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(-) Description

Title :  3D STRUCTURE OF A THERMOPHILIC FAMILY GH11 XYLANASE FROM THERMOBIFIDA FUSCA
 
Authors :  A. Lammerts Van Bueren, S. Otani, E. P. Friis, K. S Wilson, G. J. Davie
Date :  27 Jun 11  (Deposition) - 08 Feb 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Glycoside Hydrolase, Plant Cell Wall (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Lammerts Van Bueren, S. Otani, E. P. Friis, K. S. Wilson, G. J. Davies
Three-Dimensional Structure Of A Thermophilic Family Gh11 Xylanase From Thermobifida Fusca.
Acta Crystallogr. , Sect. F V. 68 141 2012
PubMed-ID: 22297985  |  Reference-DOI: 10.1107/S1744309111049608

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE
    Chains: A
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Taxid: 1423
    Fragment: CATALYTIC DOMAIN, RESIDUES 43-236
    Organism Scientific: THERMOBIFIDA FUSCA
    Organism Taxid: 2021
    Other Details: COVALENT GLYCOSYL-ENZYME INTERMEDIATE TO GLU127
    Synonym: XYLANASE 11

 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
1EDO5Ligand/Ion1,2-ETHANEDIOL
2FXP1Ligand/Ion2-DEOXY-2-FLUORO-4-O-BETA-D-XYLOPYRANOSYL-ALPHA-D-XYLOPYRANOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:60 , VAL A:88 , TYR A:118 , TRP A:120 , GLU A:127 , TYR A:129 , ARG A:161 , PRO A:165 , SER A:166 , PHE A:173 , GLN A:175 , TYR A:210 , HOH A:2022 , HOH A:2023 , HOH A:2044 , HOH A:2144BINDING SITE FOR RESIDUE FXP A1207
2AC2SOFTWAREGLY A:96 , GLY A:97 , ARG A:98 , ARG A:99 , SER A:166 , ILE A:167 , GLY A:169 , HOH A:2111 , HOH A:2144BINDING SITE FOR RESIDUE EDO A1230
3AC3SOFTWARESER A:68 , SER A:80BINDING SITE FOR RESIDUE EDO A1231
4AC4SOFTWAREASN A:112 , TYR A:114 , TYR A:137 , GLU A:216 , TYR A:218 , HOH A:2075 , HOH A:2082 , HOH A:2108 , HOH A:2145BINDING SITE FOR RESIDUE EDO A1232
5AC5SOFTWAREMET A:144 , ARG A:200 , HIS A:201BINDING SITE FOR RESIDUE EDO A1233
6AC6SOFTWAREGLY A:54 , TYR A:55 , TRP A:93BINDING SITE FOR RESIDUE EDO A1234

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZSE)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:123 -Pro A:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZSE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZSE)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZSE)

(-) 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:188
 aligned with Q5RZ98_THEFU | Q5RZ98 from UniProtKB/TrEMBL  Length:338

    Alignment length:188
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        
         Q5RZ98_THEFU    43 AVTSNETGYHDGYFYSFWTDAPGTVSMELGPGGNYSTSWRNTGNFVAGKGWATGGRRTVTYSASFNPSGNAYLTLYGWTRNPLVEYYIVESWGTYRPTGTYMGTVTTDGGTYDIYKTTRYNAPSIEGTRTFDQYWSVRQSKRTSGTITAGNHFDAWARHGMHLGTHDYMIMATEGYQSSGSSNVTLGT 230
               SCOP domains d3zsea_ A: automated matches                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..eeeeeee.....eeeee....eeeeee....eeeeeeee......eeeeeeee....eeeeeeeeeee...eeeeeeeee.......eeeeeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeeehhhhhhhhhhh.....eeeeeeeeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zse A  43 AVTSNQTGYHDGYFYSFWTDAPGTVSMELGPGGNYSTSWRNTGNFVAGKGWATGGRRTVTYSASFNPSGNAYLTLYGWTRNPLVEYYIVESWGTYRPTGTYMGTVTTDGGTYDIYKTTRYNAPSIEGTRTFDQYWSVRQSKRTSGTITAGNHFDAWARHGMHLGTHDYMIMATEGYQSSGSSNVTLGT 230
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZSE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZSE)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5RZ98_THEFU | Q5RZ98)
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:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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.

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