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(-) Description

Title :  BINDING SUB-SITE DISSECTION OF A FAMILY 6 CARBOHYDRATE-BINDING MODULE BY X-RAY CRYSTALLOGRAPHY AND ISOTHERMAL TITRATION CALORIMETRY
 
Authors :  A. L. Van Bueren, A. B. Boraston
Date :  01 Mar 04  (Deposition) - 18 Jun 04  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Carbohydrate-Binding Module, Thermodynamics, Protein Structure, Xylan, Protein-Carbohydrate Interactions (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. L. Van Bueren, A. B. Boraston
Binding Sub-Site Dissection Of A Carbohydrate-Binding Modul Reveals The Contribution Of Entropy To Oligosaccharide Recognition At "Non-Primary" Binding Subsites.
J. Mol. Biol. V. 340 869 2004
PubMed-ID: 15223327  |  Reference-DOI: 10.1016/J.JMB.2004.05.038

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-CBM6-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET 28
    FragmentCARBOHYDRATE-BINDING MODULE, RESIDUES 1-139
    Organism ScientificCLOSTRIDIUM STERCORARIUM
    Organism Taxid1510
    StrainNCIB 11745
    SynonymCSCBM6-1,1,4-BETA-D-XYLAN XYLANOHYDROLASE A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4XYP2Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:50 , TYR A:51 , TRP A:107 , PRO A:133 , ASN A:135 , XYP A:1148 , HOH A:2145 , HOH A:2155BINDING SITE FOR RESIDUE XYP A1147
2AC2SOFTWARETRP A:107 , ASN A:108 , XYP A:1147 , HOH A:2157BINDING SITE FOR RESIDUE XYP A1148
3AC3SOFTWARESER A:35 , THR A:98 , THR A:115 , HOH A:2107 , HOH A:2126 , HOH A:2127BINDING SITE FOR RESIDUE NA A1145
4AC4SOFTWAREGLU A:25 , GLU A:27 , ARG A:47 , ASP A:137 , HOH A:2057BINDING SITE FOR RESIDUE CA A1146
5AC5SOFTWARESER A:88 , ASP A:89 , SER A:90 , PRO A:91 , THR A:92 , THR A:94 , HIS A:124 , HOH A:2129 , HOH A:2158 , HOH A:2159BINDING SITE FOR RESIDUE GOL A1149

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UY2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UY2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UY2)

(-) 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
  1A:22-142
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1UY2)

(-) 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:131
 aligned with XYNA1_CLOSR | Q8GJ44 from UniProtKB/Swiss-Prot  Length:651

    Alignment length:131
                                   251       261       271       281       291       301       311       321       331       341       351       361       371 
          XYNA1_CLOSR   242 SPIRRDAFSIIEAEEYNSTNSSTLQVIGTPNNGRGIGYIENGNTVTYSNIDFGSGATGFSATVATEVNTSIQIRSDSPTGTLLGTLYVSSTGSWNTYQTVSTNISKITGVHDIVLVFSGPVNVDNFIFSRS 372
               SCOP domains d1uy2a_ A: Putative xylanase                                                                                                        SCOP domains
               CATH domains 1uy2A00 A:14-144 Galactose-binding domain-like                                                                                      CATH domains
               Pfam domains -----------CBM_6-1uy2A01 A:25-143                                                                                                 - Pfam domains
         Sec.struct. author ....ee....ee.....ee.....eeee.....eeee......eeeeeeee....eeeeeeeee....eeeeeee......eeeeeee.........eeeeeeeeee..eeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------CBM6  PDB: A:22-142 UniProt: 250-370                                                                                     -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uy2 A  14 SPIRRDAFSIIEAEEYNSTNSSTLQVIGTPNNGRGIGYIENGNTVTYSNIDFGSGATGFSATVATEVNTSIQIRSDSPTGTLLGTLYVSSTGSWNTYNTVSTNISKITGVHDIVLVFSGPVNVDNFIFSRS 144
                                    23        33        43        53        63        73        83        93       103       113       123       133       143 

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  - → 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

(-) 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 1o8p 1o8s 1od3 1uy1 1uy3 1uy4

(-) Related Entries Specified in the PDB File

1nae STRUCTURE OF CSCBM6-3 FROM CLOSTRIDIUM STERCORARIUM INCOMPLEX WITH XYLOTRIOSE
1od3 STRUCTURE OF CBM6-3 IN COMPLEX WITH LAMINARIBIOSE
1uy1 STRUCTURE OF CARBOHYDRATE-BINDING MODULE LAMINARIBIOSE
1uy3 STRUCTURE OF CARBOHYDRATE-BINDING MODULE LAMINARIBIOSE
1uy4 STRUCTURE OF CARBOHYDRATE-BINDING MODULE LAMINARIBIOSE