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(-) Description

Title :  STRUCTURAL INSIGHTS INTO A FAMILY 39 GLYCOSIDE HYDROLASE FROM THE GUT SYMBIONT BACTEROIDES CELLULOSILYTICUS WH2.
 
Authors :  A. Ali-Ahmad, M. L. Garron, V. Zamboni, N. Lenfant, Y. Bourne, F. Vincen
Date :  11 May 16  (Deposition) - 07 Dec 16  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Bacteroides, Gh39, Phylogeny, Endo-Glycoside Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ali-Ahmad, M. L. Garron, V. Zamboni, N. Lenfant, D. Nurizzo, B. Henrissat, J. G. Berrin, Y. Bourne, F. Vincent
Structural Insights Into A Family 39 Glycoside Hydrolase From The Gut Symbiont Bacteroides Cellulosilyticus Wh2.
J. Struct. Biol. V. 197 227 2017
PubMed-ID: 27890857  |  Reference-DOI: 10.1016/J.JSB.2016.11.004

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDEST17
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Gene: BCELLWH2_03314
    Organism Scientific: BACTEROIDES CELLULOSILYTICUS
    Organism Taxid: 246787

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1CXS2Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2GOL8Ligand/IonGLYCEROL
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CXS-1Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2GOL2Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1CXS1Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2GOL1Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
Biological Unit 3 (3, 7)
No.NameCountTypeFull Name
1CXS1Ligand/Ion3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2GOL5Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:287 , PRO A:291 , GLY A:328 , THR A:329 , GLY A:330 , HOH A:782binding site for residue SO4 A 651
02AC2SOFTWARETHR A:219 , GLU A:220binding site for residue SO4 A 652
03AC3SOFTWARESER A:371 , ASP A:376 , HOH A:708 , HOH A:738 , LYS C:172binding site for residue GOL A 653
04AC4SOFTWAREHIS A:137 , ARG A:160 , ASP A:162 , TYR A:201 , ASN A:248 , GLU A:366 , TYR A:402 , HOH A:737 , HOH A:808binding site for residue GOL A 654
05AC5SOFTWAREPHE B:446 , GLU B:448 , THR B:449 , HOH B:774binding site for residue SO4 B 651
06AC6SOFTWAREHIS B:137 , ASP B:162 , TYR B:201 , ASN B:248 , GLU B:366 , TYR B:402 , HOH B:751binding site for residue SO4 B 652
07AC7SOFTWARELEU B:375 , ASP B:376binding site for residue SO4 B 653
08AC8SOFTWARETYR A:394 , ASN A:443 , TYR B:182 , ARG B:240 , HOH B:750binding site for residue CXS B 654
09AC9SOFTWAREMET B:237 , ASN B:239 , ARG B:240binding site for residue GOL B 655
10AD1SOFTWAREGLU C:448 , THR C:449 , HOH C:732binding site for residue SO4 C 651
11AD2SOFTWAREGLU A:448 , THR A:449 , LEU A:450 , ASP A:452 , GLY C:288 , ALA C:318 , ASN C:320 , TYR C:326 , HOH C:714 , HOH C:779binding site for residue CXS C 652
12AD3SOFTWAREALA C:287 , GLY C:288 , GLY C:292 , THR C:329 , ILE C:333 , HOH C:721 , HOH C:807binding site for residue GOL C 653
13AD4SOFTWARETYR C:316 , GLU C:366 , TYR C:402 , GLU C:415 , GOL C:655 , GOL C:657 , HOH C:717binding site for residue GOL C 654
14AD5SOFTWAREHIS C:137 , ARG C:160 , ASP C:162 , TYR C:201 , GLU C:366 , TYR C:402 , GOL C:654 , HOH C:719binding site for residue GOL C 655
15AD6SOFTWAREPHE A:324 , GLY A:453 , GLU C:249 , ASN C:251 , HOH C:701 , HOH C:756binding site for residue GOL C 656
16AD7SOFTWAREGOL C:654 , HOH C:795 , HOH C:800binding site for residue GOL C 657

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ala A:318 -Pro A:319
2Tyr A:402 -Asp A:403
3Ala B:318 -Pro B:319
4Tyr B:402 -Asp B:403
5Ala C:318 -Pro C:319
6Tyr C:402 -Asp C:403

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JVK)

(-) Sequences/Alignments

Asymmetric 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:490
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eee..eeeeeeee......eeeeeeee.....eeeeee....eeeeee...eeeeeeeeee....eeeeeeeeeeee...hhhhh...eeee.......hhhhhhhhhhhh...eeeeeeehhhhh........hhhhhhhhhhhhhh..eeeeeee..................hhhhhhhhhhhhhhhhhhhhhhh.eeee...........hhhhhhhhhhhhhhhhh...eeee....hhhhh....hhhhhhhh.hhhhh.eeee.......................hhhhhhhhhhhhhhhh........eeeeeee.......hhhhhhhhhhhhhhhhhhh.....eee...........hhhhh..........hhhhhhhhhhhhhhh..eeeeeee...eeeeeeee..eeeeeeeee.....eeeeee...hhh.eeee.....ee.......eeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jvk A  36 KIQLNPVLVSTDIGKKNVAKNLGEGNMRLTGKLVRYGDNLTFSGVANAGKELVIDVTELGYYTLELTLADNENIIQTAVVNYAVVPEIIDEERPLDMGVCVHPPKDNDYSKTFRLIRMAGFTRIRTDLAWEHVEPAKGKYVMPEHMYQFVSASEKEGIKPLIVFGYANAIAYPNGFPTIPFPTTEESRLGCANALAYAVKEMGNRVTEWELWNEPNYADPVKDYLPLLKVVYPTVKKVNPDITLISGGGSGAGGGPGGAFIIPVLDAGGVDFQDGYSIHPYMAPNTPDFGYAGTGGPIPAVNIPTVWPYLKKISEENLRSDKKELSVWVTEIGWNSTTNLDIEQAAYLARTYLLSRRHYMSPGVFWYDFQNDGDTPDNIEHNFGLLRSDFSPKPSYQAAAVVASLLKNYTFQETLLDGVNKVLAFGQDGETTFYTAWTTKAEGTTIRVKAPTDVDKLRLIDWQGCEMPLTVDNGYLVLNLSILPQYLVVK 525
                                    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


Chain B from PDB  Type:PROTEIN  Length:490
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eee..eeeeeeee.....eeeeeeeee.....eeeeee....eeeeee...eeeeeeeeeee..eeeeeeeeeeeee...hhhhh...eeee.......hhhhhhhhhhhh...eeeeeeehhhhh........hhhhhhhhhhhhhh..eeeeeee..................hhhhhhhhhhhhhhhhhhhhhhh.eeee...........hhhhhhhhhhhhhhhhh...eeee....hhhhh....hhhhhhhh.hhhhh.eeee............ee.......eehhhhhhhhhhhhhhhh........eeeeeee.......hhhhhhhhhhhhhhhhhhh.....eee...........hhhhh..........hhhhhhhhhhhhhhh..eeeeeee...eeeeeeee..eeeeeeeee.....eeeeee.......eeee.....ee.......eeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jvk B  36 KIQLNPVLVSTDIGKKNVAKNLGEGNMRLTGKLVRYGDNLTFSGVANAGKELVIDVTELGYYTLELTLADNENIIQTAVVNYAVVPEIIDEERPLDMGVCVHPPKDNDYSKTFRLIRMAGFTRIRTDLAWEHVEPAKGKYVMPEHMYQFVSASEKEGIKPLIVFGYANAIAYPNGFPTIPFPTTEESRLGCANALAYAVKEMGNRVTEWELWNEPNYADPVKDYLPLLKVVYPTVKKVNPDITLISGGGSGAGGGPGGAFIIPVLDAGGVDFQDGYSIHPYMAPNTPDFGYAGTGGPIPAVNIPTVWPYLKKISEENLRSDKKELSVWVTEIGWNSTTNLDIEQAAYLARTYLLSRRHYMSPGVFWYDFQNDGDTPDNIEHNFGLLRSDFSPKPSYQAAAVVASLLKNYTFQETLLDGVNKVLAFGQDGETTFYTAWTTKAEGTTIRVKAPTDVDKLRLIDWQGCEMPLTVDNGYLVLNLSILPQYLVVK 525
                                    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


Chain C from PDB  Type:PROTEIN  Length:490
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eee..eeeeeeee......eeeeeeee.....eeeeee....eeeeee...eeeeeeeeeee..eeeeeeeeeeeee...hhhhh...eeee.......hhhhhhhhhhhh...eeeeeeehhhhh........hhhhhhhhhhhhhh..eeeeeee..................hhhhhhhhhhhhhhhhhhhhhhh.eeee...........hhhhhhhhhhhhhhhhh...eeee....hhhhh....hhhhhhhh.hhhhh.eeee.......................hhhhhhhhhhhhhhhh........eeeeeee.......hhhhhhhhhhhhhhhhhhh.....eee...........hhhhh..........hhhhhhhhhhhhhhh..eeeeeee...eeeeeeee..eeeeeeeee.....eeeeee...hhh.eeee.....ee...ee..eeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jvk C  36 KIQLNPVLVSTDIGKKNVAKNLGEGNMRLTGKLVRYGDNLTFSGVANAGKELVIDVTELGYYTLELTLADNENIIQTAVVNYAVVPEIIDEERPLDMGVCVHPPKDNDYSKTFRLIRMAGFTRIRTDLAWEHVEPAKGKYVMPEHMYQFVSASEKEGIKPLIVFGYANAIAYPNGFPTIPFPTTEESRLGCANALAYAVKEMGNRVTEWELWNEPNYADPVKDYLPLLKVVYPTVKKVNPDITLISGGGSGAGGGPGGAFIIPVLDAGGVDFQDGYSIHPYMAPNTPDFGYAGTGGPIPAVNIPTVWPYLKKISEENLRSDKKELSVWVTEIGWNSTTNLDIEQAAYLARTYLLSRRHYMSPGVFWYDFQNDGDTPDNIEHNFGLLRSDFSPKPSYQAAAVVASLLKNYTFQETLLDGVNKVLAFGQDGETTFYTAWTTKAEGTTIRVKAPTDVDKLRLIDWQGCEMPLTVDNGYLVLNLSILPQYLVVK 525
                                    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
   Legend:   → Mismatch (orange background)
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5JVK)

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  Cis Peptide Bonds
    Ala A:318 - Pro A:319   [ RasMol ]  
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    Tyr A:402 - Asp A:403   [ RasMol ]  
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