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(-) Description

Title :  XYLAN-BINDING DOMAIN FROM CBM 22, FORMALLY X6B DOMAIN
 
Authors :  G. J. Davies, S. J. Charnock, H. J. Gilbert, C. M. G. A. Fontes
Date :  03 Feb 00  (Deposition) - 04 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Carbohydrate-Binding Module, Xylan-Binding, Xylanase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Charnock, D. N. Bolam, J. P. Turkenburg, H. J. Gilbert, L. M. A. Ferreira, G. J. Davies, C. M. G. A. Fontes
The X6 Thermostabilising Domains Of Xylanases Are Carbohydrate Binding Modules: Structure And Biochemistry Of The Clostridium Thermocellum X6B Domain
Biochemistry V. 39 5013 2000
PubMed-ID: 10819965  |  Reference-DOI: 10.1021/BI992821Q

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE Y
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: XYLAN-BINDING DOMAIN
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Synonym: CBM 22, X6B DOMAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:14 , GLU A:16 , LYS A:39 , GLU A:42 , ASP A:149BINDING SITE FOR RESIDUE CA A 300
2AC2SOFTWARETHR B:14 , GLU B:16 , LYS B:39 , GLU B:42 , ASP B:149 , HOH B:2147BINDING SITE FOR RESIDUE CA B 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DYO)

(-) Exons   (0, 0)

(no "Exon" information available for 1DYO)

(-) Sequences/Alignments

Asymmetric 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:156
 aligned with XYNY_CLOTM | P51584 from UniProtKB/Swiss-Prot  Length:1077

    Alignment length:157
                                   571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       
           XYNY_CLOTM   562 PDANGYYYHDTFEGSVGQWTARGPAEVLLSGRTAYKGSESLLVRNRTAAWNGAQRALNPRTFVPGNTYCFSVVASFIEGASSTTFCMKLQYVDGSGTQRYDTIDMKTVGPNQWVHLYNPQYRIPSDATDMYVYVETADDTINFYIDEAIGAVAGTVI 718
               SCOP domains d1d yoa_ A: Xylan-binding domain                                                                                                                              SCOP domains
               CATH domains 1dy oA00 A:5-160 Galactose-binding domain-like                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-.eeeee.........eee...eeeee.........eeeee.......eeeeee.........eeeeeeeee.......eeeeeeeeee.....eeeeeeeeeee.....eeeeeeeee.....eeeeeeeee......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dyo A   5 PDA-GYYYHDTFEGSVGQWTARGPAEVLLSGRTAYKGSESLLVRNRTAAWNGAQRALNPRTFVPGNTYCFSVVASFIEGASSTTFCmKLQYVDGSGTQRYDTIDmKTVGPNQWVHLYNPQYRIPSDATDmYVYVETADDTINFYIDEAIGAVAGTVI 160
                              | |   13        23        33        43        53        63        73        83      | 93       103    |  113       123       133       143       153       
                              7 8                                                                                90-MSE           108-MSE                  133-MSE                       


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with XYNY_CLOTM | P51584 from UniProtKB/Swiss-Prot  Length:1077

    Alignment length:157
                                   571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       
           XYNY_CLOTM   562 PDANGYYYHDTFEGSVGQWTARGPAEVLLSGRTAYKGSESLLVRNRTAAWNGAQRALNPRTFVPGNTYCFSVVASFIEGASSTTFCMKLQYVDGSGTQRYDTIDMKTVGPNQWVHLYNPQYRIPSDATDMYVYVETADDTINFYIDEAIGAVAGTVI 718
               SCOP domains d1d yob_ B: Xylan-binding domain                                                                                                                              SCOP domains
               CATH domains 1dy oB00 B:5-160 Galactose-binding domain-like                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-.eeeee.........eee...eeeee.........eeeee.......eeeee..........eeeeeeeee.......eeeeeeeeee.....eeeeeeeeeee.....eeeeeeeee.....eeeeeeeee......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dyo B   5 PDA-GYYYHDTFEGSVGQWTARGPAEVLLSGRTAYKGSESLLVRNRTAAWNGAQRALNPRTFVPGNTYCFSVVASFIEGASSTTFCmKLQYVDGSGTQRYDTIDmKTVGPNQWVHLYNPQYRIPSDATDmYVYVETADDTINFYIDEAIGAVAGTVI 160
                              | |   13        23        33        43        53        63        73        83      | 93       103    |  113       123       133       143       153       
                              7 8                                                                                90-MSE           108-MSE                  133-MSE
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (XYNY_CLOTM | P51584)
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:0043263    cellulosome    An extracellular multi-enzyme complex containing up to 11 different enzymes aligned on a non-catalytic scaffolding glycoprotein. Functions to hydrolyze cellulose.

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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNY_CLOTM | P51584: 1gkk 1gkl 1h6x 1h6y 1ohz 1wb4 1wb5 1wb6 2ccl 2w5f 2wys 2wze 3zi7 4bag 4h35 5fxm

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