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(-) Description

Title :  CRYSTAL STRUCTURE OF A FAMILY 6 CARBOHYDRATE-BINDING MODULE FROM CLOSTRIDIUM CELLULOLYTICUM IN COMPLEX WITH XYLOSE
 
Authors :  D. W. Abbott, E. Ficko-Blean, A. Lammerts Van Bueren, P. M. Coutinho, B. Henrissat, H. J. Gilbert, A. B. Boraston
Date :  29 Sep 08  (Deposition) - 13 Oct 09  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Family 6 Carbohydrate Binding Module, Cccbm6 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Abbott, E. Ficko-Blean, A. L. Van Bueren, A. Rogowski, A. Cartmell, P. M. Coutinho, B. Henrissat, H. J. Gilbert, A. B. Boraston
Analysis Of The Structural And Functional Diversity Of Plant Cell Wall Specific Family 6 Carbohydrate Binding Modules.
Biochemistry V. 48 10395 2009
PubMed-ID: 19788273  |  Reference-DOI: 10.1021/BI9013424

(-) Compounds

Molecule 1 - GH59 GALACTOSIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Fragment: CCCBM6, RESIDUES 922-1050
    Organism Scientific: CLOSTRIDIUM CELLULOLYTICUM
    Synonym: FAMILY 59 GLYCOSIDE HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:942 , GLU A:949 , PHE A:953 , ASN A:1042 , HOH A:2158 , HOH A:2159 , HOH A:2160 , HOH A:2161 , HOH A:2162BINDING SITE FOR RESIDUE XYP A3051
2AC2SOFTWAREGLU A:929 , GLU A:931 , GLU A:949 , ASN A:1044 , HOH A:2030BINDING SITE FOR RESIDUE NA A3052

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V4V)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:129
 aligned with Q0PRN1_CLOCE | Q0PRN1 from UniProtKB/TrEMBL  Length:1122

    Alignment length:129
                                   931       941       951       961       971       981       991      1001      1011      1021      1031      1041         
        Q0PRN1_CLOCE    922 QSAYSRIEAESYSNQSGIQTETCSEGGEDVGFVENGDYTVYNNVDFGDGVGGFQARVASATSGGNIEIRLDSSTGTLIGTCPVAGTGDWQTYTDAKCTVSGVTGKHDVYLVFKGDSGYLFNLNWFTFSE 1050
               SCOP domains d2v4va_ A: automated matches                                                                                                      SCOP domains
               CATH domains 2v4vA00 A:922-1050 Galactose-binding domain-like                                                                                  CATH domains
               Pfam domains -------CBM_6-2v4vA01 A:929-1050                                                                                                   Pfam domains
         Sec.struct. author ......ee.hhh.eee..eeee.....eeee......eeeeeeeeeee...eeeeeee.....eeeeeee......eeeeeee........eeeeeee....eeeeeeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                2v4v A  922 QSAYSRIEAESYSNQSGIQTETCSEGGEDVGFVENGDYTVYNNVDFGDGVGGFQARVASATSGGNIEIRLDSSTGTLIGTCPVAGTGDWQTYTDAKCTVSGVTGKHDVYLVFKGDSGYLFNLNWFTFSE 1050
                                   931       941       951       961       971       981       991      1001      1011      1021      1031      1041
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: GBD (153)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q0PRN1_CLOCE | Q0PRN1)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0004336    galactosylceramidase activity    Catalysis of the reaction: D-galactosyl-N-acylsphingosine + H2O = D-galactose + N-acylsphingosine.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0006683    galactosylceramide catabolic process    The chemical reactions and pathways resulting in the breakdown of galactosylceramides, any compound formed by the replacement of the glycosidic hydroxyl group of a cyclic form of galactose by a ceramide group.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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