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(-) Description

Title :  CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH ALPHA-CYCLODEXTRIN
 
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 :  1.21
Chains :  Asym./Biol. Unit :  A
Keywords :  Carbohydrate Metabolism, Hydrolase, 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  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACX1Ligand/IonALPHA-CYCLODEXTRIN (CYCLOHEXA-AMYLOSE)
2EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:99 , GLN A:192 , PHE A:198 , HIS A:298 , ALA A:380 , LEU A:381 , PRO A:382 , SER A:404 , HOH A:2400 , HOH A:2616 , HOH A:2661 , HOH A:2806 , HOH A:2807 , HOH A:2808 , HOH A:2809 , HOH A:2810 , HOH A:2811 , HOH A:2812 , HOH A:2813 , HOH A:2814BINDING SITE FOR RESIDUE ACX A 600
2AC2SOFTWARETHR A:127 , ASN A:129 , PRO A:188 , PRO A:191 , TYR A:236 , HOH A:2406 , HOH A:2815BINDING SITE FOR RESIDUE EDO A1490
3AC3SOFTWAREGLN A:212 , PHE A:215 , GLU A:228 , PHE A:229 , HOH A:2816 , HOH A:2817BINDING SITE FOR RESIDUE EDO A1491

(-) SS Bonds  (0, 0)

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

(-) 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 2XFY)

(-) 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 2XFY)

(-) 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:486
 aligned with AMYB_HORVU | P16098 from UniProtKB/Swiss-Prot  Length:535

    Alignment length:486
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483      
           AMYB_HORVU     4 NVKGNYVQVYVMLPLDAVSVNNRFEKGDELRAQLRKLVEAGVDGVMVDVWWGLVEGKGPKAYDWSAYKQLFELVQKAGLKLQAIMSFHQCGGNVGDAVNIPIPQWVRDVGTRDPDIFYTDGHGTRNIEYLTLGVDNQPLFHGRSAVQMYADYMTSFRENMKDFLDAGVIVDIEVGLGPAGEMRYPSYPQSHGWSFPGIGEFICYDKYLQADFKAAAAAVGHPEWEFPNDVGQYNDTPERTQFFRDNGTYLSEKGRFFLAWYSNNLIKHGDRILDEANKVFLGYKVQLAIKISGIHWWYKVPSHAAELTAGYYNLHDRDGYRTIARMLKRHRASINFTCAEMRDLEQSSQAMSAPEELVQQVLSAGWREGLNVACENALPRYDPTAYNTILRNARPHGINQSGPPEHKLFGFTYLRLSNQLVEGQNYVNFKTFVDRMHANLPRDPYVDPMAPLPRSGPEISIEMILQAAQPKLQPFPFQEHTDLPVG 489
               SCOP domains d2xfya_ 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
                 2xfy A   4 NVKGNYVQVYVMLPLDAVSVNNRFEKGDELRAQLRKLVEAGVDGVMVDVWWGLVEGKGPKAYDWSAYKQLFELVQKAGLKLQAIMSFHQCGGNVGDAVNIPIPQWVRDVGTRDPDIFYTDGHGTRNIEYLTLGVDNQPLFHGRSAVQMYADYMTSFRENMKEFLDAGVIVDIEVGLGPAGEMRYPSYPQSHGWSFPGIGEFICYDKYLQADFKAAAAAVGHPEWEFPNDVGQYNDTPERTQFFRDNGTYLSEKGRFFLAWYSNNLIKHGDRILDEANKVFLGYKVQLAIKISGIHWWYKVPSHAAELTAGYYNLHDRDGYRTIARMLKRHRASINFTCAEMRDSEQSSQAMSAPEELVQQVLSAGWREGLNVACENALPRYDPTAYNTILRNARPHGINQSGPPEHKLFGFTYLRLSNQLVEGQNYANFKTFVDRMHANLPRDPYVDPMAPLPRSGPEISIEMILQAAQPKLQPFPFQEHTDLPVG 489
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483
   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 2XFY)

(-) Pfam Domains  (0, 0)

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

(-) 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 2xfr 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
2xfr TOWARDS THE DISSECTION OF CEREAL STARCH METABOLISM THROUGH CHEMICAL GENETICS: STRUCTURAL BASIS OF THE NON-COVALENT AND COVALENT INHIBITION OF BARLEY BETA-AMYLASE
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