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(-) Description

Title :  BACILLUS STEAROTHERMOPHILUS ALPHA-AMYLASE
 
Authors :  D. Suvd, Z. Fujimoto, K. Takase, M. Matsumura, H. Mizuno
Date :  08 Jan 01  (Deposition) - 31 Jan 01  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Glycosyltransferase, Alpha-Amylase, Starch Degradation, Alpha-1, 4-Glucan-4-Glucanohydrolase, Thermostability (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Suvd, Z. Fujimoto, K. Takase, M. Matsumura, H. Mizuno
Crystal Structure Of Bacillus Stearothermophilus Alpha-Amylase: Possible Factors Determining The Thermostability
J. Biochem. V. 129 461 2001
PubMed-ID: 11226887
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE
    Chains: A
    EC Number: 3.2.1.1
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PTUB617
    Expression System Strain: A631
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Gene: AMYT631
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2NA1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:162 , ALA A:184 , ASP A:186 , ASP A:205 , HOH A:655 , HOH A:727BINDING SITE FOR RESIDUE CA A 516
2AC2SOFTWAREASP A:105 , ASP A:197 , ASP A:203 , HIS A:238 , HOH A:609BINDING SITE FOR RESIDUE CA A 517
3AC3SOFTWAREGLY A:303 , PHE A:305 , SER A:406 , ASP A:407 , ASP A:430 , HOH A:941BINDING SITE FOR RESIDUE CA A 518
4AC4SOFTWAREASP A:162 , ASP A:186 , ASP A:197 , ASP A:203 , LEU A:204BINDING SITE FOR RESIDUE NA A 519

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:187 -Glu A:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1HVX)

(-) 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:483
 aligned with AMY_GEOSE | P06279 from UniProtKB/Swiss-Prot  Length:549

    Alignment length:483
                                    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       514   
            AMY_GEOSE    35 AAPFNGTMMQYFEWYLPDDGTLWTKVANEANNLSSLGITALWLPPAYKGTSRSDVGYGVYDLYDLGEFNQKGAVRTKYGTKAQYLQAIQAAHAAGMQVYADVVFDHKGGADGTEWVDAVEVNPSDRNQEISGTYQIQAWTKFDFPGRGNTYSSFKWRWYHFDGVDWDESRKLSRIYKFRGIGKAWDWEVDTENGNYDYLMYADLDMDHPEVVTELKSWGKWYVNTTNIDGFRLDAVKHIKFSFFPDWLSDVRSQTGKPLFTVGEYWSYDINKLHNYIMKTNGTMSLFDAPLHNKFYTASKSGGTFDMRTLMTNTLMKDQPTLAVTFVDNHDTEPGQALQSWVDPWFKPLAYAFILTRQEGYPCVFYGDYYGIPQYNIPSLKSKIDPLLIARRDYAYGTQHDYLDHSDIIGWTREGVTEKPGSGLAALITDGPGGSKWMYVGKQHAGKVFYDLTGNRSDTVTINSDGWGEFKVNGGSVSVWVPR 517
               SCOP domains d1hvxa2 A:1-393 Bacterial alpha-amylase                                                                                                                                                                                                                                                                                                                                                                  d1hvxa1 A:394-483 Bacterial alpha-Amylase                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1hvxA03 A:397-483 Golgi alpha-mannosidase II                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..........hhhhhhhhhhhhhhhh...eeee....ee.........eee..................hhhhhhhhhhhhhhh..eeeeee...ee....eeeeeeeeeee..eeeee....eeeeeeee...............hhh.eeeeeee....eeeeeee.......................eee...hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh....eeehhhhhhhhhhhhhh....hhhhh...hhhhhh...eee....................hhhhhhhhhhhh...eeeeehhhhhh.hhhh...hhhhhhhhhhhhhhh....eeee.....eeeeee..........eeeeee....eeeeee.hhhhh..eeee.......eee.....eeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hvx A   1 AAPFNGTMMQYFEWYLPDDGTLWTKVANEANNLSSLGITALWLPPAYKGTSRSDVGYGVYDLYDLGEFNQKGAVRTKYGTKAQYLQAIQAAHAAGMQVYADVVFDHKGGADGTEWVDAVEVNPSDRNQEISGTYQIQAWTKFDFPGRGNTYSSFKWRWYHFDGVDWDESRKLSRIYKFRGIGKAWDWEVDTENGNYDYLMYADLDMDHPEVVTELKSWGKWYVNTTNIDGFRLDAVKHIKFSFFPDWLSYVRSQTGKPLFTVGEYWSYDINKLHNYIMKTNGTMSLFDAPLHNKFYTASKSGGTFDMRTLMTNTLMKDQPTLAVTFVDNHDTEPGQALQSWVDPWFKPLAYAFILTRQEGYPCVFYGDYYGIPQYNIPSLKSKIDPLLIARRDYAYGTQHDYLDHSDIIGWTREGVTEKPGSGLAALITDGPGGSKWMYVGKQHAGKVFYDLTGNRSDTVTINSDGWGEFKVNGGSVSVWVPR 483
                                    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       410       420       430       440       450       460       470       480
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  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
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMY_GEOSE | P06279)
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: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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-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.

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        AMY_GEOSE | P06279: 4uzu

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