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(-) Description

Title :  HIGH-RESOLUTION STRUCTURES OF XYLANASES FROM B. CIRCULANS AND T. HARZIANUM IDENTIFY A NEW FOLDING PATTERN AND IMPLICATIONS FOR THE ATOMIC BASIS OF THE CATALYSIS
 
Authors :  R. L. Campbell
Date :  01 Jun 94  (Deposition) - 20 Dec 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Campbell, D. R. Rose, W. W. Wakarchuk, R. J. To, W. Sung, M. Yaguchi
High-Resolution Structures Of Xylanases From B. Circulans And T. Harzianum Identify A New Folding Pattern And Implications For The Atomic Basis Of The Catalysis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - XYLANASE
    Chains: A
    EC Number: 3.2.1.8
    Engineered: YES
    Organism Scientific: BACILLUS CIRCULANS
    Organism Taxid: 1397

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:1 , GLY A:96 , THR A:97 , HIS A:156 , HOH A:242 , HOH A:403BINDING SITE FOR RESIDUE SO4 A 191
2AS1AUTHORGLU A:78 , GLU A:172CATALYTIC ACIDIC RESIDUES
3AS2AUTHORTYR A:5 , TYR A:69 , TYR A:80 , TYR A:166GROUP OF TYROSINE RESIDUES IN THE ACTIVE SITE THAT APPEAR TO BE IMPORTANT FOR SUBSTRATE BINDING

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH11_1PS00776 Glycosyl hydrolases family 11 (GH11) active site signature 1.XYNA_BACCI103-113  1A:75-85
2GH11_2PS00777 Glycosyl hydrolases family 11 (GH11) active site signature 2.XYNA_BACCI197-208  1A:169-180

(-) Exons   (0, 0)

(no "Exon" information available for 1XNB)

(-) 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:185
 aligned with XYNA_BACCI | P09850 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_BACCI    29 ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 213
               SCOP domains d1xnba_ A: Xylanase II                                                                                                                                                                    SCOP domains
               CATH domains 1xnbA00 A:1-185  [code=2.60.120.180, no name defined]                                                                                                                                     CATH domains
               Pfam domains Glyco_hydro_11-1xnbA01 A:1-184                                                                                                                                                          - Pfam domains
         Sec.struct. author .eeeeeeeee....eeeeeee...eeeeeee...eeee..........eeeeeeeeeeee..eeee.eeeeee...eeeee..eee.........eeeee..eeeeeeeeeee...........eeeeeee.........eeeeeehhhhhhhh........eeeeee.eeeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------GH11_1     -----------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xnb A   1 ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYNA_BACCI | P09850)
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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  1xnb
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNA_BACCI | P09850: 1bcx 1bvv 1c5h 1c5i 1hv0 1hv1 1xnc 2bvv 3lb9 3vzj 3vzk 3vzl 3vzm 3vzn 3vzo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1XNB)