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(-) Description

Title :  CRYSTAL STRUCTURES AND BIOCHEMICAL CHARACTERIZATION OF THE BACTERIAL SOLUTE RECEPTOR ACBH REVEAL AN UNPRECEDENTED EXCLUSIVE SUBSTRATE PREFERENCE FOR B-D-GALACTOPYRANOSE
 
Authors :  A. Vahedi-Faridi, H. Bulut, A. Licht
Date :  30 Aug 10  (Deposition) - 29 Dec 10  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Class 2 Sbp Fold, Abc Transporter Extracellular Solute Binding Protein, D-Galactose Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Licht, H. Bulut, F. Scheffel, O. Daumke, U. F. Wehmeier, W. Saenger, E. Schneider, A. Vahedi-Faridi
Crystal Structures Of The Bacterial Solute Receptor Acbh Displaying An Exclusive Substrate Preference For Beta-D-Galactopyranose
J. Mol. Biol. V. 406 92 2011
PubMed-ID: 21168419  |  Reference-DOI: 10.1016/J.JMB.2010.11.048

(-) Compounds

Molecule 1 - ABC TRANSPORTER BINDING PROTEIN ACBH
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAL8, PET15B
    Expression System Strain: ROSETTA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUE IN UNP 39-433
    Gene: ACBH
    Mutation: YES
    Organism Scientific: ACTINOPLANES
    Organism Taxid: 134676
    Strain: SE50/110

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GAL2Ligand/IonBETA-D-GALACTOSE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:56 , GLN A:60 , ARG A:82 , TYR A:129 , TRP A:131 , TRP A:177 , GLN A:255 , PRO A:288 , PHE A:359 , ASP A:361 , ARG A:362 , HOH A:636BINDING SITE FOR RESIDUE GAL A 405
2AC2SOFTWAREHIS B:56 , GLN B:60 , ARG B:82 , TYR B:129 , TRP B:131 , TRP B:177 , GLN B:255 , PRO B:288 , PHE B:359 , ASP B:361 , ARG B:362 , HOH B:414 , HOH B:495BINDING SITE FOR RESIDUE GAL B 405
3AC3SOFTWARELYS A:31 , VAL A:51 , ASN A:52 , THR A:53 , LYS B:31 , VAL B:51 , THR B:53 , HOH B:409 , HOH B:467BINDING SITE FOR RESIDUE SO4 B 406
4AC4SOFTWAREALA A:149 , SER A:150 , ALA A:153 , HOH A:468 , GLN B:279 , HOH B:476BINDING SITE FOR RESIDUE SO4 B 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OO6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OO6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OO6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OO6)

(-) Exons   (0, 0)

(no "Exon" information available for 3OO6)

(-) 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:390
 aligned with Q27GR2_ACTS5 | Q27GR2 from UniProtKB/TrEMBL  Length:433

    Alignment length:390
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433
         Q27GR2_ACTS5    44 GNGPITFGSNYSDEAPKAAFASLMQQATTSTTVPVTVNTTDHNTFQNNISNYLQGTPDSLATWFAGYRLQFFAAQGLLTPIDDVWDKIGGTFNDAAKSLSKGLDGHYYLVPLYNYPWVVFYNKSVFQSKGYEVPASWEAFIALARKMQSDGLVPLAFADKDGWPALGTFDILNLRINGYDYHIKLMKHEVPWTDPGVTKVFDQWRELAAYQQKGANGRTWQDAAKALENKQAGMMFQGSNQVAANYSAKNLPDLDFFVFPAINPQYGTDYMDAPTDGFILPKKGKNAAAAKKVLQYIGTAEAEAAFLKTDHWDVGLANGLIAPTYNDIQKKSVAEIGKCKSVSQFMDRDTVPDMANAMIKLIQQFIDQPTPETIATVQKSAEDQAKTIFR 433
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhh..........eeeee..eeeeeehhhhhhhh.....hhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeeeeehhhhhhhh...hhh.eeee............eee..eeeee......hhhhhhhhhhhhhhhhhhhhhhh.....ee..........hhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oo6 A  15 GNGPITFGSNYSDEAPKAAFASLMQQATTSTTVPVTVNTTDHNTFQNNISNYLQGTPDSLATWFAGYRLQFFAAQGLLTPIDDVWDKIGGTFNDAAKSLSKGLDGHYYLVPLYNYPWVVFYNKSVFQSKGYEVPASWEAFIALARKMQSDGLVPLAFADKDGWPALGTFDILNLRINGYDYHIKLMKHEVPWTDPGVTKVFDQWRELAAYQQKGANGRTWQDAAKALENKQAGMMFQGSNQVAANYSAKNLPDLDFFVFPAINPQYGTDYMDAPTDGFILPKKGKNAAAAKKVLQYIGTAEAEAAFLKTDHWDVGLANGLIAPTYNDIQKKSVAEIGKCKSVSQFMDRDTVPDMANAMIKLIQQFIDQPTPETIATVQKSAEDQAKTIFR 404
                                    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


Chain B from PDB  Type:PROTEIN  Length:390
 aligned with Q27GR2_ACTS5 | Q27GR2 from UniProtKB/TrEMBL  Length:433

    Alignment length:390
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433
         Q27GR2_ACTS5    44 GNGPITFGSNYSDEAPKAAFASLMQQATTSTTVPVTVNTTDHNTFQNNISNYLQGTPDSLATWFAGYRLQFFAAQGLLTPIDDVWDKIGGTFNDAAKSLSKGLDGHYYLVPLYNYPWVVFYNKSVFQSKGYEVPASWEAFIALARKMQSDGLVPLAFADKDGWPALGTFDILNLRINGYDYHIKLMKHEVPWTDPGVTKVFDQWRELAAYQQKGANGRTWQDAAKALENKQAGMMFQGSNQVAANYSAKNLPDLDFFVFPAINPQYGTDYMDAPTDGFILPKKGKNAAAAKKVLQYIGTAEAEAAFLKTDHWDVGLANGLIAPTYNDIQKKSVAEIGKCKSVSQFMDRDTVPDMANAMIKLIQQFIDQPTPETIATVQKSAEDQAKTIFR 433
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------SBP_bac_1-3oo6B01 B:23-318                                                                                                                                                                                                                                                                              -------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------SBP_bac_1-3oo6B02 B:23-318                                                                                                                                                                                                                                                                              -------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhh..........eeeee..eeeeeehhhhhhhh.....hhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeeeeehhhhhhhh...hhh.eeee............eee..eeeee......hhhhhhhhhhhhhhhhhhhhhh......ee..........hhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oo6 B  15 GNGPITFGSNYSDEAPKAAFASLMQQATTSTTVPVTVNTTDHNTFQNNISNYLQGTPDSLATWFAGYRLQFFAAQGLLTPIDDVWDKIGGTFNDAAKSLSKGLDGHYYLVPLYNYPWVVFYNKSVFQSKGYEVPASWEAFIALARKMQSDGLVPLAFADKDGWPALGTFDILNLRINGYDYHIKLMKHEVPWTDPGVTKVFDQWRELAAYQQKGANGRTWQDAAKALENKQAGMMFQGSNQVAANYSAKNLPDLDFFVFPAINPQYGTDYMDAPTDGFILPKKGKNAAAAKKVLQYIGTAEAEAAFLKTDHWDVGLANGLIAPTYNDIQKKSVAEIGKCKSVSQFMDRDTVPDMANAMIKLIQQFIDQPTPETIATVQKSAEDQAKTIFR 404
                                    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
   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 3OO6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OO6)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q27GR2_ACTS5 | Q27GR2)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0045493    xylan catabolic process    The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.

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 Related Entries

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

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        Q27GR2_ACTS5 | Q27GR2: 3oo7 3oo8 3oo9 3ooa

(-) Related Entries Specified in the PDB File

3oo7 3oo8 3oo9 3ooa