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(-) Description

Title :  BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE
 
Authors :  A. Kadziola, R. Haser
Date :  05 Jun 98  (Deposition) - 15 Jun 99  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, O-Glycosyl (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kadziola, M. Sogaard, B. Svensson, R. Haser
Molecular Structure Of A Barley Alpha-Amylase-Inhibitor Complex: Implications For Starch Binding And Catalysis.
J. Mol. Biol. V. 278 205 1998
PubMed-ID: 9571044  |  Reference-DOI: 10.1006/JMBI.1998.1683
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE
    Chains: A
    EC Number: 3.2.1.1
    Organ: GERMINATED SEEDS
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
    Synonym: ALPHA-AMYLASE, HIGH PI ISOZYME
    Variant: CULTIVAR MENUET

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1AF11Ligand/Ion4,6-DIDEOXY-4-{[(1S,4S,5S,6S)-4,5,6-TRIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}-BETA-D-GLUCOPYRANOSE
2BGC1Ligand/IonBETA-D-GLUCOSE
3CA3Ligand/IonCALCIUM ION
4DAF1Ligand/Ion1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX-5-ENYL)AMINO)FRUCTOSE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1AF12Ligand/Ion4,6-DIDEOXY-4-{[(1S,4S,5S,6S)-4,5,6-TRIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}-BETA-D-GLUCOPYRANOSE
2BGC2Ligand/IonBETA-D-GLUCOSE
3CA-1Ligand/IonCALCIUM ION
4DAF2Ligand/Ion1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX-5-ENYL)AMINO)FRUCTOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1ASUNKNOWNASP A:179 , GLU A:204 , ASP A:289NULL
2SSUNKNOWNTRP A:276 , TRP A:277NULL

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BG9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:128 -Pro A:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BG9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BG9)

(-) Exons   (0, 0)

(no "Exon" information available for 1BG9)

(-) Sequences/Alignments

Asymmetric 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:403
 aligned with AMY2_HORVU | P04063 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:403
                                    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   
           AMY2_HORVU    25 QVLFQGFNWESWKHNGGWYNFLMGKVDDIAAAGITHVWLPPASQSVAEQGYMPGRLYDLDASKYGNKAQLKSLIGALHGKGVKAIADIVINHRTAEHKDGRGIYCIFEGGTPDARLDWGPHMICRDDRPYADGTGNPDTGADFGAAPDIDHLNLRVQKELVEWLNWLKADIGFDGWRFDFAKGYSADVAKIYIDRSEPSFAVAEIWTSLAYGGDGKPNLNQDQHRQELVNWVDKVGGKGPATTFDFTTKGILNVAVEGELWRLRGTDGKAPGMIGWWPAKAVTFVDNHDTGSTQHMWPFPSDRVMQGYAYILTHPGTPCIFYDHFFDWGLKEEIDRLVSVRTRHGIHNESKLQIIEADADLYLAEIDGKVIVKLGPRYDVGNLIPGGFKVAAHGNDYAVWEKI 427
               SCOP domains d1bg9a2 A:1-346 Plant alpha-amylase                                                                                                                                                                                                                                                                                                                       d1bg9a1 A:347-403 Plant alpha-amylase                     SCOP domains
               CATH domains 1bg9A01 A:1-345 Glycosidases                                                                                                                                                                                                                                                                                                                             1bg9A02 A:346-403 Golgi alpha-mannosidase II               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeee..........hhhhhhhhhhhhhhhh..eeeee..........................hhhhhhhhhhhhhhh..eeeeee................................................................hhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhhhh......eeehhhhhhhhhhh................hhhhh..eeee...hhhhh............hhhhhhhhhhh..-----hhhhhh..hhhhhhhhhhhhhhh......eeeeeeee..eeeeeee.eeeeeee...........eeeeeeee.eeeeeeee Sec.struct. author (1)
     Sec.struct. author (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeee--------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bg9 A   1 QVLFQGFNWESWKHNGGWYNFLMGKVDDIAAAGITHVWLPPASQSVAEQGYMPGRLYDLDASKYGNKAQLKSLIGALHGKGVKAIADIVINHRTAEHKDGRGIYCIFEGGTPDARLDWGPHMICRDDRPYADGTGNPDTGADFGAAPDIDHLNLRVQKELVEWLNWLKADIGFDGWRFDFAKGYSADVAKIYIDRSEPSFAVAEIWTSLAYGGDGKPNLNQDQHRQELVNWVDKVGGKGPATTFDFTTKGILNVAVEGELWRLRGTDGKAPGMIGWWPAKAVTFVDNHDTGSTQHMWPFPSDRVMQGYAYILTHPGTPCIFYDHFFDWGLKEEIDRLVSVRTRHGIHNESKLQIIEADADLYLAEIDGKVIVKLGPRYDVGNLIPGGFKVAAHGNDYAVWEKI 403
                                    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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BG9)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (AMY2_HORVU | P04063)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMY2_HORVU | P04063: 1amy 1ava

(-) Related Entries Specified in the PDB File

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