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(-) Description

Title :  BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1) H395A MUTANT
 
Authors :  N. Aghajari, X. Robert, R. Haser
Date :  24 Dec 07  (Deposition) - 26 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Barley Alpha-Amylase, Amy1, Mutant, Calcium, Carbohydrate Metabolism, Germination, Glycosidase, Hydrolase, Metal- Binding, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. M. Nielsen, E. S. Seo, S. Bozonnet, N. Aghajari, X. Robert, R. Haser, B. Svensson
Multi-Site Substrate Binding And Interplay In Barley Alpha-Amylase 1
Febs Lett. V. 582 2567 2008
PubMed-ID: 18588886  |  Reference-DOI: 10.1016/J.FEBSLET.2008.06.027
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE TYPE A ISOZYME
    ChainsA
    EC Number3.2.1.1
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPICZA
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonBARLEY
    Organism ScientificHORDEUM VULGARE
    Organism Taxid4513
    SynonymALPHA-AMYLASE ISOZYME 1, 1,4-ALPHA-D- GLUCAN GLUCANOHYDROLASE, AMY1, LOW PI ALPHA-AMYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:92 , ASP A:139 , ALA A:142 , ASP A:149 , GLY A:184 , HOH A:630BINDING SITE FOR RESIDUE CA A 500
2AC2SOFTWAREGLU A:109 , THR A:112 , ASP A:114 , ASP A:118 , HOH A:604BINDING SITE FOR RESIDUE CA A 501
3AC3SOFTWAREASP A:128 , ASP A:143 , PHE A:144 , ALA A:147 , ASP A:149 , HOH A:788BINDING SITE FOR RESIDUE CA A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BSG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BSG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BSG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BSG)

(-) Exons   (0, 0)

(no "Exon" information available for 3BSG)

(-) 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:404
 aligned with AMY1_HORVU | P00693 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:404
                                    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    
           AMY1_HORVU    25 HQVLFQGFNWESWKQSGGWYNMMMGKVDDIAAAGVTHVWLPPPSHSVSNEGYMPGRLYDIDASKYGNAAELKSLIGALHGKGVQAIADIVINHRCADYKDSRGIYCIFEGGTSDGRLDWGPHMICRDDTKYSDGTANLDTGADFAAAPDIDHLNDRVQRELKEWLLWLKSDLGFDAWRLDFARGYSPEMAKVYIDGTSPSLAVAEVWDNMATGGDGKPNYDQDAHRQNLVNWVDKVGGAASAGMVFDFTTKGILNAAVEGELWRLIDPQGKAPGVMGWWPAKAATFVDNHDTGSTQAMWPFPSDKVMQGYAYILTHPGIPCIFYDHFFNWGFKDQIAALVAIRKRNGITATSALKILMHEGDAYVAEIDGKVVVKIGSRYDVGAVIPAGFVTSAHGNDYAVWEK 428
               SCOP domains d3bsga2 A:1-347 automated matches                                                                                                                                                                                                                                                                                                                          d3bsga1 A:348-404 automated matches                       SCOP domains
               CATH domains -3bsgA01 A:2-347 Glycosidases                                                                                                                                                                                                                                                                                                                              3bsgA02 A:348-404 Golgi alpha-mannosidase II              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....hhhhh..hhhhhhh.hhhhhhhh...eeee..................hhhhh...hhhhhhhhhhhhhhh..eeeeee........ee.....eee............hhhhh.............................hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh...eee.................hhhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhh..hhhhhh.......hhhhhh...eeee..................hhhhhhhhhhhh..eeeeehhhhhh..hhhhhhhhhhhhhhh.......eeeeeee..eeeeee...eeeee.....hhhhh....eeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bsg A   1 HQVLFQGFNWESWKQSGGWYNMMMGKVDDIAAAGVTHVWLPPPSHSVSNEGYMPGRLYDIDASKYGNAAELKSLIGALHGKGVQAIADIVINHRCADYKDSRGIYCIFEGGTSDGRLDWGPHMICRDDTKYSDGTANLDTGADFAAAPDIDHLNDRVQRELKEWLLWLKSDLGFDAWRLDFARGYSPEMAKVYIDGTSPSLAVAEVWDNMATGGDGKPNYDQDAHRQNLVNWVDKVGGAASAGMVFDFTTKGILNAAVEGELWRLIDPQGKAPGVMGWWPAKAVTFVDNHDTGSTQAMWPFPSDKVMQGYAYILTHPGIPCIFYDHFFNWGFKDQIAALVAIRKRNGITATSALKILMHEGDAYVAEIDGKVVVKIGSRYDVGAVIPAGFVTSAAGNDYAVWEK 404
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400    

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BSG)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMY1_HORVU | P00693)
molecular function
    GO:0004556    alpha-amylase activity    Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0043169    cation binding    Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMY1_HORVU | P006931ht6 1p6w 1rp8 1rp9 1rpk 2qps 2qpu 3bsh

(-) Related Entries Specified in the PDB File

1ht6 NATIVE BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1)
3bsh