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(-) Description

Title :  CRYSTAL STRUCTURE OF GAMMA-CGTASE FROM ALKALOPHILIC BACILLUS CLARKII AT 1.65 ANGSTROM RESOLUTION
 
Authors :  L. Wu, D. Yang, J. Zhou, J. Wu, J. Chen
Date :  22 Feb 13  (Deposition) - 26 Feb 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Ibeta/Alpha J8 Barrel, Alpha-Amylase Family, Cyclization, Binding Glucose, Binding Cation Calcium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Wu, D. Yang, J. Li, J. Zhou, J. Wu
The Crystal Structure Of Gamma-Cgtase From Alkalophilic Bacillus Clarkii At 1. 65 Angstrom Resolution.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYCLODEXTRIN GLUCANOTRANSFERASE
    Chains: A
    EC Number: 2.4.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CGT
    Organism Scientific: BACILLUS CLARKII
    Organism Taxid: 79879

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 50)

Asymmetric/Biological Unit (6, 50)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2CL13Ligand/IonCHLORIDE ION
3EDO7Ligand/Ion1,2-ETHANEDIOL
4GOL9Ligand/IonGLYCEROL
5NA1Ligand/IonSODIUM ION
6SO414Ligand/IonSULFATE ION

(-) Sites  (50, 50)

Asymmetric Unit (50, 50)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:27 , ASP A:29 , ASN A:32 , ASN A:33 , GLY A:51 , ASP A:53 , HOH A:909BINDING SITE FOR RESIDUE CA A 701
02AC2SOFTWAREGLU A:62BINDING SITE FOR RESIDUE CA A 702
03AC3SOFTWAREGLU A:144 , TYR A:149 , HIS A:157 , GOL A:735BINDING SITE FOR RESIDUE CA A 703
04AC4SOFTWARETHR A:433BINDING SITE FOR RESIDUE CA A 704
05AC5SOFTWARETYR A:165 , HIS A:195BINDING SITE FOR RESIDUE CA A 705
06AC6SOFTWAREASN A:136 , ILE A:181 , HIS A:224 , HOH A:828 , HOH A:832 , HOH A:947BINDING SITE FOR RESIDUE CA A 706
07AC7SOFTWAREARG A:402 , GLU A:440BINDING SITE FOR RESIDUE CL A 707
08AC8SOFTWARESER A:515BINDING SITE FOR RESIDUE CL A 708
09AC9SOFTWAREALA A:634BINDING SITE FOR RESIDUE CL A 709
10BC1SOFTWAREARG A:669BINDING SITE FOR RESIDUE CL A 710
11BC2SOFTWARELEU A:7 , SER A:8 , LYS A:507BINDING SITE FOR RESIDUE CL A 711
12BC3SOFTWAREGLY A:288BINDING SITE FOR RESIDUE CL A 712
13BC4SOFTWAREHOH A:1033BINDING SITE FOR RESIDUE CL A 713
14BC5SOFTWAREASN A:41BINDING SITE FOR RESIDUE CL A 714
15BC6SOFTWAREASN A:590BINDING SITE FOR RESIDUE CL A 715
16BC7SOFTWAREHIS A:224 , HOH A:929 , HOH A:1276BINDING SITE FOR RESIDUE CL A 716
17BC8SOFTWAREASP A:533 , ASP A:534BINDING SITE FOR RESIDUE CL A 717
18BC9SOFTWAREASN A:427BINDING SITE FOR RESIDUE CL A 718
19CC1SOFTWARESER A:235 , ASP A:239 , ASP A:504BINDING SITE FOR RESIDUE CL A 719
20CC2SOFTWAREGLY A:228 , VAL A:627 , SER A:628 , HOH A:839 , HOH A:849 , HOH A:1103BINDING SITE FOR RESIDUE NA A 720
21CC3SOFTWAREGLY A:36 , ASN A:41 , EDO A:747 , HOH A:1215 , HOH A:1226BINDING SITE FOR RESIDUE SO4 A 721
22CC4SOFTWAREGLU A:62 , HIS A:125 , LYS A:359 , HOH A:1012BINDING SITE FOR RESIDUE SO4 A 722
23CC5SOFTWAREASP A:176 , TYR A:177 , HIS A:258 , HOH A:863BINDING SITE FOR RESIDUE SO4 A 723
24CC6SOFTWARETYR A:294 , GLU A:401BINDING SITE FOR RESIDUE SO4 A 724
25CC7SOFTWARETYR A:355 , THR A:375 , THR A:376 , HOH A:1088 , HOH A:1207 , HOH A:1208BINDING SITE FOR RESIDUE SO4 A 725
26CC8SOFTWAREASN A:464 , THR A:531 , TRP A:532 , HOH A:1004 , HOH A:1149BINDING SITE FOR RESIDUE SO4 A 726
27CC9SOFTWAREGLU A:401 , TYR A:521 , LYS A:526BINDING SITE FOR RESIDUE SO4 A 727
28DC1SOFTWAREHIS A:584 , TYR A:620BINDING SITE FOR RESIDUE SO4 A 728
29DC2SOFTWARETYR A:618 , ARG A:669 , HOH A:1213BINDING SITE FOR RESIDUE SO4 A 729
30DC3SOFTWARETYR A:446 , HIS A:447 , HOH A:848 , HOH A:1196 , HOH A:1210BINDING SITE FOR RESIDUE SO4 A 730
31DC4SOFTWARETRP A:249 , SER A:256 , HIS A:258 , HOH A:1137 , HOH A:1286BINDING SITE FOR RESIDUE SO4 A 731
32DC5SOFTWAREPRO A:67 , HIS A:125 , LYS A:287 , HOH A:1017 , HOH A:1180BINDING SITE FOR RESIDUE SO4 A 732
33DC6SOFTWAREARG A:284 , VAL A:324 , LYS A:359 , HOH A:904 , HOH A:1253BINDING SITE FOR RESIDUE SO4 A 733
34DC7SOFTWAREGLY A:358 , LYS A:359 , LYS A:366 , HOH A:1248 , HOH A:1270 , HOH A:1282BINDING SITE FOR RESIDUE SO4 A 734
35DC8SOFTWARETYR A:149 , LEU A:154 , HIS A:157 , ALA A:634 , ARG A:659 , CA A:703 , HOH A:870BINDING SITE FOR RESIDUE GOL A 735
36DC9SOFTWARETHR A:105 , ASP A:111 , PHE A:112 , HOH A:815 , HOH A:935 , HOH A:1038BINDING SITE FOR RESIDUE GOL A 736
37EC1SOFTWAREARG A:523 , ALA A:549 , GLN A:550BINDING SITE FOR RESIDUE GOL A 737
38EC2SOFTWARETRP A:603 , LYS A:638 , ASN A:655 , HOH A:1219BINDING SITE FOR RESIDUE GOL A 738
39EC3SOFTWAREHIS A:482 , SER A:484 , GLU A:485BINDING SITE FOR RESIDUE GOL A 739
40EC4SOFTWARELYS A:203 , GLN A:207 , SER A:236 , LYS A:572BINDING SITE FOR RESIDUE GOL A 740
41EC5SOFTWAREASN A:596 , TRP A:603BINDING SITE FOR RESIDUE GOL A 741
42EC6SOFTWAREASP A:6 , TYR A:240 , PRO A:242 , HOH A:1016 , HOH A:1072 , HOH A:1242BINDING SITE FOR RESIDUE GOL A 742
43EC7SOFTWAREASN A:164 , ASN A:192 , GLN A:194 , HIS A:195 , HOH A:822 , HOH A:827 , HOH A:880 , HOH A:1206 , HOH A:1274BINDING SITE FOR RESIDUE GOL A 743
44EC8SOFTWAREASP A:239 , TYR A:587 , GLY A:588BINDING SITE FOR RESIDUE EDO A 744
45EC9SOFTWAREGLU A:463BINDING SITE FOR RESIDUE EDO A 745
46FC1SOFTWARELYS A:507 , THR A:536BINDING SITE FOR RESIDUE EDO A 746
47FC2SOFTWAREGLY A:36 , SO4 A:721BINDING SITE FOR RESIDUE EDO A 747
48FC3SOFTWAREHIS A:291 , ASN A:405 , ASP A:406BINDING SITE FOR RESIDUE EDO A 748
49FC4SOFTWAREARG A:327 , ASP A:328 , VAL A:428BINDING SITE FOR RESIDUE EDO A 749
50FC5SOFTWAREGLN A:37BINDING SITE FOR RESIDUE EDO A 750

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:171 -Ser A:172
2Asp A:361 -Pro A:362
3Gly A:496 -Pro A:497
4Gly A:610 -Pro A:611
5Tyr A:620 -Pro A:621

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JCM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JCM)

(-) Exons   (0, 0)

(no "Exon" information available for 4JCM)

(-) 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:669
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4jcma1 A:6-396 automated matches                                                                                                                                                                                                                                                                                                                                                                      d4jcma2 A:397-486 automated matches                                                       d4jcma3 A:487-568 automated matches                                               d4jcma4 A:569-674 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee.hhhhh...hhhhh.hhhhhhhhhh........hhhhhhhhhhhhhhhhh...eeee...eee................eeeeeee.....hhhhhhhhhhhhhhh..eeeeee...eeeehhhhh..eee..eeee...................hhhhhhhh....eee....hhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhh..ee.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhh.ee................hhhhhhhhhhhhhh..eeeee.hhhhh...................hhhhhhhhhhhhhhhhhhhhhhheeeeeee...eeeeeeee..eeeeeeee......eee.........eee............eee........eee....eeeeee........eeeeee..ee....eeeeeee.......eeee..ee.eeeee...eeeee......eeeeeeee.........eeeee....eeeeeeeee........eeeeee.hhhhh..hhhhh..............eeeeeeee...eeeeeeeee.....eee.....eeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jcm A   6 DLSNVNYAEEVIYHIVTDRFKDGDPDNNPQGQLFSNGCSDLTKYCGGDWQGIIDEIESGYLPDMGITALWISPPVENVFDLHPEGFSSYHGYWARDFKKTNPFFGDFDDFSRLIETAHAHDIKVVIDFVPNHTSPVDIEDGALYDNGTLLGHYSTDANNYFYNYGGSDFSDYENSIYRNLYDLASLNQQHSFIDKYLKESIQLWLDTGIDGIRVDAVAHMPLGWQKAFISSVYDYNPVFTFGEWFTGAQGSNHYHHFVNNSGMSALDFRYAQVAQDVLRNQKGTMHDIYDMLASTQLDYERPQDQVTFIDNHDIDRFTVEGRDTRTTDIGLAFLLTSRGVPAIYYGTENYMTGKGDPGNRKMMESFDQTTTAYQVIQKLAPLRQENKAVAYGSTKERWINDDVLIYERSFNGDYLLVAINKNVNQAYTISGLLTEMPAQVYHDVLDSLLDGQSLAVKENGTVDSFLLGPGEVSVWQHISESGSAPVIGQVGPPMGKPGDAVKISGSGFGSEPGTVYFRDTKIDVLTWDDETIVITLPETLGGKAQISVTNSDGVTSNGYDFQLLTGKQESVRFVVDNAHTNYGENVYLVGNVPELGNWNPADAIGPMFNQVVYSYPTWYYDVSVPADTALEFKFIIVDGNGNVTWESGGNHNYRVTSGSTDTVRVSFRR 674
                                    15        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       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665
   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  (0, 0)

(no "CATH Domain" information available for 4JCM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JCM)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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