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(-) Description

Title :  BACILLUS CIRCULANS STRAIN 251 MUTANT A230V
 
Authors :  H. J. Rozeboom, B. W. Dijkstra
Date :  23 May 03  (Deposition) - 28 Oct 03  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosyltransferase, Transferase, Cyclodextrin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Leemhuis, H. J. Rozeboom, M. Wilbrink, G. J. Euverink, B. W. Dijkstra, L. Dijkhuizen
Conversion Of Cyclodextrin Glycosyltransferase Into A Starch Hydrolase By Directed Evolution: The Role Of Alanine 230 In Acceptor Subsite +1
Biochemistry V. 42 7518 2003
PubMed-ID: 12809508  |  Reference-DOI: 10.1021/BI034439Q
(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: ESCHERICHIA COLI
    Expression System Plasmid: PDP66K-
    Expression System Strain: MC1061
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BACILLUS CIRCULANS
    Organism Taxid: 1397
    Strain: 251
    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, 20)

Asymmetric/Biological Unit (7, 20)
No.NameCountTypeFull Name
1ACY8Ligand/IonACETIC ACID
2BGC1Ligand/IonBETA-D-GLUCOSE
3CA3Ligand/IonCALCIUM ION
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5GLC4Ligand/IonALPHA-D-GLUCOSE
6MAL2Ligand/IonMALTOSE
7MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:411 , ARG A:412 , TRP A:413 , ILE A:414 , SER A:445 , GLY A:446 , ALA A:539 , ASP A:540 , HOH A:918 , HOH A:921 , HOH A:1126 , HOH A:1145 , HOH A:1402 , HOH A:1467BINDING SITE FOR RESIDUE MAL A 887
02AC2SOFTWARETHR A:598 , ALA A:599 , LEU A:600 , GLY A:601 , GLN A:602 , ASN A:603 , ASN A:627 , GLN A:628 , TYR A:633 , HOH A:1650BINDING SITE FOR RESIDUE MAL A 889
03AC3SOFTWARETYR A:100 , HIS A:140 , ARG A:227 , ASP A:229 , VAL A:230 , GLU A:257 , HIS A:327 , ASP A:328 , ARG A:375 , GLC A:896BINDING SITE FOR RESIDUE BGC A 895
04AC4SOFTWARETRP A:101 , ASP A:371 , ARG A:375 , BGC A:895 , HOH A:1002 , HOH A:1116BINDING SITE FOR RESIDUE GLC A 896
05AC5SOFTWAREARG A:339 , TYR A:365 , SER A:384 , THR A:386 , GLC A:898 , HOH A:1341BINDING SITE FOR RESIDUE GLC A 897
06AC6SOFTWARELYS A:651 , GLU A:663 , GLC A:897 , GLC A:899 , HOH A:1205 , HOH A:1229 , HOH A:1514 , HOH A:1521BINDING SITE FOR RESIDUE GLC A 898
07AC7SOFTWAREASN A:667 , GLC A:898 , HOH A:1149 , HOH A:1473BINDING SITE FOR RESIDUE GLC A 899
08AC8SOFTWAREASP A:27 , ASN A:29 , ASN A:32 , ASN A:33 , GLY A:51 , ASP A:53 , HOH A:1063BINDING SITE FOR RESIDUE CA A 890
09AC9SOFTWAREASN A:139 , ILE A:190 , ASP A:199 , HIS A:233 , HOH A:926 , HOH A:949 , HOH A:969BINDING SITE FOR RESIDUE CA A 891
10BC1SOFTWAREALA A:315 , ASP A:577 , HOH A:973 , HOH A:1013 , HOH A:1264 , HOH A:1267 , HOH A:1444BINDING SITE FOR RESIDUE CA A 892
11BC2SOFTWAREGLY A:532 , ALA A:557 , GLY A:558 , ASN A:560 , TYR A:561 , ASN A:562 , HOH A:963 , HOH A:1080 , HOH A:1356BINDING SITE FOR RESIDUE EPE A 911
12BC3SOFTWAREGLN A:586 , VAL A:587 , SER A:674 , HOH A:1098 , HOH A:1102BINDING SITE FOR RESIDUE MPD A 901
13BC4SOFTWARESER A:450BINDING SITE FOR RESIDUE ACY A 902
14BC5SOFTWAREASP A:220BINDING SITE FOR RESIDUE ACY A 903
15BC6SOFTWAREARG A:377 , ILE A:378 , HOH A:1075 , HOH A:1542BINDING SITE FOR RESIDUE ACY A 905
16BC7SOFTWAREMET A:366 , SER A:367 , ALA A:376 , HOH A:968BINDING SITE FOR RESIDUE ACY A 906
17BC8SOFTWAREPHE A:236BINDING SITE FOR RESIDUE ACY A 907
18BC9SOFTWAREALA A:555 , HOH A:1513BINDING SITE FOR RESIDUE ACY A 908

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBM20PS51166 CBM20 (carbohydrate binding type-20) domain profile.CDGT2_BACCI608-713  1A:581-686

(-) Exons   (0, 0)

(no "Exon" information available for 1PEZ)

(-) 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 CDGT2_BACCI | P43379 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      
          CDGT2_BACCI    28 APDTSVSNKQNFSTDVIYQIFTDRFSDGNPANNPTGAAFDGTCTNLRLYCGGDWQGIINKINDGYLTGMGVTAIWISQPVENIYSIINYSGVNNTAYHGYWARDFKKTNPAYGTIADFQNLIAAAHAKNIKVIIDFAPNHTSPASSDQPSFAENGRLYDNGTLLGGYTNDTQNLFHHNGGTDFSTTENGIYKNLYDLADLNHNNSTVDVYLKDAIKMWLDLGIDGIRMDAVKHMPFGWQKSFMAAVNNYKPVFTFGEWFLGVNEVSPENHKFANESGMSLLDFRFAQKVRQVFRDNTDNMYGLKAMLEGSAADYAQVDDQVTFIDNHDMERFHASNANRRKLEQALAFTLTSRGVPAIYYGTEQYMSGGTDPDNRARIPSFSTSTTAYQVIQKLAPLRKCNPAIAYGSTQERWINNDVLIYERKFGSNVAVVAVNRNLNAPASISGLVTSLPQGSYNDVLGGLLNGNTLSVGSGGAASNFTLAAGGTAVWQYTAATATPTIGHVGPMMAKPGVTITIDGRGFGSSKGTVYFGTTAVSGADITSWEDTQIKVKIPAVAGGNYNIKVANAAGTASNVYDNFEVLSGDQVSVRFVVNNATTALGQNVYLTGSVSELGNWDPAKAIGPMYNQVVYQYPNWYYDVSVPAGKTIEFKFLKKQGSTVTWEGGSNHTFTAPSSGTATINVNWQP 713
               SCOP domains d1peza4 A:1-406 Cyclodextrin glycosyltransferase                                                                                                                                                                                                                                                                                                                                                                      d1peza3 A:407-495 Cyclodextrin glycosyltransferase                                       d1peza1 A:496-581 Cyclomaltodextrin glycanotransferase, domain D                      d1peza2 A:582-686 Cyclodextrin glycosyltransferase, C-terminal domain                                     SCOP domains
               CATH domains 1pezA01 A:1-400 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                    1pezA02 A:401-495 Golgi alpha-mannosidase II                                                   1pezA03 A:496-582 Immunoglobulins                                                      1pezA04 A:583-685 Immunoglobulins                                                                      - CATH domains
               Pfam domains ---------------------------------------------------Alpha-amylase-1pezA04 A:52-372                                                                                                                                                                                                                                                                                                   ----------------------------------------Alpha-amylase_C-1pezA02 A:413-495                                                  ---TIG-1pezA01 A:499-581                                                              ----CBM_20-1pezA03 A:586-682                                                                         ---- Pfam domains
         Sec.struct. author ................eeeehhhhhh..hhhhh.hhhhh.............hhhhhhhhhhhhhhhhhh..eeee...eee....eee..eee.......eeeeeee.....hhhhhhhhhhhhhhh..eeeeee...eeee.............eee..eeee...................hhhhhhh.....eee....hhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhh..ee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhh.ee...............hhhhhhhhhhhhhhh..eeeee.hhhhh...................hhhhhhhhhhhhhhhhhhhhhhheeeeeee...eeeeeee...eeeeeeee......eee.........eee............eeehhhhh...eee....eeeeeee......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: A:581-686 UniProt: 608-713                                                                     PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pez A   1 APDTSSSNKQNFSTDVIYQIFTDRFSDGNPANNPTGAAFDGTCTNLRLYCGGDWQGIINKINDGYLTGMGVTAIWISQPVENIYSIINYSGVNNTAYHGYWARDFKKTNPAYGTIADFQNLIAAAHAKNIKVIIDFAPNHTSPASSDQPSFAENGRLYDNGTLLGGYTNDTQNLFHHNGGTDFSTTENGIYKNLYDLADLNHNNSTVDVYLKDAIKMWLDLGIDGIRMDVVKHMPFGWQKSFMAAVNNYKPVFTFGEWFLGVNEVSPENHKFANESGMSLLDFRFAQKVRQVFRDNTDNMYGLKAMLEGSAADYAQVDDQVTFIDNHDMERFHASNANRRKLEQALAFTLTSRGVPAIYYGTEQYMSGGTDPDNRARIPSFSTSTTAYQVIQKLAPLRKSNPAIAYGSTQERWINNDVLIYERKFGSNVAVVAVNRNLNAPASISGLVTSLPQGSYNDVLGGLLNGNTLSVGSGGAASNFTLAAGGTAVWQYTAATATPTIGHVGPMMAKPGVTITIDGRGFGSSKGTVYFGTTAVSGADITSWEDTQIKVKIPAVAGGNYNIKVANAAGTASNVYDNFEVLSGDQVSVRFVVNNATTALGQNVYLTGSVSELGNWDPAKAIGPMYNQVVYQYPNWYYDVSVPAGKTIEFKFLKKQGSTATWEGGSNHTFTAPSSGTGTINVNWQP 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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 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  (4, 4)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)
(-)
Family: TIG (28)
(-)
Clan: GHD (106)
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CDGT2_BACCI | P43379)
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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  CDGT2_BACCI | P43379
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 Related Entries

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

UniProtKB/Swiss-Prot
        CDGT2_BACCI | P43379: 1cdg 1cgv 1cgw 1cgx 1cgy 1cxe 1cxf 1cxh 1cxi 1cxk 1cxl 1d3c 1dtu 1eo5 1eo7 1kck 1kcl 1ot1 1ot2 1pj9 1tcm 2cxg 2dij

(-) Related Entries Specified in the PDB File

1cdg NUCLEOTIDE SEQUENCE AND X-RAY STRUCTURE OF CYCLODEXTRIN GLYCOSYL TRANSFERASE FROM BACILLUS CIRCULANS STRAIN 251 IN A MALTOSE-DEPENDENT CRYSTAL FORM