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(-) Description

Title :  STRUCTURE OF CSCBM6-3 FROM CLOSTRIDIUM STERCORARIUM IN COMPLEX WITH XYLOTRIOSE
 
Authors :  A. B. Boraston, V. Notenboom, R. A. J. Warren, D. G. Kilburn, D. R. Rose, G. Davies
Date :  27 Nov 02  (Deposition) - 18 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Carbohydrate-Binding Module, Beta-Sandwich, Xylan, Xylooligosaccharide, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. B. Boraston, V. Notenboom, R. A. J. Warren, D. G. Kilburn, D. R. Rose, G. 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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE XYLANASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A
    Expression System StrainBL21/DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL CARBOHYDRATE-BINDING MODULE
    GenePUTATIVE XYLANASE
    Organism ScientificCLOSTRIDIUM STERCORARIUM
    Organism Taxid1510

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2XYP3Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREXYP A:801 , HOH A:994 , HOH A:1070BINDING SITE FOR RESIDUE XYP A 802
2AC2SOFTWAREGLY A:55 , TYR A:56 , PHE A:112 , ASN A:140 , XYP A:800 , XYP A:802 , HOH A:924 , HOH A:957BINDING SITE FOR RESIDUE XYP A 801
3AC3SOFTWAREPHE A:45 , THR A:99 , ASP A:113 , ASN A:140 , XYP A:801BINDING SITE FOR RESIDUE XYP A 800
4AC4SOFTWAREGLN A:30 , GLU A:32 , SER A:52 , ASP A:142 , HOH A:992BINDING SITE FOR RESIDUE CA A 900

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1NAE)

(-) 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:129
 aligned with XYNA1_CLOSR | Q8GJ44 from UniProtKB/Swiss-Prot  Length:651

    Alignment length:129
                                   529       539       549       559       569       579       589       599       609       619       629       639         
          XYNA1_CLOSR   520 GGTRSAFSNIQAEDYDSSYGPNLQIFSLPGGGSAIGYIENGYSTTYKNIDFGDGATSVTARVATQNATTIQVRLGSPSGTLLGTIYVGSTGSFDTYRDVSATISNTAGVKDIVLVFSGPVNVDWFVFSK 648
               SCOP domains d1naea_ A: Putative xylanase                                                                                                      SCOP domains
               CATH domains 1naeA00 A:20-148 Galactose-binding domain-like                                                                                    CATH domains
               Pfam domains ----------CBM_6-1naeA01 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
                 1nae A  20 GGTRSAFSNIQAEDYDSSYGPNLQIFSLPGGGSAIGYIENGYSTTYKNIDFGDGATSVTARVATQNATTIQVRLGSPSGTLLGTIYVGSTGSFDTYRDVSATISNTAGVKDIVLVFSGPVNVDWFVFSK 148
                                    29        39        49        59        69        79        89        99       109       119       129       139         

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  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  (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 | Q8GJ441o8p 1o8s 1od3 1uy1 1uy2 1uy3 1uy4

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