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(-) Description

Title :  SUCROSE PHOSPHORYLASE FROM BIFIDOBACTERIUM ADOLESCENTIS REACTED WITH SUCROSE
 
Authors :  L. K. Skov, O. Mirza, M. Gajhede, J. S. Katsrup
Date :  17 Mar 06  (Deposition) - 26 Sep 06  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Alpha-Barrels, Dimer, Glycoside Hydrolase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Mirza, L. K. Skov, D. Sprogoe, L. A. M. Van Den Broek, A. G. J. Voragen, J. S. Katsrup, M. Gajhede
Structural Rearrangements Of Sucrose Phosphorylase From Bifidobacterium Adolescentis During Sucrose Conversion
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUCROSE PHOSPHORYLASE
    Chains: A, B
    EC Number: 2.4.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBLUESCRIPT
    Expression System Strain: XL-1 BLUE MRF
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BIFIDOBACTERIUM ADOLESCENTIS
    Organism Taxid: 1680

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:50 , PHE A:53 , HIS A:88 , ARG A:190 , ASP A:192 , GLU A:232 , HIS A:289 , ASP A:290 , ARG A:399 , HOH A:971BINDING SITE FOR RESIDUE BGC A 700
2AC2SOFTWAREASP B:50 , PHE B:53 , HIS B:88 , ARG B:135 , PHE B:156 , ARG B:190 , ASP B:192 , GLU B:232 , HIS B:289 , ASP B:290 , ARG B:399 , HOH B:835 , HOH B:908 , HOH B:1515BINDING SITE FOR RESIDUE BGC B 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:44 -Pro A:45
2Thr B:44 -Pro B:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GDV)

(-) 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:504
 aligned with Q84HQ2_BIFAD | Q84HQ2 from UniProtKB/TrEMBL  Length:504

    Alignment length:504
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500    
         Q84HQ2_BIFAD     1 MKNKVQLITYADRLGDGTIKSMTDILRTRFDGVYDGVHILPFFTPFDGADAGFDPIDHTKVDERLGSWDDVAELSKTHNIMVDAIVNHMSWESKQFQDVLAKGEESEYYPMFLTMSSVFPNGATEEDLAGIYRPRPGLPFTHYKFAGKTRLVWVSFTPQQVDIDTDSDKGWEYLMSIFDQMAASHVSYIRLDAVGYGAKEAGTSCFMTPKTFKLISRLREEGVKRGLEILIEVHSYYKKQVEIASKVDRVYDFALPPLLLHALSTGHVEPVAHWTDIRPNNAVTVLDTHDGIGVIDIGSDQLDRSLKGLVPDEDVDNLVNTIHANTHGESQAATGAAASNLDLYQVNSTYYSALGCNDQHYIAARAVQFFLPGVPQVYYVGALAGKNDMELLRKTNNGRDINRHYYSTAEIDENLKRPVVKALNALAKFRNELDAFDGTFSYTTDDDTSISFTWRGETSQATLTFEPKRGLGVDNTTPVAMLEWEDSAGDHRSDDLIANPPVVA 504
               SCOP domains d2gdva2 A:1-434 Sucrose phosphorylase                                                                                                                                                                                                                                                                                                                                                                                                             d2gdva1 A:435-504 Sucrose phosphorylase                                SCOP domains
               CATH domains 2gdvA01 A:1-85,A:167-432 Glycosidases                                                2gdvA02 A:86-166 Oligo-1,6-glucosidase; Domain 2                                 2gdvA01 A:1-85,A:167-432 Glycosidases                                                                                                                                                                                                                                     ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee........hhhhhhhhhhhhh.....eeee...ee............eeeee.....hhhhhhhhh...eeeeeee..eee..hhhhhhhhhhhhhh.hhhhh.hhhhhh....hhhhhhh.........eeeeee..eeeeee......eee....hhhhhhhhhhhhhhhhhh...eeeeehhhhh..........hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh.eeee.hhhhhhhhhhhhh.hhhhhhhhhhh...eee..........................hhhhhhhhhhhhhhhh.hhhhhhhhhhh..........hhhhhh..hhhhhhhhhhhhhhh..eeeeehhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhheeeeeee...eeeeeee....eeeeee.hhhhh........eeeeeee..eeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gdv A   1 MKNKVQLITYADRLGDGTIKSMTDILRTRFDGVYDGVHILPFFTPFDGADAGFDPIDHTKVDERLGSWDDVAELSKTHNIMVDAIVNHMSWESKQFQDVLAKGEESEYYPMFLTMSSVFPNGATEEDLAGIYRPRPGLPFTHYKFAGKTRLVWVSFTPQQVDIDTDSDKGWEYLMSIFDQMAASHVSYIRLDAVGYGAKEAGTSCFMTPKTFKLISRLREEGVKRGLEILIEVHSYYKKQVEIASKVDRVYDFALPPLLLHALSTGHVEPVAHWTDIRPNNAVTVLDTHDGIGVIDIGSDQLDRSLKGLVPDEDVDNLVNTIHANTHGESQAATGAAASNLDLYQVNSTYYSALGCNDQHYIAARAVQFFLPGVPQVYYVGALAGKNDMELLRKTNNGRDINRHYYSTAEIDENLKRPVVKALNALAKFRNELDAFDGTFSYTTDDDTSISFTWRGETSQATLTFEPKRGLGVDNTTPVAMLEWEDSAGDHRSDDLIANPPVVA 504
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500    


Chain B from PDB  Type:PROTEIN  Length:504
 aligned with Q84HQ2_BIFAD | Q84HQ2 from UniProtKB/TrEMBL  Length:504

    Alignment length:504
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500    
         Q84HQ2_BIFAD     1 MKNKVQLITYADRLGDGTIKSMTDILRTRFDGVYDGVHILPFFTPFDGADAGFDPIDHTKVDERLGSWDDVAELSKTHNIMVDAIVNHMSWESKQFQDVLAKGEESEYYPMFLTMSSVFPNGATEEDLAGIYRPRPGLPFTHYKFAGKTRLVWVSFTPQQVDIDTDSDKGWEYLMSIFDQMAASHVSYIRLDAVGYGAKEAGTSCFMTPKTFKLISRLREEGVKRGLEILIEVHSYYKKQVEIASKVDRVYDFALPPLLLHALSTGHVEPVAHWTDIRPNNAVTVLDTHDGIGVIDIGSDQLDRSLKGLVPDEDVDNLVNTIHANTHGESQAATGAAASNLDLYQVNSTYYSALGCNDQHYIAARAVQFFLPGVPQVYYVGALAGKNDMELLRKTNNGRDINRHYYSTAEIDENLKRPVVKALNALAKFRNELDAFDGTFSYTTDDDTSISFTWRGETSQATLTFEPKRGLGVDNTTPVAMLEWEDSAGDHRSDDLIANPPVVA 504
               SCOP domains d2gdvb2 B:1-434 Sucrose phosphorylase                                                                                                                                                                                                                                                                                                                                                                                                             d2gdvb1 B:435-504 Sucrose phosphorylase                                SCOP domains
               CATH domains 2gdvB01 B:1-85,B:167-432 Glycosidases                                                2gdvB02 B:86-166 Oligo-1,6-glucosidase; Domain 2                                 2gdvB01 B:1-85,B:167-432 Glycosidases                                                                                                                                                                                                                                     ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee........hhhhhhhhhhhhh.....eeee...ee............eeeee.....hhhhhhhhh...eeeeeee..eee..hhhhhhhhhhhhhh.hhhhh.hhhhhh....hhhhhhh.........eeeeee..eeeeee......eee....hhhhhhhhhhhhhhhhhh...eeeeehhhhh..........hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhh...eeee.hhhhhhhhhhhhh.hhhhhhhhhhh...eee.......ee.................hhhhhhhhhhhhhhhh.hhhhhhh..........ee..hhhhhh..hhhhhhhhhhhhhhh..eeeeehhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhheeeeee.....eeeeee....eeeeee.hhhh.........eeeeeee..eeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gdv B   1 MKNKVQLITYADRLGDGTIKSMTDILRTRFDGVYDGVHILPFFTPFDGADAGFDPIDHTKVDERLGSWDDVAELSKTHNIMVDAIVNHMSWESKQFQDVLAKGEESEYYPMFLTMSSVFPNGATEEDLAGIYRPRPGLPFTHYKFAGKTRLVWVSFTPQQVDIDTDSDKGWEYLMSIFDQMAASHVSYIRLDAVGYGAKEAGTSCFMTPKTFKLISRLREEGVKRGLEILIEVHSYYKKQVEIASKVDRVYDFALPPLLLHALSTGHVEPVAHWTDIRPNNAVTVLDTHDGIGVIDIGSDQLDRSLKGLVPDEDVDNLVNTIHANTHGESQAATGAAASNLDLYQVNSTYYSALGCNDQHYIAARAVQFFLPGVPQVYYVGALAGKNDMELLRKTNNGRDINRHYYSTAEIDENLKRPVVKALNALAKFRNELDAFDGTFSYTTDDDTSISFTWRGETSQATLTFEPKRGLGVDNTTPVAMLEWEDSAGDHRSDDLIANPPVVA 504
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500
   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/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GDV)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q84HQ2_BIFAD | Q84HQ2)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0009018    sucrose phosphorylase activity    Catalysis of the reaction: sucrose + phosphate = D-fructose + alpha-D-glucose 1-phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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:0005985    sucrose metabolic process    The chemical reactions and pathways involving sucrose, the disaccharide fructofuranosyl-glucopyranoside.

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  2.4.1.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q84HQ2_BIFAD | Q84HQ2: 5c8b
UniProtKB/TrEMBL
        Q84HQ2_BIFAD | Q84HQ2: 1r7a 2gdu

(-) Related Entries Specified in the PDB File

1r7a NATIVE STRUCTURE
2gdu E232Q MUTANT IN COMPLEX WITH SUCROSE