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(-) Description

Title :  CYCLODEXTRIN GLYCOSYL TRANSFERASE FROM THERMOANEROBACTERIUM THERMOSULFURIGENES EM1 MUTANT S77P COMPLEXED WITH A MALTOHEPTAOSE INHIBITOR
 
Authors :  H. J. Rozeboom, N. Van Oosterwijk, B. W. Dijkstra
Date :  13 Dec 07  (Deposition) - 27 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosidase, Thermostable, Family 13 Glycosyl Hydrolas, Ligand, Substrate, Acarbose, Glycosyltransferase, Metal-Binding, Secreted, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Kelly, H. Leemhuis, H. J. Rozeboom, N. Van Oosterwijk, B. W. Dijkstra, L. Dijkhuizen
Elimination Of Competing Hydrolysis And Coupling Side Reactions Of A Cyclodextrin Glucanotransferase By Directed Evolution.
Biochem. J. V. 413 517 2008
PubMed-ID: 18422488  |  Reference-DOI: 10.1042/BJ20080353
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYCLOMALTODEXTRIN GLUCANOTRANSFERASE
    Chains: A
    EC Number: 2.4.1.19
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PCSCGT-TT
    Expression System Strain: DB104A
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Gene: AMYA
    Mutation: YES
    Organism Scientific: THERMOANAEROBACTERIUM THERMOSULFURIGENES
    Organism Taxid: 33950
    Strain: EM1
    Synonym: CYCLODEXTRIN-GLYCOSYLTRANSFERASE, CGTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 21)

Asymmetric/Biological Unit (7, 21)
No.NameCountTypeFull Name
1ACI1Ligand/Ion6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
2CA2Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4G6D1Ligand/Ion6-DEOXY-ALPHA-D-GLUCOSE
5GLC7Ligand/IonALPHA-D-GLUCOSE
6GOL6Ligand/IonGLYCEROL
7SO43Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:413 , ILE A:414 , THR A:445 , HOH A:1238 , HOH A:1306 , HOH A:1326 , HOH A:1541BINDING SITE FOR RESIDUE GLC A 687
02AC2SOFTWAREGLN A:411 , ARG A:412 , GLY A:446 , HOH A:844 , HOH A:1332 , HOH A:1442 , HOH A:1600 , HOH A:1768BINDING SITE FOR RESIDUE GLC A 688
03AC3SOFTWAREGLY A:262 , GLU A:265 , HOH A:1272 , HOH A:1275 , HOH A:1305 , HOH A:1401 , HOH A:1564 , HOH A:1586 , HOH A:1652BINDING SITE FOR RESIDUE GLC A 691
04AC4SOFTWAREPHE A:184 , PHE A:196 , LYS A:233 , HOH A:1305 , HOH A:1586BINDING SITE FOR RESIDUE GLC A 692
05AC5SOFTWAREPHE A:196 , ALA A:231 , LYS A:233 , HIS A:234 , GLU A:258 , ASP A:329 , HOH A:770BINDING SITE FOR RESIDUE G6D A 693
06AC6SOFTWARETYR A:101 , HIS A:141 , ARG A:228 , ASP A:230 , GLU A:258 , HIS A:328 , ASP A:329 , ARG A:375BINDING SITE FOR RESIDUE ACI A 694
07AC7SOFTWARETYR A:101 , TRP A:102 , ASP A:371 , ARG A:375 , HOH A:736BINDING SITE FOR RESIDUE GLC A 695
08AC8SOFTWARELYS A:47 , PHE A:196 , ASP A:371 , HOH A:976 , HOH A:1217 , HOH A:1357 , HOH A:1660 , HOH A:1665BINDING SITE FOR RESIDUE GLC A 696
09AC9SOFTWAREHOH A:1066 , HOH A:1278 , HOH A:1357 , HOH A:1760BINDING SITE FOR RESIDUE GLC A 697
10BC1SOFTWAREASN A:140 , ILE A:191 , ASP A:200 , HIS A:234 , HOH A:734 , HOH A:808 , HOH A:834BINDING SITE FOR RESIDUE CA A 698
11BC2SOFTWAREASP A:27 , ASN A:29 , ASN A:32 , ASN A:33 , GLY A:51 , ASP A:53 , HOH A:857BINDING SITE FOR RESIDUE CA A 699
12BC3SOFTWAREARG A:104 , GLU A:154 , ARG A:157 , HOH A:948 , HOH A:1052 , HOH A:1523BINDING SITE FOR RESIDUE SO4 A 701
13BC4SOFTWAREHIS A:665 , THR A:666 , HOH A:788 , HOH A:1057 , HOH A:1183BINDING SITE FOR RESIDUE SO4 A 702
14BC5SOFTWARETYR A:492 , SER A:494 , SER A:495 , SER A:496 , HOH A:1490BINDING SITE FOR RESIDUE SO4 A 703
15BC6SOFTWAREPRO A:144 , TYR A:152 , ASP A:197 , HOH A:760 , HOH A:1195 , HOH A:1665BINDING SITE FOR RESIDUE GOL A 704
16BC7SOFTWAREHIS A:127 , ALA A:128 , ASN A:130 , LYS A:648 , TRP A:659 , HOH A:1271 , HOH A:1313 , HOH A:1445 , HOH A:1614BINDING SITE FOR RESIDUE GOL A 705
17BC8SOFTWARETYR A:187 , ILE A:191 , TYR A:192 , PRO A:236 , PHE A:237 , GLY A:238 , PHE A:623 , TYR A:635 , ASP A:636BINDING SITE FOR RESIDUE GOL A 706
18BC9SOFTWAREARG A:295 , ASP A:296 , ASN A:335 , THR A:595 , GLU A:599 , TYR A:630 , HOH A:1009 , HOH A:1028 , HOH A:1039 , HOH A:1192BINDING SITE FOR RESIDUE GOL A 707
19CC1SOFTWARESER A:441 , TYR A:442 , ASN A:443 , ILE A:678 , HOH A:799 , HOH A:965 , HOH A:981 , HOH A:1722BINDING SITE FOR RESIDUE GOL A 708
20CC2SOFTWAREARG A:193 , ASN A:297 , ASP A:299 , ARG A:436 , GLN A:625 , HOH A:1279 , HOH A:1775BINDING SITE FOR RESIDUE GOL A 709

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BMW)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:371 -Pro A:372
2Gly A:505 -Pro A:506
3Gly A:620 -Pro A:621
4Tyr A:630 -Pro A:631

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBM20PS51166 CBM20 (carbohydrate binding type-20) domain profile.CDGT_THETU605-710  1A:578-683

(-) Exons   (0, 0)

(no "Exon" information available for 3BMW)

(-) 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:683
 aligned with CDGT_THETU | P26827 from UniProtKB/Swiss-Prot  Length:710

    Alignment length:683
                                    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_THETU    28 ASDTAVSNVVNYSTDVIYQIVTDRFVDGNTSNNPTGDLYDPTHTSLKKYFGGDWQGIINKINDGYLTGMGVTAIWISQPVENIYAVLPDSTFGGSTSYHGYWARDFKRTNPYFGSFTDFQNLINTAHAHNIKVIIDFAPNHTSPASETDPTYAENGRLYDNGTLLGGYTNDTNGYFHHYGGTDFSSYEDGIYRNLFDLADLNQQNSTIDSYLKSAIKVWLDMGIDGIRLDAVKHMPFGWQKNFMDSILSYRPVFTFGEWFLGTNEIDVNNTYFANESGMSLLDFRFSQKVRQVFRDNTDTMYGLDSMIQSTASDYNFINDMVTFIDNHDMDRFYNGGSTRPVEQALAFTLTSRGVPAIYYGTEQYMTGNGDPYNRAMMTSFNTSTTAYNVIKKLAPLRKSNPAIAYGTTQQRWINNDVYIYERKFGNNVALVAINRNLSTSYNITGLYTALPAGTYTDVLGGLLNGNSISVASDGSVTPFTLSAGEVAVWQYVSSSNSPLIGHVGPTMTKAGQTITIDGRGFGTTSGQVLFGSTAGTIVSWDDTEVKVKVPSVTPGKYNISLKTSSGATSNTYNNINILTGNQICVRFVVNNASTVYGENVYLTGNVAELGNWDTSKAIGPMFNQVVYQYPTWYYDVSVPAGTTIQFKFIKKNGNTITWEGGSNHTYTVPSSSTGTVIVNWQQ 710
               SCOP domains d3bmwa4 A:1-406 Cyclodextrin glycosyltransferase                                                                                                                                                                                                                                                                                                                                                                      d3bmwa3 A:407-495 Cyclodextrin glycosyltransferase                                       d3bmwa1 A:496-578 Cyclomaltodextrin glycanotransferase, domain D                   d3bmwa2 A:579-683 Cyclodextrin glycosyltransferase, C-terminal domain                                     SCOP domains
               CATH domains 3bmwA01 A:1-400 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                    3bmwA02 A:401-495 Golgi alpha-mannosidase II                                                   3bmwA03 A:496-579 Immunoglobulins                                                   3bmwA04 A:580-682 Immunoglobulins                                                                      - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.hhhhh...hhhhh.hhhhh.............hhhhhhhhhhh..hhhhh..eeee...eee....eee...eee.......eeeeeee.....hhhhhhhhhhhhhhh..eeeeee...eeee.............eee..eeee...................hhhhhhhh....eee....hhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhh..ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhh.ee...............hhhhhhhhhhhhhh..eeeee.hhhhh......hhhhh........hhhhhhhhhhhhhhhhhhhhhhheeeeeee...eeeeeeee..eeeeeeee......eee.........eee............eee........eee....eeeeee.......eeeeee..ee....eeeeeee.......eeee..ee.eeeee...eeeee......eeeeeeee.........eeeeee....eeeeeeeee........eeeeee.hhhhh..hhhhh..............eeeeeeee...eeeeeeeee....eee.....eeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBM20  PDB: A:578-683 UniProt: 605-710                                                                     PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bmw A   1 ASDTAVSNVVNYSTDVIYQIVTDRFVDGNTSNNPTGDLYDPTHTSLKKYFGGDWQGIINKINDGYLTGMGVTAIWIPQPVENIYAVLPDSTFGGSTSYHGYWARDFKRTNPYFGSFTDFQNLINTAHAHNIKVIIDFAPNHTSPASETDPTYAENGRLYDNGTLLGGYTNDTNGYFHHYGGTDFSSYEDGIYRNLFDLADLNQQNSTIDSYLKSAIKVWLDMGIDGIRLDAVKHMPFGWQKNFMDSILSYRPVFTFGEWFLGTNEIDVNNTYFANESGMSLLDFRFSQKVRQVFRDNTDTMYGLDSMIQSTASDYNFINDMVTFIDNHDMDRFYNGGSTRPVEQALAFTLTSRGVPAIYYGTEQYMTGNGDPYNRAMMTSFNTSTTAYNVIKKLAPLRKSNPAIAYGTTQQRWINNDVYIYERKFGNNVALVAINRNLSTSYNITGLYTALPAGTYTDVLGGLLNGNSISVASDGSVTPFTLSAGEVAVWQYVSSSNSPLIGHVGPTMTKAGQTITIDGRGFGTTSGQVLFGSTAGTIVSWDDTEVKVKVPSVTPGKYNISLKTSSGATSNTYNNINILTGNQICVRFVVNNASTVYGENVYLTGNVAELGNWDTSKAIGPMFNQVVYQYPTWYYDVSVPAGTTIQFKFIKKNGNTITWEGGSNHTYTVPSSSTGTVIVNWQQ 683
                                    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
   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  (4, 4)

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

(-) CATH Domains  (3, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CDGT_THETU | P26827)
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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  CDGT_THETU | P26827
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 Related Entries

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

UniProtKB/Swiss-Prot
        CDGT_THETU | P26827: 1a47 1ciu 3bmv

(-) Related Entries Specified in the PDB File

1ciu THE WILD-TYPE PROTEIN
1a47 THE WILD-TYPE PROTEIN IN COMPLEX WITH A MALTOHEXOASE INHIBITOR
3bmv