Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  SUCROSE PHOSPHORYLASE FROM BIFIDOBACTERIUM ADOLESCENTIS
 
Authors :  D. Sprogoe, L. A. M. Van Den Broek, O. Mirza, J. S. Kastrup, A. G. J. Vora M. Gajhede, L. K. Skov
Date :  21 Oct 03  (Deposition) - 10 Feb 04  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Alpha-Barrels, Dimer, Glycoside Hydrolase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Sprogoe, L. A. Van Den Broek, O. Mirza, J. S. Kastrup, A. G. Voragen M. Gajhede, L. K. Skov
Crystal Structure Of Sucrose Phosphorylase From Bifidobacterium Adolescentis.
Biochemistry V. 43 1156 2004
PubMed-ID: 14756551  |  Reference-DOI: 10.1021/BI0356395

(-) 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  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CSD2Mod. Amino Acid3-SULFINOALANINE
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:50 , PHE A:53 , HIS A:88 , GLN A:160 , ASP A:192 , ALA A:193 , GLU A:232 , ARG A:399 , HOH A:857 , HOH A:1110 , HOH A:1380BINDING SITE FOR RESIDUE TRS A 700
2AC2SOFTWAREASP B:50 , PHE B:53 , HIS B:88 , PHE B:156 , GLN B:160 , ASP B:192 , ALA B:193 , GLU B:232 , ARG B:399 , HOH B:895 , HOH B:1031 , HOH B:1759BINDING SITE FOR RESIDUE TRS B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R7A)

(-) 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 1R7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R7A)

(-) Exons   (0, 0)

(no "Exon" information available for 1R7A)

(-) 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 d1r7aa2 A:1-434 Sucrose phosphorylase                                                                                                                                                                                                                                                                                                                                                                                                             d1r7aa1 A:435-504 Sucrose phosphorylase                                SCOP domains
               CATH domains 1r7aA01 A:1-85,A:167-432 Glycosidases                                                1r7aA02 A:86-166 Oligo-1,6-glucosidase; Domain 2                                 1r7aA01 A:1-85,A:167-432 Glycosidases                                                                                                                                                                                                                                     ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee........hhhhhhhhhhhhh.....eeee...ee............eeeee.....hhhhhhhhhh..eeeeeee..eee..hhhhhhhhhhhhhh.hhhhh.hhhhhh....hhhhhhh.........eeeeee..eeeeee......eee....hhhhhhhhhhhhhhhhhh...eeeeehhhhh..........hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhh...eeee.hhhhhhhhhhhhh.hhhhhhhhhhh...eee..........................hhhhhhhhhhhhhhhh.hhhhhhhhhhh..........hhhhhh..hhhhhhhhhhhhhhh..eeeeehhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhheeeeeee...eeeeeee....eeeeee.hhhh.........eeeeeee..eeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r7a 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    
                                                                                                                                                                                                                                                                                                                                                                                             356-CSD                                                                                                                                                


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 d1r7ab2 B:1-434 Sucrose phosphorylase                                                                                                                                                                                                                                                                                                                                                                                                             d1r7ab1 B:435-504 Sucrose phosphorylase                                SCOP domains
               CATH domains 1r7aB01 B:1-85,B:167-432 Glycosidases                                                1r7aB02 B:86-166 Oligo-1,6-glucosidase; Domain 2                                 1r7aB01 B:1-85,B:167-432 Glycosidases                                                                                                                                                                                                                                     ------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------Alpha-amylase-1r7aB01 B:32-388                                                                                                                                                                                                                                                                                                                                       ----------------------------------------------DUF1964-1r7aB03 B:435-502                                           -- Pfam domains (1)
           Pfam domains (2) -------------------------------Alpha-amylase-1r7aB02 B:32-388                                                                                                                                                                                                                                                                                                                                       ----------------------------------------------DUF1964-1r7aB04 B:435-502                                           -- Pfam domains (2)
         Sec.struct. author .....eeee........hhhhhhhhhhhhh.....eeee...ee............eeeee.....hhhhhhhhhh..eeeeee...eee..hhhhhhhhhhhhhh.hhhhh.hhhhhh....hhhhhhh.........eeeeee..eeeeee......eee....hhhhhhhhhhhhhhhhhh...eeee.hhhhh..........hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh.eeee.hhhhhhhhhhhhh.hhhhhhhhhhh...eee..........................hhhhhhhhhhhhhhhh.hhhhhhhhhhh..........hhhhhh..hhhhhhhhhhhhhhh..eeeeehhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhheeeeeee...eeeeeee....eeeeee.hhhh.........eeeeeee..eeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r7a 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    
                                                                                                                                                                                                                                                                                                                                                                                             356-CSD
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)
(-)
Clan: no clan defined [family: DUF1964] (1)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CSD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:44 - Pro A:45   [ RasMol ]  
    Thr B:44 - Pro B:45   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1r7a
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q84HQ2_BIFAD | Q84HQ2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.4.1.7
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q84HQ2_BIFAD | Q84HQ2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1R7A)