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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF ALPHA-AMYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH ACARBOSE
 
Authors :  M. Kagawa, Z. Fujimoto, M. Momma, K. Takase, H. Mizuno
Date :  03 Mar 03  (Deposition) - 18 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha-Barrels, Acarbose, Greek-Key Motif, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kagawa, Z. Fujimoto, M. Momma, K. Takase, H. Mizuno
Crystal Structure Of Bacillus Subtilis Alpha-Amylase In Complex With Acarbose
J. Bacteriol. V. 185 6981 2003
PubMed-ID: 14617662  |  Reference-DOI: 10.1128/JB.185.23.6981-6984.2003
(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: PNQ356
    Expression System Strain: 207-25
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 4-425
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
1ACI2Ligand/Ion6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
2BGC1Ligand/IonBETA-D-GLUCOSE
3CA3Ligand/IonCALCIUM ION
4G6D1Ligand/Ion6-DEOXY-ALPHA-D-GLUCOSE
5GLC1Ligand/IonALPHA-D-GLUCOSE
6GLD1Ligand/Ion4,6-DIDEOXYGLUCOSE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:126 , LEU A:142 , GLY A:143 , GLD A:502 , HOH A:645 , HOH A:693BINDING SITE FOR RESIDUE ACI A 501
2AC2SOFTWARELYS A:27 , GLN A:63 , PHE A:105 , LEU A:142 , ACI A:501 , GLC A:503BINDING SITE FOR RESIDUE GLD A 502
3AC3SOFTWARETRP A:58 , TYR A:59 , TYR A:62 , GLN A:63 , LEU A:142 , ASP A:269 , ASN A:273 , GLD A:502 , ACI A:504 , HOH A:692BINDING SITE FOR RESIDUE GLC A 503
4AC4SOFTWARETRP A:58 , TYR A:62 , HIS A:102 , ARG A:174 , ASP A:176 , GLU A:208 , HIS A:268 , ASP A:269 , GLC A:503 , G6D A:505BINDING SITE FOR RESIDUE ACI A 504
5AC5SOFTWAREALA A:177 , HIS A:180 , GLU A:208 , LEU A:210 , ACI A:504 , BGC A:506BINDING SITE FOR RESIDUE G6D A 505
6AC6SOFTWARETRP A:130 , LYS A:179 , ASP A:212 , G6D A:505 , HOH A:775 , HOH A:960BINDING SITE FOR RESIDUE BGC A 506
7AC7SOFTWAREASN A:101 , THR A:137 , ASP A:146 , HIS A:180 , HOH A:608 , HOH A:667 , HOH A:798BINDING SITE FOR RESIDUE CA A 601
8AC8SOFTWAREGLY A:169 , ASP A:171 , HOH A:716 , HOH A:796 , HOH A:800 , HOH A:801BINDING SITE FOR RESIDUE CA A 602
9AC9SOFTWAREGLU A:89 , GLU A:276 , GLY A:313 , HOH A:795 , HOH A:811 , HOH A:905BINDING SITE FOR RESIDUE CA A 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UA7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UA7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UA7)

(-) Exons   (0, 0)

(no "Exon" information available for 1UA7)

(-) 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:422
 aligned with AMY_BACSU | P00691 from UniProtKB/Swiss-Prot  Length:659

    Alignment length:422
                                    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  
            AMY_BACSU    45 PSIKSGTILHAWNWSFNTLKHNMKDIHDAGYTAIQTSPINQVKEGNQGDKSMSNWYWLYQPTSYQIGNRYLGTEQEFKEMCAAAEEYGIKVIVDAVINHTTSDYAAISNEVKSIPNWTHGNTQIKNWSDRWDVTQNSLLGLYDWNTQNTQVQSYLKRFLDRALNDGADGFRFDAAKHIELPDDGSYGSQFWPNITNTSAEFQYGEILQDSASRDAAYANYMDVTASNYGHSIRSALKNRNLGVSNISHYASDVSADKLVTWVESHDTYANDDEESTWMSDDDIRLGWAVIASRSGSTPLFFSRPEGGGNGVRFPGKSQIGDRGSALFEDQAITAVNRFHNVMAGQPEELSNPNGNNQIFMNQRGSHGVVLANAGSSSVSINTATKLPDGRYDNKAGAGSFQVNDGKLTGTINARSVAVLYPD 466
               SCOP domains d1ua7a2 A:4-347 Bacterial alpha-amylase                                                                                                                                                                                                                                                                                                                 d1ua7a1 A:348-425 Bacterial alpha-Amylase                                      SCOP domains
               CATH domains 1ua7A01 A:4-347 Glycosidases                                                                                                                                                                                                                                                                                                                            1ua7A02 A:348-425 Golgi alpha-mannosidase II                                   CATH domains
               Pfam domains -----------Alpha-amylase-1ua7A01 A:15-317                                                                                                                                                                                                                                                                                 ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee....hhhhhhhhhhhhhhh...eeee...eee..hhhhh.hhhhhhhhh.eeeeeeee...eehhhhhhhhhhhhh...eeeeee............hhhhhh....eee........hhhhhhhh......ee...hhhhhhhhhhhhhhhhhh...eeee.hhhhh....hhhhh.hhhhhhh.....eeee........hhhhhhh..eeehhhhhhhhhhhhhhh..hhhhhh......hhh.eee...hhhhhhh........hhhhhhhhhhhhhh....eeeee......................hhhhhhhhhhhhhhhhhhhh.....eehhhhh..eeeeee...eeeeee.....eeeeee.....eeee......eeeee..eeeeee...eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ua7 A   4 PSIKSGTILHAWNWSFNTLKHNMKDIHDAGYTAIQTSPINQVKEGNQGDKSMSNWYWLYQPTSYQIGNRYLGTEQEFKEMCAAAEEYGIKVIVDAVINHTTFDYAAISNEVKSIPNWTHGNTQIKNWSDRWDVTQNSLLGLYDWNTQNTQVQSYLKRFLERALNDGADGFRFDAAKHIELPDDGSYGSQFWPNITNTSAEFQYGEILQDSASRDAAYANYMDVTASNYGHSIRSALKNRNLGVSNISHYASDVSADKLVTWVESHDTYANDDEESTWMSDDDIRLGWAVIASRSGSTPLFFSRPEGGGNGVRFPGKSQIGDRGSALFEDQAITAVNRFHNVMAGQPEELSNPQGNNQIFMNQRGSHGVVLANAGSSSVSINTATKLPDGRYDNKAGAGSFQVNDGKLTGTINARSVAVLYPD 425
                                    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
   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
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMY_BACSU | P00691)
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: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.

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 Related Entries

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

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        AMY_BACSU | P00691: 1bag

(-) Related Entries Specified in the PDB File

1bag THE SAME PROTEIN COMPLEXED WITH MALTOPENTAOSE