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(-) Description

Title :  XYLAN-BINDING MODULE CBM15
 
Authors :  S. Szabo, S. Jamal, H. Xie, S. J. Charnock, D. N. Bolam, H. J. Gilbert, G. J. Davies
Date :  10 Oct 01  (Deposition) - 29 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A
Keywords :  Carbohydrate-Binding Module, Xylan, Xylooligosaccharide, Xylanase, Catalysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Szabo, S. Jamal, H. Xie, S. J. Charnock, D. N. Bolam, H. J. Gilbert, G. J. Davies
Structure Of A Family 15 Carbohydrate-Binding Module In Complex With Xylopentaose: Evidence That Xylan Binds In An Approximate Three-Fold Helical Conformation
J. Biol. Chem. V. 276 49061 2001
PubMed-ID: 11598143  |  Reference-DOI: 10.1074/JBC.M109558200

(-) Compounds

Molecule 1 - XYLANASE 10C
    Chains: A
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: DE3-PLYSS
    Fragment: CARBOHYDRATE BINDING MODULE 15, RESIDUES (91-244)
    Organism Scientific: PSEUDOMONAS CELLULOSA
    Organism Taxid: 155077

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2XYP5Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREXYP A:1246 , HOH A:2025 , HOH A:2227BINDING SITE FOR RESIDUE XYP A1245
2AC2SOFTWAREASN A:106 , ALA A:120 , GLN A:171 , TRP A:176 , GLN A:217 , XYP A:1245 , XYP A:1247 , HOH A:2227BINDING SITE FOR RESIDUE XYP A1246
3AC3SOFTWARESER A:108 , ASP A:121 , GLN A:171 , TRP A:176 , TRP A:181 , LYS A:233 , XYP A:1246 , XYP A:1248 , HOH A:2228BINDING SITE FOR RESIDUE XYP A1247
4AC4SOFTWARETRP A:181 , ASP A:195 , LYS A:233 , XYP A:1247 , XYP A:1249 , HOH A:2143 , HOH A:2229 , HOH A:2230BINDING SITE FOR RESIDUE XYP A1248
5AC5SOFTWARETRP A:181 , XYP A:1248 , HOH A:2229 , HOH A:2231BINDING SITE FOR RESIDUE XYP A1249
6AC6SOFTWAREASN A:154 , VAL A:155 , ALA A:192 , HOH A:2162 , HOH A:2163BINDING SITE FOR RESIDUE NA A1244

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:183 -A:200

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:140 -Pro A:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBM15PS51759 Carbohydrate-binding module 15 (CBM15) domain profile.XY10C_CELJA91-242  1A:91-242

(-) Exons   (0, 0)

(no "Exon" information available for 1GNY)

(-) 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:153
 aligned with XY10C_CELJA | Q59675 from UniProtKB/Swiss-Prot  Length:606

    Alignment length:153
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
          XY10C_CELJA    91 GNVVIEVDMANGWRGNASGSTSHSGITYSADGVTFAALGDGVGAVFDIARPTTLEDAVIAMVVNVSAEFKASEANLQIFAQLKEDWSKGEWDCLAASSELTADTDLTLTCTIDEDDDKFNQTARDVQVGIQAKGTPAGTITIKSVTITLAQEA 243
               SCOP domains d1gnya_ A: Xylan-binding module from xylanase 10c                                                                                                         SCOP domains
               CATH domains 1gnyA00 A:91-243 Galactose-binding domain-like                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......eeee.........eee..eeeee.....eeeeeee...ee....eeeeeeeehhhhhhhh.eeeeeeee..eeeeee.....hhhhh.....eeeeee........ee....eeeeeeee.....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CBM15  PDB: A:91-242 UniProt: 91-242                                                                                                                    - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gny A  91 GNVVIEVDMANGWRGNASGSTSHSGITYSADGVTFAALGDGVGAVFDIARPTTLEDAVIAMVVNVSAEFKASEANLQIFAQLKEDWSKGEWDCLAGSSELTADTDLTLTCTIDEDDDKFNQTARDVQVGIQAKGTPAGTITIKSVTITLAQEA 243
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GNY)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XY10C_CELJA | Q59675)
molecular function
    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.
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: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:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  XY10C_CELJA | Q59675
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 Related Entries

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

UniProtKB/Swiss-Prot
        XY10C_CELJA | Q59675: 1us2 1us3

(-) Related Entries Specified in the PDB File

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