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(-) Description

Title :  CRYSTAL STRUCTURE OF XYNB, A HIGHLY THERMOSTABLE BETA-1,4-XYLANASE FROM DICTYOGLOMUS THERMOPHILUM RT46B.1, AT 1.8 A RESOLUTION
 
Authors :  A. A. Mccarthy, E. N. Baker
Date :  26 Jul 00  (Deposition) - 15 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Xylanase, Beta-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Mccarthy, D. D. Morris, P. L. Bergquist, E. N. Baker
Structure Of Xynb, A Highly Thermostable Beta-1, 4-Xylanase From Dictyoglomus Thermophilum Rt46B. 1, At 1. 8 A Resolution.
Acta Crystallogr. , Sect. D V. 56 1367 2000
PubMed-ID: 11053833  |  Reference-DOI: 10.1107/S0907444900009896
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-1,4-XYLANASE
    Chains: A, B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJLA602
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: DICTYOGLOMUS THERMOPHILUM
    Organism Taxid: 14
    Strain: RT46B.1

 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
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:164 , ARG B:165 , HOH B:1061 , HOH B:1121BINDING SITE FOR RESIDUE SO4 B 1001
2AC2SOFTWAREASN A:86 , GLY B:109 , GLN B:110 , ARG B:165BINDING SITE FOR RESIDUE SO4 B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F5J)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:86 -Pro A:87
2Pro A:102 -Pro A:103
3Asn B:86 -Pro B:87
4Pro B:102 -Pro B:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F5J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F5J)

(-) Exons   (0, 0)

(no "Exon" information available for 1F5J)

(-) 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:199
 aligned with P77853_DICTH | P77853 from UniProtKB/TrEMBL  Length:360

    Alignment length:199
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218         
         P77853_DICTH    29 TLTSNASGTFDGYYYELWKDTGNTTMTVYTQGRFSCQWSNINNALFRTGKKYNQNWQSLGTIRITYSATYNPNGNSYLCIYGWSTNPLVEFYIVESWGNWRPPGATSLGQVTIDGGTYDIYRTTRVNQPSIVGTATFDQYWSVRTSKRTSGTVTVTDHFRAWANRGLNLGTIDQITLCVEGYQSSGSANITQNTFSQGS 227
               SCOP domains d1f5ja_ A: Xylanase II                                                                                                                                                                                  SCOP domains
               CATH domains 1f5jA00 A:1-199  [code=2.60.120.180, no name defined]                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..eeeeeee...eeeeee.hhh.eeeeee...eeeeeeeeeeeee.hhh.eeeeeeeeeeee...eeeeeeeeee...eeeeeeeee.........eeeeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeeehhhhhhhhhh......eeeeeeeeeeee...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f5j A   1 ALTSNASGTFDGYYYELWKDTGNTTMTVYTQGRFSCQWSNINNALFRTGKKYNQNWQSLGTIRITYSATYNPNGNSYLCIYGWSTNPLVEFYIVESWGNWRPPGATSLGQVTIDGGTYDIYRTTRVNQPSIVGTATFDQYWSVRTSKRTSGTVTVTDHFRAWANRGLNLGTIDQITLCVEGYQSSGSANITQNTFSQSS 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         


Chain B from PDB  Type:PROTEIN  Length:199
 aligned with P77853_DICTH | P77853 from UniProtKB/TrEMBL  Length:360

    Alignment length:199
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218         
         P77853_DICTH    29 TLTSNASGTFDGYYYELWKDTGNTTMTVYTQGRFSCQWSNINNALFRTGKKYNQNWQSLGTIRITYSATYNPNGNSYLCIYGWSTNPLVEFYIVESWGNWRPPGATSLGQVTIDGGTYDIYRTTRVNQPSIVGTATFDQYWSVRTSKRTSGTVTVTDHFRAWANRGLNLGTIDQITLCVEGYQSSGSANITQNTFSQGS 227
               SCOP domains d1f5jb_ B: Xylanase II                                                                                                                                                                                  SCOP domains
               CATH domains 1f5jB00 B:1-199  [code=2.60.120.180, no name defined]                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..eeeeeee...eeeeee.hhh.eeeeee...eeeeeeeeeeeee.hhh.eeeeeeeeeeee...eeeeeeeeee...eeeeeeeee.........eeeeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeeehhhhhhhhhhh.....eeeeeeeeeeee...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f5j B   1 ALTSNASGTFDGYYYELWKDTGNTTMTVYTQGRFSCQWSNINNALFRTGKKYNQNWQSLGTIRITYSATYNPNGNSYLCIYGWSTNPLVEFYIVESWGNWRPPGATSLGQVTIDGGTYDIYRTTRVNQPSIVGTATFDQYWSVRTSKRTSGTVTVTDHFRAWANRGLNLGTIDQITLCVEGYQSSGSANITQNTFSQSS 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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, 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 1F5J)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (P77853_DICTH | P77853)
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.
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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