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(-) Description

Title :  CRYSTAL STRUCTURE OF CYCLODEXTRIN GLUCANOTRANSFERASE FROM ALKALOPHILIC BACILLUS SP.#1011 COMPLEXED WITH 1-DEOXYNOJIRIMYCIN
 
Authors :  R. Kanai, K. Haga, K. Yamane, K. Harata
Date :  08 Mar 01  (Deposition) - 11 Apr 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Inhibitor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kanai, K. Haga, K. Yamane, K. Harata
Crystal Structure Of Cyclodextrin Glucanotransferase From Alkalophilic Bacillus Sp. 1011 Complexed With 1-Deoxynojirimycin At 2. 0 A Resolution.
J. Biochem. (Tokyo) V. 129 593 2001
PubMed-ID: 11275559
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYCLODEXTRIN GLUCANOTRANSFERASE
    Chains: A, B
    EC Number: 2.4.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTUE254
    Expression System Strain: ME8417
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BACCGTA
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 1409

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2NOJ4Ligand/Ion1-DEOXYNOJIRIMYCIN

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:27 , ASN A:29 , ASN A:32 , ASN A:33 , GLY A:51 , ASP A:53 , HOH A:1184BINDING SITE FOR RESIDUE CA A 1687
2AC2SOFTWAREASN A:139 , ILE A:190 , ASP A:199 , HIS A:233 , HOH A:739 , HOH A:751 , HOH A:1137BINDING SITE FOR RESIDUE CA A 1688
3AC3SOFTWAREASP B:27 , ASN B:29 , ASN B:32 , ASN B:33 , GLY B:51 , ASP B:53 , HOH B:1095BINDING SITE FOR RESIDUE CA B 1689
4AC4SOFTWAREASN B:139 , ILE B:190 , ASP B:199 , HIS B:233 , HOH B:784 , HOH B:1071 , HOH B:1082BINDING SITE FOR RESIDUE CA B 1690
5AC5SOFTWARETYR A:100 , LEU A:194 , ASP A:229 , ASP A:328 , HOH A:894 , HOH A:972 , HOH A:1015BINDING SITE FOR RESIDUE NOJ A 2691
6AC6SOFTWARELYS A:651 , ASN A:667BINDING SITE FOR RESIDUE NOJ A 2692
7AC7SOFTWARETYR B:100 , HIS B:140 , ASP B:229 , ASP B:328 , HOH B:824BINDING SITE FOR RESIDUE NOJ B 2693
8AC8SOFTWARETRP B:616 , ASN B:667BINDING SITE FOR RESIDUE NOJ B 2694

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:43 -A:50
2B:43 -B:50

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Asp A:371 -Pro A:372
2Gly A:505 -Pro A:506
3Gly A:623 -Pro A:624
4Tyr A:633 -Pro A:634
5Asp B:371 -Pro B:372
6Gly B:505 -Pro B:506
7Gly B:623 -Pro B:624
8Tyr B:633 -Pro B:634

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I75)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBM20PS51166 CBM20 (carbohydrate binding type-20) domain profile.CDGT_BACS0608-713
 		  2A:581-686
B:581-686

(-) Exons   (0, 0)

(no "Exon" information available for 1I75)

(-) 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:686
 aligned with CDGT_BACS0 | P05618 from UniProtKB/Swiss-Prot  Length:713

    Alignment length:686
                                    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       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707      
           CDGT_BACS0    28 APDTSVSNKQNFSTDVIYQIFTDRFSDGNPANNPTGAAFDGSCTNLRLYCGGDWQGIINKINDGYLTGMGITAIWISQPVENIYSVINYSGVNNTAYHGYWARDFKKTNPAYGTMQDFKNLIDTAHAHNIKVIIDFAPNHTSPASSDDPSFAENGRLYDNGNLLGGYTNDTQNLFHHYGGTDFSTIENGIYKNLYDLADLNHNNSSVDVYLKDAIKMWLDLGVDGIRVDAVKHMPFGWQKSFMATINNYKPVFTFGEWFLGVNEISPEYHQFANESGMSLLDFRFAQKARQVFRDNTDNMYGLKAMLEGSEVDYAQVNDQVTFIDNHDMERFHTSNGDRRKLEQALAFTLTSRGVPAIYYGSEQYMSGGNDPDNRARLPSFSTTTTAYQVIQKLAPLRKSNPAIAYGSTHERWINNDVIIYERKFGNNVAVVAINRNMNTPASITGLVTSLRRASYNDVLGGILNGNTLTVGAGGAASNFTLAPGGTAVWQYTTDATTPIIGNVGPMMAKPGVTITIDGRGFGSGKGTVYFGTTAVTGADIVAWEDTQIQVKIPAVPGGIYDIRVANAAGAASNIYDNFEVLTGDQVTVRFVINNATTALGQNVFLTGNVSELGNWDPNNAIGPMYNQVVYQYPTWYYDVSVPAGQTIEFKFLKKQGSTVTWEGGANRTFTTPTSGTATVNVNWQP 713
               SCOP domains d1i75a4 A:1-406 Cyclodextrin glycosyltransferase                                                                                                                                                                                                                                                                                                                                                                      d1i75a3 A:407-496 Cyclodextrin glycosyltransferase                                        d1i75a1 A:497-582 Cyclomaltodextrin glycanotransferase, domain D                      d1i75a2 A:583-686 Cyclodextrin glycosyltransferase, C-terminal domain                                    SCOP domains
               CATH domains 1i75A01 A:1-400 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                    1i75A02 A:401-495 Golgi alpha-mannosidase II                                                   1i75A03 A:496-582 Immunoglobulins                                                      1i75A04 A:583-685 Immunoglobulins                                                                      - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.hhhhh...hhhhh.hhhh..............hhhhhhhhhhhhhhhhh...eeee...eee....eee..eee.......eeeeeee.....hhhhhhhhhhhhhhh..eeeeee...eeee.............eee..eeee...................hhhhhhhh....eee....hhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhh..ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhh.ee...............hhhhhhhhhhhhhhh..eeeee.hhhhh...................hhhhhhhhhhhhhhhhhhhhhhheeeeeee...eeeeeeee..eeeeeeee......eee.........eee............eeehhhh....eee....eeeeee.......eeeeee..ee....eeeeeee.......eeee..eeehhh.eeee...eeeee......eeeeeeee.........eeeeee....eeeeeeeee........eeeeee.hhhhh..hhhhh..............eeeeeeee...eeeeeeeeee..eeee.....eeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBM20  PDB: A:581-686 UniProt: 608-713                                                                     PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i75 A   1 APDTSVSNKQNFSTDVIYQIFTDRFSDGNPANNPTGAAFDGSCTNLRLYCGGDWQGIINKINDGYLTGMGITAIWISQPVENIYSVINYSGVNNTAYHGYWARDFKKTNPAYGTMQDFKNLIDTAHAHNIKVIIDFAPNHTSPASSDDPSFAENGRLYDNGNLLGGYTNDTQNLFHHYGGTDFSTIENGIYKNLYDLADLNHNNSSVDVYLKDAIKMWLDLGVDGIRVDAVKHMPFGWQKSFMATINNYKPVFTFGEWFLGVNEISPEYHQFANESGMSLLDFRFAQKARQVFRDNTDNMYGLKAMLEGSEVDYAQVNDQVTFIDNHDMERFHTSNGDRRKLEQALAFTLTSRGVPAIYYGSEQYMSGGNDPDNRARLPSFSTTTTAYQVIQKLAPLRKSNPAIAYGSTHERWINNDVIIYERKFGNNVAVVAINRNMNTPASITGLVTSLPRGSYNDVLGGILNGNTLTVGAGGAASNFTLAPGGTAVWQYTTDATTPIIGNVGPMMAKPGVTITIDGRGFGSGKGTVYFGTTAVTGADIVAWEDTQIQVKIPAVPGGIYDIRVANAAGAASNIYDNFEVLTGDQVTVRFVINNATTALGQNVFLTGNVSELGNWDPNNAIGPMYNQVVYQYPTWYYDVSVPAGQTIEFKFLKKQGSTVTWEGGANRTFTTPTSGTATVNVNWQP 686
                                    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       590       600       610       620       630       640       650       660       670       680      


Chain B from PDB  Type:PROTEIN  Length:686
 aligned with CDGT_BACS0 | P05618 from UniProtKB/Swiss-Prot  Length:713

    Alignment length:686
                                    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       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707      
           CDGT_BACS0    28 APDTSVSNKQNFSTDVIYQIFTDRFSDGNPANNPTGAAFDGSCTNLRLYCGGDWQGIINKINDGYLTGMGITAIWISQPVENIYSVINYSGVNNTAYHGYWARDFKKTNPAYGTMQDFKNLIDTAHAHNIKVIIDFAPNHTSPASSDDPSFAENGRLYDNGNLLGGYTNDTQNLFHHYGGTDFSTIENGIYKNLYDLADLNHNNSSVDVYLKDAIKMWLDLGVDGIRVDAVKHMPFGWQKSFMATINNYKPVFTFGEWFLGVNEISPEYHQFANESGMSLLDFRFAQKARQVFRDNTDNMYGLKAMLEGSEVDYAQVNDQVTFIDNHDMERFHTSNGDRRKLEQALAFTLTSRGVPAIYYGSEQYMSGGNDPDNRARLPSFSTTTTAYQVIQKLAPLRKSNPAIAYGSTHERWINNDVIIYERKFGNNVAVVAINRNMNTPASITGLVTSLRRASYNDVLGGILNGNTLTVGAGGAASNFTLAPGGTAVWQYTTDATTPIIGNVGPMMAKPGVTITIDGRGFGSGKGTVYFGTTAVTGADIVAWEDTQIQVKIPAVPGGIYDIRVANAAGAASNIYDNFEVLTGDQVTVRFVINNATTALGQNVFLTGNVSELGNWDPNNAIGPMYNQVVYQYPTWYYDVSVPAGQTIEFKFLKKQGSTVTWEGGANRTFTTPTSGTATVNVNWQP 713
               SCOP domains d1i75b4 B:1-406 Cyclodextrin glycosyltransferase                                                                                                                                                                                                                                                                                                                                                                      d1i75b3 B:407-496 Cyclodextrin glycosyltransferase                                        d1i75b1 B:497-582 Cyclomaltodextrin glycanotransferase, domain D                      d1i75b2 B:583-686 Cyclodextrin glycosyltransferase, C-terminal domain                                    SCOP domains
               CATH domains 1i75B01 B:1-400 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                    1i75B02 B:401-495 Golgi alpha-mannosidase II                                                   1i75B03 B:496-582 Immunoglobulins                                                      1i75B04 B:583-685 Immunoglobulins                                                                      - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeehhhhh...hhhhh.hhhh..............hhhhhhhhhhhhhhhhh...eeee...eee....eee..eee.......eeeeeee.....hhhhhhhhhhhhhhh..eeeeee...eeee.............eee..eeee...................hhhhhhhh....eee....hhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhh..ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhh.ee...............hhhhhhhhhhhhhhh..eeeee.hhhhh...................hhhhhhhhhhhhhhhhhhhhhhheeeeeee...eeeeeeee..eeeeeeee......eee.........eee............eeehhhh....eee....eeeeee.......eeeeee..ee....eeeeeee.......eeee..eeehhh.eeeee..eeeee......eeeeeeee.........eeeeee....eeeeeeeee........eeeeee.hhhhh..hhhhh..............eeeeeeee...eeeeeeeeee..eeee.....eeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBM20  PDB: B:581-686 UniProt: 608-713                                                                     PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i75 B   1 APDTSVSNKQNFSTDVIYQIFTDRFSDGNPANNPTGAAFDGSCTNLRLYCGGDWQGIINKINDGYLTGMGITAIWISQPVENIYSVINYSGVNNTAYHGYWARDFKKTNPAYGTMQDFKNLIDTAHAHNIKVIIDFAPNHTSPASSDDPSFAENGRLYDNGNLLGGYTNDTQNLFHHYGGTDFSTIENGIYKNLYDLADLNHNNSSVDVYLKDAIKMWLDLGVDGIRVDAVKHMPFGWQKSFMATINNYKPVFTFGEWFLGVNEISPEYHQFANESGMSLLDFRFAQKARQVFRDNTDNMYGLKAMLEGSEVDYAQVNDQVTFIDNHDMERFHTSNGDRRKLEQALAFTLTSRGVPAIYYGSEQYMSGGNDPDNRARLPSFSTTTTAYQVIQKLAPLRKSNPAIAYGSTHERWINNDVIIYERKFGNNVAVVAINRNMNTPASITGLVTSLPRGSYNDVLGGILNGNTLTVGAGGAASNFTLAPGGTAVWQYTTDATTPIIGNVGPMMAKPGVTITIDGRGFGSGKGTVYFGTTAVTGADIVAWEDTQIQVKIPAVPGGIYDIRVANAAGAASNIYDNFEVLTGDQVTVRFVINNATTALGQNVFLTGNVSELGNWDPNNAIGPMYNQVVYQYPTWYYDVSVPAGQTIEFKFLKKQGSTVTWEGGANRTFTTPTSGTATVNVNWQP 686
                                    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       590       600       610       620       630       640       650       660       670       680
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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  (4, 8)

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

(-) CATH Domains  (3, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I75)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CDGT_BACS0 | P05618)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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:0043895    cyclomaltodextrin glucanotransferase activity    Catalysis of the cyclization of part of a 1,4-alpha-D-glucan chain by formation of a 1,4-alpha-D-glucosidic bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:2001070    starch binding    Interacting selectively and non-covalently with starch.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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: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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  1i75
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  2.4.1.19
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 Related Entries

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

UniProtKB/Swiss-Prot
        CDGT_BACS0 | P05618: 1d7f 1ded 1pam 1ukq 1uks 1ukt 1v3j 1v3k 1v3l 1v3m

(-) Related Entries Specified in the PDB File

1pam 1PAM CONTAINS THE NATIVE PROTEIN