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(-) Description

Title :  RECOMBINANT MEDAKA FISH ALPHA-AMYLASE EXPRESSED IN YEAST PICHIA PASTORIS
 
Authors :  K. Mizutani, M. Toyoda, B. Mikami
Date :  08 Dec 11  (Deposition) - 06 Jun 12  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A
Keywords :  (Alpha/Beta)8 Barrel Fold, Starch Hydrolysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Mizutani, M. Toyoda, Y. Otake, S. Yoshioka, N. Takahashi, B. Mikami
Structural And Functional Characterization Of Recombinant Medaka Fish Alpha-Amylase Expressed In Yeast Pichia Pastoris.
Biochim. Biophys. Acta V. 1824 954 2012
PubMed-ID: 22613096  |  Reference-DOI: 10.1016/J.BBAPAP.2012.05.005

(-) Compounds

Molecule 1 - ALPHA-AMYLASE
    Chains: A
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Plasmid: P9KPRAHS
    Expression System Strain: KM71
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Organism Scientific: ORYZIAS LATIPES
    Organism Taxid: 8090
    Strain: HD-RR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:100 , ARG A:158 , ASP A:167 , HIS A:201 , HOH A:552 , HOH A:553 , HOH A:554BINDING SITE FOR RESIDUE CA A 506
2AC2SOFTWAREARG A:195 , ASN A:298 , ARG A:337BINDING SITE FOR RESIDUE CL A 507

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:86
2A:70 -A:115
3A:141 -A:160
4A:379 -A:385
5A:451 -A:463

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:53 -Pro A:54
2Val A:129 -Pro A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VM5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VM5)

(-) Exons   (0, 0)

(no "Exon" information available for 3VM5)

(-) 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:499
 aligned with H2N0D4_ORYLA | H2N0D4 from UniProtKB/TrEMBL  Length:512

    Alignment length:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          512  
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505      |  
         H2N0D4_ORYLA    16 QHNPNTRDGRTAIVHLFEWRWADIAAECERFLGPKGFAGVQISPPNEHILVSSPWRPWWQRYQPISYNLCSRSGGENELRDMITRCNNVGVNVYVDAVINHMCGAGGGEGTHSSCGSWFNANNKDFPSVPYSNLDFNDGKCKTGSGNIENYGDPYQVRDCRLVGLLDLALEKDYVRGKVADFMNKLIDMGVAGFRVDACKHMWPGDLDNVYRRLNNLNTKWFPGGSRPFIFQEVIDLGGEPITTGEYVGLGRVTEFKYGARLGELFRKWNGQKLSYTKNWGEGWGFMADGNAVVFTDNHDNQRGHGAGGASILTFWDPRLYKMAVGYMLAHPYGFTRVMSSYSWDRNFVNGKDENDWIGPPSNGDGSTKPVPINPDQTCGDGWVCEHRWRQIMNMVQFRNVVNGQPHANWWDNGNNQVAFGRGNRGFIVFNNDDWALDVTLNTGLPGGTYCDVISGNKDGGSCTGKQITVGGDGRAHFYINNSEEDPFIAIHADSKL--   -
               SCOP domains d3vm5a1 A:1-404 automated matches                                                                                                                                                                                                                                                                                                                                                                                   d3vm5a2 A:405-499 automated matches                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee....hhhhhhhhhhhh.......eeee..............hhhhhhh...........hhhhhhhhhhhhhhh..eeeeee...eeee....ee........ee...........hhhhhhhhhh...........hhhhhhhh....eee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh................eeee..........hhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eee.....hhhhh...hhhhh....hhhhhhhhhhhhhhh...eeeee.............................................hhhhhhhhhhhhhhhhhhh...eeeeee....eeeeee...eeeeee.....eeeeee.....eeee......ee..ee...eeee....eeeeee.......eeeee.hhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vm5 A   1 QHNPNTRDGRTAIVHLFEWRWADIAAECERFLGPKGFAGVQISPPNEHILVSSPWRPWWQRYQPISYNLCSRSGGENELRDMITRCNNVGVNVYVDAVINHMCGAGGGEGTHSSCGSWFNANNKDFPSVPYSNLDFNDGKCKTGSGNIENYGDPYQVRDCRLVGLLDLALEKDYVRGKVADFMNKLIDMGVAGFRVDACKHMWPGDLDNVYRRLNNLNTKWFPGGSRPFIFQEVIDLGGEPITTGEYVGLGRVTEFKYGARLGELFRKWNGQKLSYTKNWGEGWGFMADGNAVVFTDNHDNQRGHGAGGASILTFWDPRLYKMAVGYMLAHPYGFTRVMSSYSWDRNFVNGKDENDWIGPPSNGDGSTKPVPINPDQTCGDGWVCEHRWRQIMNMVQFRNVVNGQPHANWWDNGNNQVAFGRGNRGFIVFNNDDWALDVTLNTGLPGGTYCDVISGNKDGGSCTGKQITVGGDGRAHFYINNSEEDPFIAIHADSKLHH 499
                                    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       490
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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  (0, 0)

(no "CATH Domain" information available for 3VM5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VM5)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (H2N0D4_ORYLA | H2N0D4)
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.

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