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(-) Description

Title :  CRYSTAL STRUCTURE OF ALPHA-AMYLASE FROM GEOBACILLUS THERMOLEOVORANS, GTA, COMPLEXED WITH ACARBOSE
 
Authors :  S. C. Mok, A. H. Teh, J. A. Saito, N. Najimudin, M. Alam
Date :  09 Mar 12  (Deposition) - 13 Mar 13  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Barrel, Calcium Binding, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Mok, A. H. Teh, J. A. Saito, N. Najimudin, M. Alam
Crystal Structure Of A Compact Alpha-Amylase From Geobacillus Thermoleovorans.
Enzyme. Microb. Technol. V. 53 46 2013
PubMed-ID: 23683704  |  Reference-DOI: 10.1016/J.ENZMICTEC.2013.03.009

(-) Compounds

Molecule 1 - ALPHA-AMYLASE
    Chains: A
    EC Number: 3.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-17XB
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 25-478
    Gene: GTCCBUS3UF5_7870
    Organism Scientific: GEOBACILLUS THERMOLEOVORANS
    Organism Taxid: 1111068
    Strain: CCB_US3_UF5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1ACI2Ligand/Ion6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
2BGC1Ligand/IonBETA-D-GLUCOSE
3CA1Ligand/IonCALCIUM ION
4G6D2Ligand/Ion6-DEOXY-ALPHA-D-GLUCOSE
5GLC1Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:143 , GLU A:177 , ASP A:186 , HIS A:221 , HOH A:701 , HOH A:702 , HOH A:703BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWARETYR A:104 , TRP A:105 , HIS A:144 , TYR A:147 , HIS A:153 , ASP A:154 , PRO A:155 , THR A:156 , LYS A:157 , TRP A:170 , TYR A:182 , LEU A:184 , ARG A:215 , ASP A:217 , THR A:218 , ARG A:220 , HIS A:221 , GLU A:246 , TRP A:248 , HIS A:313 , ASP A:314 , ASP A:362 , ARG A:366 , HOH A:818 , HOH A:862 , HOH A:868 , HOH A:979 , HOH A:994BINDING SITE FOR LINKED RESIDUES A 502-507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E2O)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:362 -Pro A:363

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E2O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E2O)

(-) Exons   (0, 0)

(no "Exon" information available for 4E2O)

(-) 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:445
 aligned with G8N704_GEOTH | G8N704 from UniProtKB/TrEMBL  Length:511

    Alignment length:451
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477 
         G8N704_GEOTH    28 ERTWQDEAIYFIMVDRFNNMDPTNDQNVNVNDPKGYFGGDLKGVTAKLDYIKEMGFTAIWLTPIFKNMPGGYHGYWIEDFYQVDPHFGTLGDLKTLVKEAHKRDMKVILDFVANHVGYNHPWLHDPTKKDWFHPKKEIFDWNDQTQLENGWVYGLPDLAQENPEVKTYLIDAAKWWIKETDIDGYRLDTVRHVPKSFWQEFAKEVKSVKKDFFLLGEVWSDDPRYIADYGKYGIDGFVDYPLYGAVKQSLARRDASLRPLYDVWEYNKTFYDRPYLLGSFLDNHDTVRFTKLAIDNRNNPISRIKLAMTYLFTAPGIPIMYYGTEIAMNGGQDPDNRRLMDFRADPEIIDYLKKIGPLRQELPSLRRGDFTLLYEKDGMAVLKRQYQDETTVIAINNTSETQHVHLTNDQLPKNKELRGFLLDDLVRGDEDGYDLVLDRETAEVYKLREKT 478
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeeehhhhh....------............hhhhhhhhhhhhhh....eeee...eee.........eeeeeee.....hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhh..........hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhh..eeehhhhhhhhhhh.......hhhhhhhhhhhhhhh.hhh.eee........hhhhhhhhh..hhhhhhhhhhhhhhhh..eeeee.hhhhh..................hhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeeeee..eeeeeeee.....eeeee.........eeee.....eee.....eeeee...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e2o A  30 ERTWQDEAIYFIMVDRFNNMD------VNVNDPKGYFGGDLKGVTAKLDYIKEMGFTAIWLTPIFKNMPGGYHGYWIEDFYQVDPHFGTLGDLKTLVKEAHKRDMKVILDFVANHVGYNHPWLHDPTKKDWFHPKKEIFDWNDQTQLENGWVYGLPDLAQENPEVKTYLIDAAKWWIKETDIDGYRLDTVRHVPKSFWQEFAKEVKSVKKDFFLLGEVWSDDPRYIADYGKYGIDGFVDYPLYGAVKQSLARRDASLRPLYDVWEYNKTFYDRPYLLGSFLDNHDTVRFTKLAIDNRNNPISRIKLAMTYLFTAPGIPIMYYGTEIAMNGGQDPDNRRLMDFRADPEIIDYLKKIGPLRQELPSLRRGDFTLLYEKDGMAVLKRQYQDETTVIAINNTSETQHVHLTNDQLPKNKELRGFLLDDLVRGDEDGYDLVLDRETAEVYKLREKT 480
                                    39        49|      |59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479 
                                               50     57
   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  (0, 0)

(no "SCOP Domain" information available for 4E2O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E2O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E2O)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (G8N704_GEOTH | G8N704)
molecular function
    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: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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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