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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH A NOVEL IMINOSUGAR FUCOSIDASE INHIBITOR
 
Authors :  A. Lammerts Van Bueren, A. Ardevol, J. Fayers-Kerr, B. Luo, Y. Zhang, M. Sollogoub, Y. Bleriot, C. Rovira, G. J. Davies
Date :  20 Oct 09  (Deposition) - 02 Feb 10  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Alpha-L-Fucose, Glycoside Hydrolase Family 29 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Lammerts Van Bueren, A. Ardevol, J. Fayers-Kerr, B. Luo, Y. Zhang, M. Sollogoub, Y. Bleriot, C. Rovira, G. J. Davies
Analysis Of The Reaction Coordinate Of Alpha-L- Fucosidases: A Combined Structural And Quantum Mechanical Approach.
J. Am. Chem. Soc. V. 132 1804 2010
PubMed-ID: 20092273  |  Reference-DOI: 10.1021/JA908908Q

(-) Compounds

Molecule 1 - ALPHA-L-FUCOSIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 31-473
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Strain: VPI-5482

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1FHN2Ligand/Ion(2S,3R,5R,6S)-3,4,5-TRIHYDROXY-2,6-BIS(HYDROXYMETHYL)PIPERIDINIUM
2GOL5Ligand/IonGLYCEROL
3IMD4Ligand/IonIMIDAZOLE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:66 , GLU A:87 , TRP A:88 , HIS A:135 , HIS A:136 , TYR A:178 , TRP A:227 , ASP A:229 , ARG A:262 , GLU A:288 , CYS A:308 , TRP A:316BINDING SITE FOR RESIDUE FHN A1473
2AC2SOFTWAREHIS B:66 , GLU B:87 , TRP B:88 , HIS B:135 , HIS B:136 , TYR B:178 , TRP B:227 , ASP B:229 , ARG B:262 , GLU B:288 , CYS B:308 , TRP B:316BINDING SITE FOR RESIDUE FHN B1474
3AC3SOFTWARETRP A:232 , ARG A:262 , ARG A:271 , HIS A:272 , GLY A:286 , HOH A:2214BINDING SITE FOR RESIDUE GOL A1474
4AC4SOFTWAREGLU A:284 , GLY A:286 , TYR A:287BINDING SITE FOR RESIDUE GOL A1475
5AC5SOFTWAREALA B:85 , GLU B:87 , TRP B:88 , ASN B:314 , TRP B:316 , HOH B:2131BINDING SITE FOR RESIDUE GOL B1475
6AC6SOFTWAREASP A:393 , VAL B:295 , LYS B:391 , GLN B:392 , ASP B:393 , HOH B:2241BINDING SITE FOR RESIDUE GOL B1476
7AC7SOFTWAREASP A:393 , ASP B:335 , LYS B:391 , GLY B:395 , TYR B:396 , ASN B:411 , HOH B:2211BINDING SITE FOR RESIDUE GOL B1477
8AC8SOFTWARELYS A:456 , LYS A:457 , ASN A:458 , HOH A:2208BINDING SITE FOR RESIDUE IMD A1477
9AC9SOFTWARELYS B:90 , SER B:91 , TYR B:191BINDING SITE FOR RESIDUE IMD B1479

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WVT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WVT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WVT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WVT)

(-) Exons   (0, 0)

(no "Exon" information available for 2WVT)

(-) 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:438
 aligned with Q8A3I4_BACTN | Q8A3I4 from UniProtKB/TrEMBL  Length:484

    Alignment length:438
                                    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        
         Q8A3I4_BACTN    35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAA 472
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhhhhhhhhhheeeee..hhhhh...ee..ee...hhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhh..eeeeeee................hhhh....hhhhhhhhhhhhh..eeeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhh...ee.hhhh................................hhhhhhh.eeeee...........hhhhh...hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhhhh.............eeeee.....eeeee.eee...eeeee.....eeeeeee........eeeee..eeeee.........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wvt A  35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAA 472
                                    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        


Chain B from PDB  Type:PROTEIN  Length:439
 aligned with Q8A3I4_BACTN | Q8A3I4 from UniProtKB/TrEMBL  Length:484

    Alignment length:439
                                    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         
         Q8A3I4_BACTN    35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAAK 473
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Alpha_L_fucos-2wvtB01 B:35-383                                                                                                                                                                                                                                                                                                                               ------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) Alpha_L_fucos-2wvtB02 B:35-383                                                                                                                                                                                                                                                                                                                               ------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ...............hhhhhhhhhhheeeee..hhhhh...ee..ee...hhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhh..eeeee..................hhhh....hhhhhhhhhhhhh..eeeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhhhhh...ee.hhhh................................hhhhhhh.eeeee...........hhhhh...hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhhhh.............eeeee.....eeeee.eee...eeeee....eeeeeeee........eeeee..eeeee.........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvt B  35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAAK 473
                                    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
   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 2WVT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WVT)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8A3I4_BACTN | Q8A3I4)
molecular function
    GO:0004560    alpha-L-fucosidase activity    Catalysis of the reaction: an alpha-L-fucoside + H2O = an alcohol + L-fucose.
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.
    GO:0006004    fucose metabolic process    The chemical reactions and pathways involving fucose, or 6-deoxygalactose, which has two enantiomers, D-fucose and L-fucose.

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  2wvt
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 Related Entries

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

UniProtKB/TrEMBL
        Q8A3I4_BACTN | Q8A3I4: 2wvs 2wvu 2wvv 2xib 2xii 4j27 4j28 4jfs 4jft 4jfu 4jfv 4jfw 4jl1 4jl2 4pcs 4pct 4pee 4wsj 4wsk 5hdr 5i5r

(-) Related Entries Specified in the PDB File

2wvs CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 TRAPPED COVALENT INTERMEDIATE FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH 2 -FLUORO-FUCOSYL FLUORIDE USING AN E288Q MUTANT
2wvu CRYSTAL STRUCTURE OF A MICHAELIS COMPLEX OF ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON WITH THE SYNTHETIC SUBSTRATE 4-NITROPHENYL-ALPHA-L-FUCOSE
2wvv CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON