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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMOPHILIC DEXTRANASE FROM THERMOANAEROBACTER PSEUDETHANOLICUS
 
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 :  1.85
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
    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, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1CXS1Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2EDO9Ligand/Ion1,2-ETHANEDIOL
3K1Ligand/IonPOTASSIUM ION
4PO48Ligand/IonPHOSPHATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:419 , LYS A:422 , SER A:461 , SER A:463 , HOH A:1115 , LYS B:99binding site for residue PO4 A 701
02AC2SOFTWAREARG A:416 , ARG B:75binding site for residue PO4 A 702
03AC3SOFTWARETYR A:188 , LYS A:189 , LYS A:192 , LYS A:247 , ASP A:248binding site for residue PO4 A 703
04AC4SOFTWAREASN A:267 , HIS A:268 , PRO A:269 , ARG A:317 , HOH A:981 , HOH A:1114binding site for residue PO4 A 704
05AC5SOFTWAREARG A:507 , GLU A:531 , HOH A:819 , HOH A:868 , HOH A:1013 , LYS B:554binding site for residue PO4 A 705
06AC6SOFTWAREHIS A:310 , ASP A:312 , ASN A:352 , TYR A:372 , GLU A:374 , ALA A:406 , TYR A:408binding site for residue EDO A 706
07AC7SOFTWAREGLU A:223 , HIS A:226 , ASN A:305 , HOH A:802binding site for residue EDO A 707
08AC8SOFTWAREARG A:53 , HIS A:226 , ASN A:229 , ILE A:230 , ASP A:307 , HOH A:956binding site for residue EDO A 708
09AC9SOFTWARELYS A:148 , GLY A:399 , LYS A:400 , ARG A:483 , HOH A:849 , HOH A:875binding site for residue EDO A 709
10AD1SOFTWAREPRO A:260 , ASN A:261 , ASN B:200 , PRO B:201 , HOH B:1128binding site for residue K B 701
11AD2SOFTWAREASN B:355 , TRP B:376 , PRO B:377 , PRO B:378 , ALA B:379 , TYR B:411 , GLU B:451 , HOH B:1103binding site for residue CXS B 702
12AD3SOFTWAREHIS B:268 , PRO B:269 , ARG B:317binding site for residue PO4 B 703
13AD4SOFTWARELYS A:554 , ARG B:507 , HOH B:807binding site for residue PO4 B 704
14AD5SOFTWAREPHE A:332 , ASN A:361 , HIS B:382 , SER B:505 , ALA B:506 , VAL B:532 , SER B:533 , HOH B:932 , HOH B:972binding site for residue PO4 B 705
15AD6SOFTWAREHIS B:310 , ASP B:312 , ASN B:352 , TYR B:372 , GLU B:374 , TYR B:408binding site for residue EDO B 706
16AD7SOFTWARELYS B:148 , GLY B:399 , LYS B:400 , ARG B:483 , HOH B:846 , HOH B:848 , HOH B:870binding site for residue EDO B 707
17AD8SOFTWAREILE B:493 , ASN B:502 , THR B:511binding site for residue EDO B 708
18AD9SOFTWARETYR B:188 , LYS B:189 , LYS B:192 , ASP B:248binding site for residue EDO B 709
19AE1SOFTWARELYS B:422 , SER B:461 , GLU B:462 , SER B:463binding site for residue EDO B 710

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 3)

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 5AXG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AXG)

(-) 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:583
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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.....................eeeeeeee......eeeeeee...hhhhh.ee..eeeeee..eeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5axg A  29 FKDDNNIVALTKGKLISDVYTDKARYYPSDKVTVKIELNNELQEDFRGTIYIFYKHLESIVGKAKIQVNIKSGQKKQLNIFWEAPKDDFKGYLVEVYAVKGNKAIDNKNTAVDVSSDWSKFPRYGYIANFPEQSKEKSALIIEDLNKYHLNGLLFYDWQYKHNKPLAGTVENPDPKWKDIANRDIYGQTVKDYIELAHSKNIMVANYNLMYGGYFDYVKDGAKPEWGLYKDPNHEEQDNHPLPHTWATDRLYLFNPANKDWQNYIFNAEKDAFRVYNFDVWHVDTLGPRGMVYDYNGNPVELSFTYADFLNNAKNALGKRIVCNTVNEYGLINVASGADVDFLYVEIWPPARAHYNFLKQTVDNGYNYSDGKKATVVAAYMNYGIADRSAEFNKHSVRLTDAAIFAAGGDHIELGDTGMLSKEYFPSANLKMSESLVKAMRNYYDFLTAYENLLRDGLKESDNKIEIPGIEISNNGSARTVWTYAKQKDGYDVIHMINLLGIEVSNWRDDLGNYSAPPIIKDFKVKYYLENDNIKNVYLASPDINDGKVMKLQFKKKEDSKGKYLEISVPELQYWDMIFIKKL 611
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608   


Chain B from PDB  Type:PROTEIN  Length:584
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh....eeeeee.........eeeeeeeee......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeee......eeeeeeeeeee..eeeeeeeeeeee.........eeee......hhhhhhhhhhhhhh....eeee....................eee.....eeehhhhhhhhhhhhhh..eeeeeee..ee..hhhhhh.hhhhh...........eee........eeee....hhhhhhhhhhhhhhhhhhh...eeeee.......ee.....eehhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhh.....eeee...hhhhh...ee.hhhhhhhhhhhhhhh..ee..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
                 5axg B  28 SFKDDNNIVALTKGKLISDVYTDKARYYPSDKVTVKIELNNELQEDFRGTIYIFYKHLESIVGKAKIQVNIKSGQKKQLNIFWEAPKDDFKGYLVEVYAVKGNKAIDNKNTAVDVSSDWSKFPRYGYIANFPEQSKEKSALIIEDLNKYHLNGLLFYDWQYKHNKPLAGTVENPDPKWKDIANRDIYGQTVKDYIELAHSKNIMVANYNLMYGGYFDYVKDGAKPEWGLYKDPNHEEQDNHPLPHTWATDRLYLFNPANKDWQNYIFNAEKDAFRVYNFDVWHVDTLGPRGMVYDYNGNPVELSFTYADFLNNAKNALGKRIVCNTVNEYGLINVASGADVDFLYVEIWPPARAHYNFLKQTVDNGYNYSDGKKATVVAAYMNYGIADRSAEFNKHSVRLTDAAIFAAGGDHIELGDTGMLSKEYFPSANLKMSESLVKAMRNYYDFLTAYENLLRDGLKESDNKIEIPGIEISNNGSARTVWTYAKQKDGYDVIHMINLLGIEVSNWRDDLGNYSAPPIIKDFKVKYYLENDNIKNVYLASPDINDGKVMKLQFKKKEDSKGKYLEISVPELQYWDMIFIKKL 611
                                    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
   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 5AXG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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: 5axh

(-) Related Entries Specified in the PDB File

5axh D312G MUTANT COMPLEXED WITH ISOMALTOHEXAOSE