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(-) Description

Title :  CRYSTAL STRUCTURE OF ALPHA-AMYLASE FROM H.ORENII
 
Authors :  N. Sivakumar, K. Swaminathan, N. Li
Date :  03 Mar 05  (Deposition) - 11 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Halothermothrix Orenii, Hydrolase, Alpha Amylase, Halophilic, Thermophilic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Sivakumar, N. Li, J. W. Tang, B. K. Patel, K. Swaminathan
Crystal Structure Of Amya Lacks Acidic Surface And Provide Insights Into Protein Stability At Poly-Extreme Condition.
Febs Lett. V. 580 2646 2006
PubMed-ID: 16647060  |  Reference-DOI: 10.1016/J.FEBSLET.2006.04.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE A
    Chains: A
    EC Number: 3.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHIS
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 28-515
    Gene: AMYA
    Organism Scientific: HALOTHERMOTHRIX ORENII
    Organism Taxid: 31909
    Other Details: HALOPHILIC AND THERMOPHILIC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:44 , ASP A:46 , ASP A:48 , ILE A:50 , ASP A:52 , HOH A:629BINDING SITE FOR RESIDUE CA A 601
2AC2SOFTWAREASP A:65 , ASP A:67 , THR A:70 , ASP A:73 , HOH A:671BINDING SITE FOR RESIDUE CA A 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WZA)

(-) 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:488
 aligned with Q8GPL8_9FIRM | Q8GPL8 from UniProtKB/TrEMBL  Length:515

    Alignment length:488
                                    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       487       497       507        
         Q8GPL8_9FIRM    28 FEKHGTYYEIFVRSFYDSDGDGIGDLKGIIEKLDYLNDGDPETIADLGVNGIWLMPIFKSPSYHGYDVTDYYKINPDYGTLEDFHKLVEAAHQRGIKVIIDLPINHTSERHPWFLKASRDKNSEYRDYYVWAGPDTDTKETKLDGGRVWHYSPTGMYYGYFWSGMPDLNYNNPEVQEKVIGIAKYWLKQGVDGFRLDGAMHIFPPAQYDKNFTWWEKFRQEIEEVKPVYLVGEVWDISETVAPYFKYGFDSTFNFKLAEAVIATAKAGFPFGFNKKAKHIYGVYDREVGFGNYIDAPFLTNHDQNRILDQLGQDRNKARVAASIYLTLPGNPFIYYGEEIGMRGQGPHEVIREPFQWYNGSGEGETYWEPAMYNDGFTSVEQEEKNLDSLLNHYRRLIHFRNENPVFYTGKIEIINGGLNVVAFRRYNDKRDLYVYHNLVNRPVKIKVASGNWTLLFNSGDKEITPVEDNNKLMYTIPAYTTIVLEKE 515
               SCOP domains d1wzaa2 A:28-436 Bacterial alpha-amylase                                                                                                                                                                                                                                                                                                                                                                                 d1wzaa1 A:437-515 Bacterial alpha-Amylase                                       SCOP domains
               CATH domains -----1wzaA01 A:33-132,A:197-436 Glycosidases                                                             1wzaA02 A:133-196 Oligo-1,6-glucosidase; Domain 2               1wzaA01 A:33-132,A:197-436 Glycosidases                                                                                                                                                                                                         ------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------Alpha-amylase-1wzaA02 A:51-380                                                                                                                                                                                                                                                                                                            -----------------------------------------------------------Alpha-amylase_C-1wzaA01 A:440-515                                            Pfam domains
         Sec.struct. author ......eeeehhhhh.........hhhhhhhhhhhhh.............eeee...ee..........eeeee.hhhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhh.....hhhhh...................eeee..eeee.............hhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhh....ee.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.................hhhhhh..hhhhhhhhhhhhh......eee.hhhhh.....hhhhhh..........................hhhhhh....hhhhhhhhhhhhhhhhhhhhhheeeee.....eeeeeee....eeeeeee.....eeeeee...eeeeee........ee...eeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wza A  28 FEKHGTYYEIFVRSFYDSDGDGIGDLKGIIEKLDYLNDGDPETIADLGVNGIWLMPIFKSPSYHGYDVTDYYKINPDYGTLEDFHKLVEAAHQRGIKVIIDLPINHTSERHPWFLKASRDKNSEYRDYYVWAGPDTDTKETKLDGGRVWHYSPTGMYYGYFWSGMPDLNYNNPEVQEKVIGIAKYWLKQGVDGFRLDGAMHIFPPAQYDKNFTWWEKFRQEIEEVKPVYLVGEVWDISETVAPYFKYGFDSTFNFKLAEAVIATAKAGFPFGFNKKAKHIYGVYDREVGFGNYIDAPFLTNHDQNRILDQLGQDRNKARVAASIYLTLPGNPFIYYGEEIGMRGQGPHEVIREPFQWYNGSGEGETYWEPAMYNDGFTSVEQEEKNLDSLLNHYRRLIHFRNENPVFYTGKIEIINGGLNVVAFRRYNDKRDLYVYHNLVNRPVKIKVASGNWTLLFNSGDKEITPVEDNNKLMYTIPAYTTIVLEKE 515
                                    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       487       497       507
   Legend:   → Mismatch (orange background)
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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  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: GHD (106)
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8GPL8_9FIRM | Q8GPL8)
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.

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  3.2.1.1
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 Related Entries

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(-) Related Entries Specified in the PDB File

1gvi THERMUS MOLTOGENIC AMYLASE
1sma MALTOGENIC AMYLASE