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(-) Description

Title :  THERMUS MALTOGENIC AMYLASE IN COMPLEX WITH BETA-CD
 
Authors :  M. -S. Kim, J. -I. Kim, B. -H. Oh
Date :  14 Feb 02  (Deposition) - 06 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Amylase, Transglycosylation, Beta-Cyclodextrin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. -S. Lee, M. -S. Kim, H. -S. Cho, J. -I. Kim, T. -J. Kim, H. -S. Lee, B. -H. Oh, K. -H. Park
Cyclomaltodextrinase, Neopullulanase, And Maltogenic Amylase Are Nearly Indistinguishable From Each Other
J. Biol. Chem. V. 277 21891 2002
PubMed-ID: 11923309  |  Reference-DOI: 10.1074/JBC.M201623200

(-) Compounds

Molecule 1 - MALTOGENIC AMYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMUS SP.
    Organism Taxid: 275

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1BCD2Ligand/IonBETA-CYCLODEXTRIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:205 , TYR A:207 , HIS A:247 , PHE A:289 , MET A:295 , ASP A:328 , TRP A:359 , TYR A:377 , HIS A:423 , ASP A:424 , ASP A:468 , ARG A:472 , TYR B:45 , TRP B:47 , ARG B:83 , ASP B:110 , THR B:111BINDING SITE FOR RESIDUE BCD A1589
2AC2SOFTWARETYR A:45 , TRP A:47 , ASP A:110 , THR A:111 , HIS B:205 , TYR B:207 , HIS B:247 , PHE B:289 , MET B:295 , ASP B:328 , TRP B:359 , TYR B:377 , HIS B:423 , ASP B:424 , ASP B:468 , ARG B:472BINDING SITE FOR RESIDUE BCD B1589

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:468 -Pro A:469
2Asp B:468 -Pro B:469

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GVI)

(-) 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:588
 aligned with O69007_9DEIN | O69007 from UniProtKB/TrEMBL  Length:588

    Alignment length:588
                                    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       500       510       520       530       540       550       560       570       580        
         O69007_9DEIN     1 MRKEAIHHRSTDNFAYAYDSETLHLRLQTKKNDVDHVELLFGDPYEWHDGAWQFQTMPMRKTGSDGLFDYWLAEVKPPYRRLRYGFVLRAGGEKLVYTEKGFYHEAPSDDTAYYFCFPFLHRVDLFQAPDWVKDTVWYQIFPERFANGNPAISPKGARPWGSEDPTPTSFFGGDLQGIIDHLDYLADLGITGIYLTPIFRAPSNHKYDTADYFEIDPHFGDKETLKTLVKRCHEKGIRVMLDAVFNHCGYEFAPFQDVLKNGAASRYKDWFHIREFPLQTEPRPNYDTFAFVPHMPKLNTAHPEVKRYLLDVATYWIREFDIDGWRLDVANEIDHQFWREFRQAVKALKPDVYILGEIWHDAMPWLRGDQFDAVMNYPLADAALRFFAKEDMSASEFADRLMHVLHSYPKQVNEAAFNLLGSHDTPRLLTVCGGDVRKVKLLFLFQLTFTGSPCIYYGDEIGMTGGNDPECRKCMVWDPEKQNKELYEHVKQLIALRKQYRALRRGDVAFLTADDEVNHLVYAKTDGNETVMIIINRSNEAAEIPMPIDARGKWLVNLLTGERFAAEAETLCVSLPPYGFVLYAVESW 588
               SCOP domains d1gvia1 A:1-123 Maltogenic amylase, N-terminal domain N                                                                    d1gvia3 A:124-505 Maltogenic amylase, central domain                                                                                                                                                                                                                                                                                                                                          d1gvia2 A:506-588 Maltogenic amylase                                                SCOP domains
               CATH domains 1gviA01 A:1-125 Immunoglobulins                                                                                              1gviA02 A:126-245,A:300-505 Glycosidases                                                                                ------------------------------------------------------1gviA02 A:126-245,A:300-505 Glycosidases                                                                                                                                                                      1gviA04 A:506-588 Golgi alpha-mannosidase II                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhh.eee.....eee.eeee.......eeeee....ee..ee..eeee.eeeee...eeeee.ee.....eeeeeeeeee..eeeeee..eee...........eeeee.........hhhhhh..eee.hhhhh............................hhhhhhhhhhhhhhhh..eee..........................hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhh.hhhh...............................hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhh...eeee................ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhh...........hhhhhh..hhhhhhhhhhhhhh.....eee.hhhhh......hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh............eeeeeeee..eeeeeeee.....eeeeee.......eee.....ee.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gvi A   1 MRKEAIHHRSTDNFAYAYDSETLHLRLQTKKNDVDHVELLFGDPYEWHDGAWQFQTMPMRKTGSDGLFDYWLAEVKPPYRRLRYGFVLRAGGEKLVYTEKGFYHEAPSDDTAYYFCFPFLHRVDLFQAPDWVKDTVWYQIFPERFANGNPAISPKGARPWGSEDPTPTSFFGGDLQGIIDHLDYLADLGITGIYLTPIFRAPSNHKYDTADYFEIDPHFGDKETLKTLVKRCHEKGIRVMLDAVFNHCGYEFAPFQDVLKNGAASRYKDWFHIREFPLQTEPRPNYDTFAFVPHMPKLNTAHPEVKRYLLDVATYWIREFDIDGWRLDVANEIDHQFWREFRQAVKALKPDVYILGLIWHDAMPWLRGDQFDAVMNYPLADAALRFFAKEDMSASEFADRLMHVLHSYPKQVNEAAFNLLGSHDTPRLLTVCGGDVRKVKLLFLFQLTFTGSPCIYYGDEIGMTGGNDPECRKCMVWDPEKQNKELYEHVKQLIALRKQYRALRRGDVAFLTADDEVNHLVYAKTDGNETVMIIINRSNEAAEIPMPIDARGKWLVNLLTGERFAAEAETLCVSLPPYGFVLYAVESW 588
                                    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       500       510       520       530       540       550       560       570       580        


Chain B from PDB  Type:PROTEIN  Length:588
 aligned with O69007_9DEIN | O69007 from UniProtKB/TrEMBL  Length:588

    Alignment length:588
                                    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       500       510       520       530       540       550       560       570       580        
         O69007_9DEIN     1 MRKEAIHHRSTDNFAYAYDSETLHLRLQTKKNDVDHVELLFGDPYEWHDGAWQFQTMPMRKTGSDGLFDYWLAEVKPPYRRLRYGFVLRAGGEKLVYTEKGFYHEAPSDDTAYYFCFPFLHRVDLFQAPDWVKDTVWYQIFPERFANGNPAISPKGARPWGSEDPTPTSFFGGDLQGIIDHLDYLADLGITGIYLTPIFRAPSNHKYDTADYFEIDPHFGDKETLKTLVKRCHEKGIRVMLDAVFNHCGYEFAPFQDVLKNGAASRYKDWFHIREFPLQTEPRPNYDTFAFVPHMPKLNTAHPEVKRYLLDVATYWIREFDIDGWRLDVANEIDHQFWREFRQAVKALKPDVYILGEIWHDAMPWLRGDQFDAVMNYPLADAALRFFAKEDMSASEFADRLMHVLHSYPKQVNEAAFNLLGSHDTPRLLTVCGGDVRKVKLLFLFQLTFTGSPCIYYGDEIGMTGGNDPECRKCMVWDPEKQNKELYEHVKQLIALRKQYRALRRGDVAFLTADDEVNHLVYAKTDGNETVMIIINRSNEAAEIPMPIDARGKWLVNLLTGERFAAEAETLCVSLPPYGFVLYAVESW 588
               SCOP domains d1gvib1 B:1-123 Maltogenic amylase, N-terminal domain N                                                                    d1gvib3 B:124-505 Maltogenic amylase, central domain                                                                                                                                                                                                                                                                                                                                          d1gvib2 B:506-588 Maltogenic amylase                                                SCOP domains
               CATH domains 1gviB01 B:1-125 Immunoglobulins                                                                                              1gviB02 B:126-245,B:300-505 Glycosidases                                                                                ------------------------------------------------------1gviB02 B:126-245,B:300-505 Glycosidases                                                                                                                                                                      1gviB04 B:506-588 Golgi alpha-mannosidase II                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhh.eeeee..eeeeeeeee.....eeeeee.....ee..ee..eeee.eeeee...eeeeeeee.hhhhheeeeeeee....eeeee..eee......hhhhheee............hhhhhh.eeeehhhhh............................hhhhhhhhhhhhhhhh..eeee....................hhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhh..hhhhhhh..............................hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhh......ee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhh............hhhhhh..hhhhhhhhhhhhh......eee.hhhhh......hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeeee..eeeeeeee.....eeeeee........ee............eeeeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gvi B   1 MRKEAIHHRSTDNFAYAYDSETLHLRLQTKKNDVDHVELLFGDPYEWHDGAWQFQTMPMRKTGSDGLFDYWLAEVKPPYRRLRYGFVLRAGGEKLVYTEKGFYHEAPSDDTAYYFCFPFLHRVDLFQAPDWVKDTVWYQIFPERFANGNPAISPKGARPWGSEDPTPTSFFGGDLQGIIDHLDYLADLGITGIYLTPIFRAPSNHKYDTADYFEIDPHFGDKETLKTLVKRCHEKGIRVMLDAVFNHCGYEFAPFQDVLKNGAASRYKDWFHIREFPLQTEPRPNYDTFAFVPHMPKLNTAHPEVKRYLLDVATYWIREFDIDGWRLDVANEIDHQFWREFRQAVKALKPDVYILGLIWHDAMPWLRGDQFDAVMNYPLADAALRFFAKEDMSASEFADRLMHVLHSYPKQVNEAAFNLLGSHDTPRLLTVCGGDVRKVKLLFLFQLTFTGSPCIYYGDEIGMTGGNDPECRKCMVWDPEKQNKELYEHVKQLIALRKQYRALRRGDVAFLTADDEVNHLVYAKTDGNETVMIIINRSNEAAEIPMPIDARGKWLVNLLTGERFAAEAETLCVSLPPYGFVLYAVESW 588
                                    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       500       510       520       530       540       550       560       570       580
   Legend:   → Mismatch (orange background)
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  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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O69007_9DEIN | O69007)
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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
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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 Related Entries

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

UniProtKB/TrEMBL
        O69007_9DEIN | O69007: 1sma

(-) Related Entries Specified in the PDB File

1sma CRYSTAL STRUCTURE OF A MALTOGENIC AMYLASE