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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENGINEERED UNINHIBITED BACILLUS SUBTILIS XYLANASE IN SUBSTRATE BOUND STATE
 
Authors :  S. Sansen, M. Dewilde, C. J. De Ranter, J. F. Sorensen, O. Sibbesen, K. Gebruers, K. Brijs, C. M. Courtin, J. A. Delcour, A. Rabijns
Date :  22 Sep 05  (Deposition) - 19 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym./Biol. Unit :  X
Keywords :  Beta-Jelly Roll Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sansen, M. Dewilde, C. J. De Ranter, K. Gebruers, K. Brijs, C. M. Courtin, J. A. Delcour, A. Rabijns
Crystal Structure Of The Triticum Xylanse Inhibitor-I In Complex With Bacillus Subtilis Xylanase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE A
    Chains: X
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: XYNA
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: XYLANASE A;
1,4- BETA-D-XYLAN XYLANOHYDROLASE A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1XYP2Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP X:9 , VAL X:37 , TYR X:69 , TRP X:71 , GLU X:78 , TYR X:80 , ARG X:112 , PRO X:116 , GLN X:127 , GLU X:172 , XYP X:501 , HOH X:510 , HOH X:525 , HOH X:547BINDING SITE FOR RESIDUE XYP X 502
2AC2SOFTWAREGLN X:7 , TRP X:9 , TYR X:69 , PRO X:116 , SER X:117 , TYR X:166 , XYP X:502 , HOH X:525 , HOH X:544BINDING SITE FOR RESIDUE XYP X 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B46)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser X:74 -Pro X:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B46)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH11_1PS00776 Glycosyl hydrolases family 11 (GH11) active site signature 1.XYNA_BACSU103-113  1X:75-85
2GH11_2PS00777 Glycosyl hydrolases family 11 (GH11) active site signature 2.XYNA_BACSU197-208  1X:169-180

(-) Exons   (0, 0)

(no "Exon" information available for 2B46)

(-) 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 X from PDB  Type:PROTEIN  Length:185
 aligned with XYNA_BACSU | P18429 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:185
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208     
           XYNA_BACSU    29 ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFSNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 213
               SCOP domains d2b46x_ X: Xylanase II                                                                                                                                                                    SCOP domains
               CATH domains 2b46X00 X:1-185  [code=2.60.120.180, no name defined]                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...eeeeee....eeeeeee...eeeeeeee.......eeeeeeeeeeee..eeeeeeeeee...eeeeeeeee.......eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeeee.........eeeehhhhhhhhhhh......eeeeeeeeeeee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------GH11_1     -----------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b46 X   1 ASTDYWQNWTFGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDDTTFTQYWSVRQSKRPTGSNATITFSNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
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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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B46)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (XYNA_BACSU | P18429)
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.

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  2b46
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNA_BACSU | P18429: 1axk 1xxn 2b42 2b45 2dcy 2dcz 2qz3 2z79 3exu 3hd8 5k9y

(-) Related Entries Specified in the PDB File

1t6e STRUCTURE OF TRITICUM AESTIVUM XYLANASE INHIBITOR-I
1t6g STRUCTURE OF TRITICUM AESTIVUM XYLANASE INHIBITOR-I IN COMPLEX WITH ASPERGILLUS NIGER XYLANASE-I
2b42 STRUCTURE OF TRITICUM AESTIVUM XYLANASE INHIBITOR-I IN COMPLEX WITH BACILLUS SUBTILIS XYLANASE
2b45 STRUCTURE OF AN ENGINEERED UNINHIBITED BACILLUS SUBTILIS XYLANASE IN FREE STATE