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(-) Description

Title :  UNBOUND STRUCTURE OF CSCBM6-3 FROM CLOSTRIDIUM STERCORARIUM
 
Authors :  A. B. Boraston, V. Notenboom, R. A. J. Warren, D. G. Kilbrun, D. R. Rose, G. J. Davies
Date :  28 Nov 02  (Deposition) - 13 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Carbohydrate-Binding Module, Xylan, Cellulose, Beta- Sandwich, Glycosidase, Xylan Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. B. Boraston, V. Notenboom, R. A. J. Warren, D. G. Kilburn, D. R. Rose, G. J. Davies
Structure And Ligand Binding Of Carbohydrate-Binding Module Cscbm6-3 Reveals Similarities With Fucose-Specific Lectins And Galactose-Binding Domains
J. Mol. Biol. V. 327 659 2003
PubMed-ID: 12634060  |  Reference-DOI: 10.1016/S0022-2836(03)00152-9

(-) Compounds

Molecule 1 - PUTATUVE ENDO-XYLANASE
    ChainsA
    EC Number3.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCARBOHYDRATE-BINDING DOMAIN, RESIDUES 273-417
    Organism ScientificCLOSTRIDIUM STERCORARIUM
    Organism Taxid1510
    StrainNCIB11745
    SynonymCSCBM6-3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:30 , GLU A:32 , SER A:52 , ASP A:142 , HOH A:2020BINDING SITE FOR RESIDUE CA A1149

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O8P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O8P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O8P)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBM6PS51175 CBM6 (carbohydrate binding type-6) domain profile.XYNA1_CLOSR250-370
387-507
527-647
  1-
-
A:27-147

(-) Exons   (0, 0)

(no "Exon" information available for 1O8P)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:131
 aligned with XYNA1_CLOSR | Q8GJ44 from UniProtKB/Swiss-Prot  Length:651

    Alignment length:131
                                   527       537       547       557       567       577       587       597       607       617       627       637       647 
          XYNA1_CLOSR   518 PVGGTRSAFSNIQAEDYDSSYGPNLQIFSLPGGGSAIGYIENGYSTTYKNIDFGDGATSVTARVATQNATTIQVRLGSPSGTLLGTIYVGSTGSFDTYRDVSATISNTAGVKDIVLVFSGPVNVDWFVFSK 648
               SCOP domains d1o8pa_ A: Putative xylanase                                                                                                        SCOP domains
               CATH domains 1o8pA00 A:18-148 Galactose-binding domain-like                                                                                      CATH domains
               Pfam domains ------------CBM_6-1o8pA01 A:30-148                                                                                                  Pfam domains
         Sec.struct. author .....ee....ee.....eee....eeee.....eeee......eeeeeeee....eeeeeeeee....eeeeeee......eeeeeee.........eeeeeeeeee..eeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------CBM6  PDB: A:27-147 UniProt: 527-647                                                                                     - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o8p A  18 PVGGTRSAFSNIQAEDYDSSYGPNLQIFSLPGGGSAIGYIENGYSTTYKNIDFGDGATSVTARVATQNATTIQVRLGSPSGTLLGTIYVGSTGSFDTYRDVSATISNTAGVKDIVLVFSGPVNVDWFVFSK 148
                                    27        37        47        57        67        77        87        97       107       117       127       137       147 

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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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYNA1_CLOSR | Q8GJ44)
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:0031176    endo-1,4-beta-xylanase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
    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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    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: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.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNA1_CLOSR | Q8GJ441nae 1o8s 1od3 1uy1 1uy2 1uy3 1uy4

(-) Related Entries Specified in the PDB File

1o8s STRUCTURE OF CSCBM6-3 FROM CLOSTRIDIUM STERCORARIUM IN COMPLEX WITH CELLOBIOSE
1od3 STRUCTURE OF CBM6-3 IN COMPLEX WITH LAMINARIBIOSE