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(-) Description

Title :  THERMOTOGA MARITIMA ALPHA-L-FUCOSYNTHASE, TMD224G, IN COMPLEX WITH ALPHA-L-FUC-(1-2)-BETA-L-FUC-N3
 
Authors :  G. Sulzenbacher, A. Lipski, B. Cobucci-Ponzano, F. Conte, E. Bedini, M. M. Corsaro, M. Parrilli, F. Dal Piaz, L. Lepore, M. Rossi, M. Moracci
Date :  08 Sep 09  (Deposition) - 19 Jan 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Hydrolase, Glycoside Hydrolase, Carbohydrate Synthesis, Thermophilic Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Cobucci-Ponzano, F. Conte, E. Bedini, M. M. Corsaro, M. Parrilli, G. Sulzenbacher, A. Lipski, F. Dal Piaz, L. Lepore, M. Rossi, M. Moracci
Beta-Glycosyl Azides As Substrates For Alpha- Glycosynthases: Preparation Of Novel Efficient Alpha-L-Fucosynthases
Chem. Biol. V. 16 1097 2009
PubMed-ID: 19875083  |  Reference-DOI: 10.1016/J.CHEMBIOL.2009.09.013

(-) Compounds

Molecule 1 - ALPHA-L-FUCOSIDASE, PUTATIVE
    Chains: A, B
    EC Number: 3.2.1.51
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PDEST17
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8
    Synonym: ALPHA-L-FUCOSYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2FUY2Ligand/IonBETA-L-FUCOSYL-AZIDE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1FUC3Ligand/IonALPHA-L-FUCOSE
2FUY3Ligand/IonBETA-L-FUCOSYL-AZIDE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1FUC3Ligand/IonALPHA-L-FUCOSE
2FUY3Ligand/IonBETA-L-FUCOSYL-AZIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:34 , GLU A:66 , TRP A:67 , HIS A:128 , HIS A:129 , ARG A:254 , PHE A:290 , FUY A:1448BINDING SITE FOR RESIDUE FUC A1447
2AC2SOFTWAREHIS B:34 , GLU B:66 , TRP B:67 , HIS B:128 , HIS B:129 , ARG B:254 , FUY B:1448BINDING SITE FOR RESIDUE FUC B1447
3AC3SOFTWARETYR A:64 , TRP A:67 , ARG A:254 , GLU A:266 , FUC A:1447BINDING SITE FOR RESIDUE FUY A1448
4AC4SOFTWARETRP B:58 , TYR B:64 , TRP B:67 , ARG B:254 , GLU B:266 , FUC B:1447BINDING SITE FOR RESIDUE FUY B1448

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:364 -A:365
2A:380 -B:380
3B:364 -B:365

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WSP)

(-) 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:435
 aligned with Q9WYE2_THEMA | Q9WYE2 from UniProtKB/TrEMBL  Length:449

    Alignment length:443
                                    14        24        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   
         Q9WYE2_THEMA     5 KPRYKPDWESLREHTVPKWFDKAKFGIFIHWGIYSVPGWATPTGELGKVPMDAWFFQNPYAEWYENSLRIKESPTWEYHVKTYGENFEYEKFADLFTAEKWDPQEWADLFKKAGAKYVIPTTKHHDGFCLWGTKYTDFNSVKRGPKRDLVGDLAKAVREAGLRFGVYYSGGLDWRFTTEPIRYPEDLSYIRPNTYEYADYAYKQVMELVDLYLPDVLWNDMGWPEKGKEDLKYLFAYYYNKHPEGSVNDRWGVPHWDFKTAEYHVNYPGDLPGYKWEFTRGIGLSFGYNRNEGPEHMLSVEQLVYTLVDVVSKGGNLLLNVGPKGDGTIPDLQKERLLGLGEWLRKYGDAIYGTSVWERCCAKTEDGTEIRFTRKCNRIFVIFLGIPTGEKIVIEDLNLSAGTVRHFLTGERLSFKNVGKNLEITVPKKLLETDSITLVLEAV 447
               SCOP domains d2wspa1 A:5-356 automated matches                                                                                                                                                                                                                                                                                                                               d2wspa2 A:357-447 automated matches                                                         SCOP domains
               CATH domains 2wspA01 A:5-356 Glycosidases                                                                                                                                                                                                                                                                                                                                    2wspA02 A:357-447 Golgi alpha-mannosidase II                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh....hhhhhhhheeeee..hhhhh...........-...........hhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....hhhhhhhhhhhh...eeeeeee........................hhhhhhhhhhhhh..ee.eee..............hhhhhhh....hhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...ee...........eee..-------.....eeeeee...........hhhhh.hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhhhhh........eeee....eeeeeee..eeeeee.......eeeee.........ee........eeee..eeeee.hhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsp A   5 KPRYKPDWESLREHTVPKWFDKAKFGIFIHWGIYSVPGWATPTGELG-VPMDAWFFQNPYAEWYENSLRIKESPTWEYHVKTYGENFEYEKFADLFTAEKWDPQEWADLFKKAGAKYVIPTTKHHDGFCLWGTKYTDFNSVKRGPKRDLVGDLAKAVREAGLRFGVYYSGGLDWRFTTEPIRYPEDLSYIRPNTYEYADYAYKQVMELVDLYLPDVLWNGMGWPEKGKEDLKYLFAYYYNKHPEGSVNDRWGVPHWDFKTAEY-------LPGYKWEFTRGIGLSFGYNRNEGPEHMLSVEQLVYTLVDVVSKGGNLLLNVGPKGDGTIPDLQKERLLGLGEWLRKYGDAIYGTSVWERCCAKTEDGTEIRFTRKCNRIFVIFLGIPTGEKIVIEDLNLSAGTVRHFLTGERLSFKNVGKNLEITVPKKLLETDSITLVLEAV 447
                                    14        24        34        44      | 54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264  |      -|      284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444   
                                                                         51 |                                                                                                                                                                                                                   267     275                                                                                                                                                                            
                                                                           53                                                                                                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:434
 aligned with Q9WYE2_THEMA | Q9WYE2 from UniProtKB/TrEMBL  Length:449

    Alignment length:443
                                    14        24        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   
         Q9WYE2_THEMA     5 KPRYKPDWESLREHTVPKWFDKAKFGIFIHWGIYSVPGWATPTGELGKVPMDAWFFQNPYAEWYENSLRIKESPTWEYHVKTYGENFEYEKFADLFTAEKWDPQEWADLFKKAGAKYVIPTTKHHDGFCLWGTKYTDFNSVKRGPKRDLVGDLAKAVREAGLRFGVYYSGGLDWRFTTEPIRYPEDLSYIRPNTYEYADYAYKQVMELVDLYLPDVLWNDMGWPEKGKEDLKYLFAYYYNKHPEGSVNDRWGVPHWDFKTAEYHVNYPGDLPGYKWEFTRGIGLSFGYNRNEGPEHMLSVEQLVYTLVDVVSKGGNLLLNVGPKGDGTIPDLQKERLLGLGEWLRKYGDAIYGTSVWERCCAKTEDGTEIRFTRKCNRIFVIFLGIPTGEKIVIEDLNLSAGTVRHFLTGERLSFKNVGKNLEITVPKKLLETDSITLVLEAV 447
               SCOP domains d2wspb1 B:5-356 automated matches                                                                                                                                                                                                                                                                                                                               d2wspb2 B:357-447 automated matches                                                         SCOP domains
               CATH domains 2wspB01 B:5-356 Glycosidases                                                                                                                                                                                                                                                                                                                                    2wspB02 B:357-447 Golgi alpha-mannosidase II                                                CATH domains
           Pfam domains (1) Alpha_L_fucos-2wspB01 B:5-357                                                                                                                                                                                                                                                                                                                                    ------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) Alpha_L_fucos-2wspB02 B:5-357                                                                                                                                                                                                                                                                                                                                    ------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ......hhhhhh....hhhhhhhheeeee..hhhhh..........--.hhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhhhhhh..eeeeeee........................hhhhhhhhhhhhh..ee.eee..............hhhhhhh....hhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...ee...........eee..-------.....eeeeee...........hhhhh.hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhhhh.........eee.....eeeeeee..eeeeee.......eeee.........eee.......eeeee..eeeee.hhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsp B   5 KPRYKPDWESLREHTVPKWFDKAKFGIFIHWGIYSVPGWATPTGEL--VPMDAWFFQNPYAEWYENSLRIKESPTWEYHVKTYGENFEYEKFADLFTAEKWDPQEWADLFKKAGAKYVIPTTKHHDGFCLWGTKYTDFNSVKRGPKRDLVGDLAKAVREAGLRFGVYYSGGLDWRFTTEPIRYPEDLSYIRPNTYEYADYAYKQVMELVDLYLPDVLWNGMGWPEKGKEDLKYLFAYYYNKHPEGSVNDRWGVPHWDFKTAEY-------LPGYKWEFTRGIGLSFGYNRNEGPEHMLSVEQLVYTLVDVVSKGGNLLLNVGPKGDGTIPDLQKERLLGLGEWLRKYGDAIYGTSVWERCCAKTEDGTEIRFTRKCNRIFVIFLGIPTGEKIVIEDLNLSAGTVRHFLTGERLSFKNVGKNLEITVPKKLLETDSITLVLEAV 447
                                    14        24        34        44     |  54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264  |      -|      284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444   
                                                                        50 53                                                                                                                                                                                                                   267     275
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9WYE2_THEMA | Q9WYE2)
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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  2wsp
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  Q9WYE2_THEMA | Q9WYE2
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 Related Entries

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

UniProtKB/TrEMBL
        Q9WYE2_THEMA | Q9WYE2: 1hl8 1hl9 1odu 2zwy 2zwz 2zx5 2zx6 2zx7 2zx8 2zx9 2zxa 2zxb 2zxd

(-) Related Entries Specified in the PDB File

1hl8 CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA -FUCOSIDASE
1hl9 CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA -FUCOSIDASE IN COMPLEX WITH A MECHANISM BASED INHIBITOR
1odu CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA ALPHA -FUCOSIDASE IN COMPLEX WITH FUCOSE