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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMOPHILIC DEXTRANASE FROM THERMOANAEROBACTER PSEUDETHANOLICUS, D312G MUTANT IN COMPLEX WITH ISOMALTOHEXAOSE
 
Authors :  N. Suzuki, N. Kishine, Z. Fujimoto, M. Sakurai, M. Momma, J. A. Ko, S. H. N A. Kimura, Y. M. Kim
Date :  29 Jul 15  (Deposition) - 11 Nov 15  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycoside Hydrolase Family 66, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Suzuki, N. Kishine, Z. Fujimoto, M. Sakurai, M. Momma, J. A. Ko, S. H. Nam, A. Kimura, Y. M. Kim
Crystal Structure Of Thermophilic Dextranase From Thermoanaerobacter Pseudethanolicus
J. Biochem. V. 159 331 2016
PubMed-ID: 26494689  |  Reference-DOI: 10.1093/JB/MVV104

(-) Compounds

Molecule 1 - DEXTRANASE
    Atcc: 33223
    Chains: A, B
    EC Number: 3.2.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET23D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 3-610
    Gene: TETH39_0264
    Mutation: YES
    Organism Scientific: THERMOANAEROBACTER PSEUDETHANOLICUS ATCC 33223
    Organism Taxid: 340099
    Strain: ATCC 33223

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GLC9Ligand/IonALPHA-D-GLUCOSE
3GOL2Ligand/IonGLYCEROL
4PO44Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:422 , SER A:461 , SER A:463 , HOH A:1003 , LYS B:99binding site for residue PO4 A 705
2AC2SOFTWARETYR A:188 , LYS A:189 , LYS A:247 , ASP A:248 , HOH A:1057binding site for residue PO4 A 706
3AC3SOFTWAREASP A:172 , ASP A:444 , GLY A:446binding site for residue GOL A 707
4AC4SOFTWARELYS A:136 , ASN A:137 , LYS A:466 , ARG A:469 , ASN A:470 , ASP A:473 , ASP A:574 , HOH A:898 , HOH A:932binding site for residue GOL A 708
5AC5SOFTWARELYS B:422 , SER B:461 , SER B:463binding site for residue PO4 B 707
6AC6SOFTWARELYS B:287 , ASP B:336 , ASN B:340 , ASP B:587 , SER B:588 , HOH B:904binding site for residue PO4 B 708
7AC7SOFTWARETYR A:184 , ASP A:185 , HIS A:190 , TYR A:235 , LEU A:237 , HIS A:268 , TRP A:274 , THR A:313 , LEU A:314 , ASN A:352 , GLU A:374 , ASP A:415 , LYS A:450 , GLU A:451 , TYR A:452 , PHE A:453 , HOH A:830 , HOH A:935 , HOH A:1020 , HOH A:1053 , HOH A:1060binding site for Poly-Saccharide residues GLC A 701 through GLC A 704
8AC8SOFTWARETYR A:184 , ASP A:185 , TYR A:188 , LYS A:189 , HIS A:190 , TYR A:235 , LEU A:237 , LYS A:247 , ASP A:248 , HIS A:268 , TRP A:274 , THR A:313 , LEU A:314 , ASN A:352 , GLU A:374 , ASP A:415 , LYS A:422 , LYS A:450 , GLU A:451 , TYR A:452 , PHE A:453 , SER A:461 , SER A:463 , HOH A:830 , HOH A:935 , HOH A:1003 , HOH A:1020 , HOH A:1053 , HOH A:1057 , HOH A:1060 , LYS B:99 , TYR B:184 , ASP B:185 , HIS B:190 , TYR B:235 , LEU B:237 , HIS B:268 , LEU B:270 , TRP B:274 , THR B:313 , LEU B:314 , GLY B:315 , PRO B:316 , VAL B:354 , GLU B:374 , TRP B:376 , TYR B:408 , ASP B:415 , LYS B:450 , GLU B:451 , TYR B:452 , HOH B:839 , HOH B:952 , HOH B:966binding site for Poly-Saccharide residues GLC B 701 through BGC B 706

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AXH)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:377 -Pro A:378
2Pro B:377 -Pro B:378

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AXH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AXH)

(-) Exons   (0, 0)

(no "Exon" information available for 5AXH)

(-) 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:586
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh...eeeeee.........eeeeeeeee......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeee......eeeeeeeeeee..eeeeeeeeeeee.........eeee......hhhhhhhhhhhhhh....eeee....................eee.....eeehhhhhhhhhhhhhh..eeeeeee..ee.........hhhhh...........eee........eeee....hhhhhhhhhhhhhhhhhhh...eeeee................hhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhh.....eeee...hhhhh...ee.hhhhhhhhhhhhhhh..ee..ee..ee..........ee.hhhhhhhhhhhhhhhhhhhhhhh...ee....ee.....ee.......eeeeeeee..eeeeeeee.....................eeeeeeee........eeeee...hhhhh.ee..eeeeee..eeeeeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5axh A  26 IFSFKDDNNIVALTKGKLISDVYTDKARYYPSDKVTVKIELNNELQEDFRGTIYIFYKHLESIVGKAKIQVNIKSGQKKQLNIFWEAPKDDFKGYLVEVYAVKGNKAIDNKNTAVDVSSDWSKFPRYGYIANFPEQSKEKSALIIEDLNKYHLNGLLFYDWQYKHNKPLAGTVENPDPKWKDIANRDIYGQTVKDYIELAHSKNIMVANYNLMYGGYFDYVKDGAKPEWGLYKDPNHEEQDNHPLPHTWATDRLYLFNPANKDWQNYIFNAEKDAFRVYNFDVWHVGTLGPRGMVYDYNGNPVELSFTYADFLNNAKNALGKRIVCNTVNEYGLINVASGADVDFLYVEIWPPARAHYNFLKQTVDNGYNYSDGKKATVVAAYMNYGIADRSAEFNKHSVRLTDAAIFAAGGDHIELGDTGMLSKEYFPSANLKMSESLVKAMRNYYDFLTAYENLLRDGLKESDNKIEIPGIEISNNGSARTVWTYAKQKDGYDVIHMINLLGIEVSNWRDDLGNYSAPPIIKDFKVKYYLENDNIKNVYLASPDINDGKVMKLQFKKKEDSKGKYLEISVPELQYWDMIFIKKL 611
                                    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      


Chain B from PDB  Type:PROTEIN  Length:587
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh...eeeeee.........eeeeeeeee......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeee......eeeeeeeeeee..eeeeeeeeeeee.........eeee......hhhhhhhhhhhhhh....eeee....................eee.....eeehhhhhhhhhhhhhh..eeeeeee..ee.........hhhhh...........eee........eeee....hhhhhhhhhhhhhhhhhhh...eeeee.......ee.....eehhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhh.....eeee...hhhhh...ee.hhhhhhhhhhhhhhh.eee..ee..ee..........ee.hhhhhhhhhhhhhhhhhhhhhhh...ee....ee.....ee.......eeeeeeee..eeeeeeee.....................eeeeeeeee.....eeeeeee...hhhhh.ee..eeeeee..eeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5axh B  25 NIFSFKDDNNIVALTKGKLISDVYTDKARYYPSDKVTVKIELNNELQEDFRGTIYIFYKHLESIVGKAKIQVNIKSGQKKQLNIFWEAPKDDFKGYLVEVYAVKGNKAIDNKNTAVDVSSDWSKFPRYGYIANFPEQSKEKSALIIEDLNKYHLNGLLFYDWQYKHNKPLAGTVENPDPKWKDIANRDIYGQTVKDYIELAHSKNIMVANYNLMYGGYFDYVKDGAKPEWGLYKDPNHEEQDNHPLPHTWATDRLYLFNPANKDWQNYIFNAEKDAFRVYNFDVWHVGTLGPRGMVYDYNGNPVELSFTYADFLNNAKNALGKRIVCNTVNEYGLINVASGADVDFLYVEIWPPARAHYNFLKQTVDNGYNYSDGKKATVVAAYMNYGIADRSAEFNKHSVRLTDAAIFAAGGDHIELGDTGMLSKEYFPSANLKMSESLVKAMRNYYDFLTAYENLLRDGLKESDNKIEIPGIEISNNGSARTVWTYAKQKDGYDVIHMINLLGIEVSNWRDDLGNYSAPPIIKDFKVKYYLENDNIKNVYLASPDINDGKVMKLQFKKKEDSKGKYLEISVPELQYWDMIFIKKL 611
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604
   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  (0, 0)

(no "SCOP Domain" information available for 5AXH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AXH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AXH)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Pro A:377 - Pro A:378   [ RasMol ]  
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        B0KBZ7_THEP3 | B0KBZ7: 5axg

(-) Related Entries Specified in the PDB File

5axg WILD-TYPE ENZYME