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(-) Description

Title :  THE ROLE OF CONSERVED AMINO ACIDS IN THE CLEFT OF THE C-TERMINAL FAMILY 22 CARBOHYDRATE BINDING MODULE OF CLOSTRIDIUM THERMOCELLUM XYN10B IN LIGAND BINDING
 
Authors :  H. Xie, D. N. Bolam, S. J. Charnock, G. J. Davies, M. P. Williamson, P. J. Simpson, C. M. G. A. Fontes, L. M. A. Ferreira, H. J. Gilbert
Date :  29 Jun 01  (Deposition) - 27 Jun 02  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Xylan Degradation, Hydrolase, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Xie, H. J. Gilbert, S. J. Charnock, G. J. Davies, M. P. Williamson, P. J. Simpson, S. Raghothama, C. M. G. A. Fontes, F. M. Dias, L. M. A. Ferreira, D. N. Bolam
Clostridium Thermocellum Xyn10B Carbohydrate- Binding Module 22-2: The Role Of Conserved Amino Acids In Ligand Binding
Biochemistry V. 40 9167 2001
PubMed-ID: 11478884  |  Reference-DOI: 10.1021/BI0106742
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE Y
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: XYLAN BINDING DOMAIN RESIDUE 560-720
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Strain: YS
    Synonym: CBM22-2,XYLANASE Y, XYLY, 1,4-BETA-D-XYLAN XYLANOHYDROLASE Y

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:14 , GLU A:16 , LYS A:39 , GLU A:42 , ASP A:149 , HOH A:2046BINDING SITE FOR RESIDUE CA A1161
2AC2SOFTWARETHR B:14 , GLU B:16 , LYS B:39 , GLU B:42 , ASP B:149 , HOH B:2156BINDING SITE FOR RESIDUE CA B1161

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H6Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H6Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H6Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H6Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1H6Y)

(-) 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:157
 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 d1h6ya_ A: Xylan-binding domain                                                                                                                               SCOP domains
               CATH domains 1h6yA00 A:4-160 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
                 1h6y A   4 PDANGYYYHDTFEGSVGQWTARGPAEVLLSGRTAYKGSESLLVRNRTAAWNGAQRALNPRTFVPGNTYCFSVVASFIEGASSTTFCMKLQYVDGSGTQRYDTIDMKTVGPNQWVHLYNPQYRIPSDATDMYVYVATADDTINFYIDEAIGAVAGTVI 160
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       


Chain B from PDB  Type:PROTEIN  Length:157
 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 d1h6yb_ B: Xylan-binding domain                                                                                                                               SCOP domains
               CATH domains 1h6yB00 B:4-160 Galactose-binding domain-like                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee........eeee...eeeee.........eeeee.......eeeee..........eeeeeeeee.......eeeeeeeeee.....eeeeeeeeeee.....eeeeeeeee.....eeeeeeeee......eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h6y B   4 PDANGYYYHDTFEGSVGQWTARGPAEVLLSGRTAYKGSESLLVRNRTAAWNGAQRALNPRTFVPGNTYCFSVVASFIEGASSTTFCMKLQYVDGSGTQRYDTIDMKTVGPNQWVHLYNPQYRIPSDATDMYVYVATADDTINFYIDEAIGAVAGTVI 160
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153
   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 1H6Y)

(-) 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: 1dyo 1gkk 1gkl 1h6x 1ohz 1wb4 1wb5 1wb6 2ccl 2w5f 2wys 2wze 3zi7 4bag 4h35 5fxm

(-) Related Entries Specified in the PDB File

1dyo XYLAN-BINDING DOMAIN FROM CBM 22, FORMALLY X6B DOMAIN
1h6x THE ROLE OF CONSERVED AMONI ACIDS IN THE CLEFT OF THE C-TERMINAL FAMILY 22 CARBOHYDRATE BINDING MODULE OF CLOSTRIDIUM THERMOCELLUM XYN10B IN LIGAND BINDING