGHGTRNIEYLTLGVDNQPLFHGRSAVQMYADYMTSFRENMKEFLDAGVIVDIEVGLGPAGEMRYPSYPQSHGWSFPGIGEFICYDKYLQADFKAAAAAVGHPEWEFPNDVGQYNDTPERTQFFRDNGTYLSEKGRFFLAWYSNNLIKHGDRILDEANKVFLGYKVQLAIKISGIHWWYKVPSHAAELTAGYYNLHDRDGYRTIARMLKRHRASINFTCAEMRDSEQSSQAMSAPEELVQQVLSAGWREGLNVACENALPRYDPTAYNTILRNARPHGINQSGPPEHKLFGFTYLRLSNQLVEGQNYANFKTFVDRMHANLPRDPYVDPMAPLPRSGPEISIEMILQAAQPKLQPFPFQEHTDLPVG 489
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (0, 0)

(no "CATH Domain" information available for 2XFR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XFR)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        AMYB_HORVU | P16098: 1b1y 2xff 2xfy 2xg9 2xgb 2xgi

(-) Related Entries Specified in the PDB File

1b1y SEVENFOLD MUTANT OF BARLEY BETA-AMYLASE
2xff CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH ACARBOSE
2xfy CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH ALPHA-CYCLODEXTRIN
2xg9 CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH 4-O-ALPHA-D- GLUCOPYRANOSYLMORANOLINE
2xgb CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH 2,3-EPOXYPROPYL-ALPHA-D- GLUCOPYRANOSIDE
2xgi CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH 3,4-EPOXYBUTYL ALPHA-D- GLUCOPYRANOSIDE