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(-) Description

Title :  XYLANASE10C (MUTANT E385A) FROM CELLVIBRIO JAPONICUS IN COMPLEX WITH XYLOPENTAOSE
 
Authors :  G. Pell, L. Szabo, S. J. Charnock, H. Xie, T. M. Gloster, G. J. Davies, H.
Date :  17 Nov 03  (Deposition) - 18 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Carbohydrate Binding Module, Xylan Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Pell, L. Szabo, S. J. Charnock, H. Xie, T. M. Gloster, G. J. Davies, H. J. Gilbert
Structural And Biochemical Analysis Of Cellvibrio Japonicus Xylanase 10C: How Variation In Substrate-Binding Cleft Influences The Catalytic Profile Of Family Gh-10 Xylanases
J. Biol. Chem. V. 279 11777 2004
PubMed-ID: 14670951  |  Reference-DOI: 10.1074/JBC.M311947200

(-) Compounds

Molecule 1 - ENDO-BETA-1,4-XYLANASE
    Chains: A
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TUNER:PLYSS
    Expression System Taxid: 562
    Expression System Vector: PET 22B
    Fragment: CARBOHYDRATE BINDING MODULE AND CATALYTIC MODULE, RESIDUES (86-606)
    Mutation: YES
    Organism Scientific: CELLVIBRIO JAPONICUS
    Organism Taxid: 155077
    Synonym: XYLANASE10C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1XYP8Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:299 , HIS A:332 , ASN A:384 , GLN A:466 , GLU A:497 , TRP A:552 , TRP A:560 , XYP A:1607 , HOH A:2831BINDING SITE FOR RESIDUE XYP A1609
2AC2SOFTWAREASN A:296 , LYS A:299 , TYR A:340 , VAL A:543 , ASN A:544 , TRP A:552 , TRP A:560 , XYP A:1609 , HOH A:2306 , HOH A:2487 , HOH A:2822 , HOH A:2824 , HOH A:2826 , HOH A:2827 , HOH A:2828 , HOH A:2829 , HOH A:2830BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1606 TO 1608
3AC3SOFTWAREASN A:106 , SER A:108 , GLN A:171 , TRP A:176 , TRP A:181 , GLN A:217 , ALA A:350 , HOH A:2833BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1610 TO 1613

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:183 -A:200
2A:470 -A:507
3A:531 -A:602

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Arg A:140 -Pro A:141
2His A:332 -Ala A:333
3Ser A:391 -Pro A:392
4Tyr A:473 -Pro A:474
5Tyr A:510 -Pro A:511
6Asn A:516 -Pro A:517

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1US2)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH10_2PS51760 Glycosyl hydrolases family 10 (GH10) domain profile.XY10C_CELJA245-596  1A:245-596
2GH10_1PS00591 Glycosyl hydrolases family 10 (GH10) active site.XY10C_CELJA490-500  1A:490-500

(-) Exons   (0, 0)

(no "Exon" information available for 1US2)

(-) 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:507
 aligned with XY10C_CELJA | Q59675 from UniProtKB/Swiss-Prot  Length:606

    Alignment length:512
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604  
          XY10C_CELJA    95 IEVDMANGWRGNASGSTSHSGITYSADGVTFAALGDGVGAVFDIARPTTLEDAVIAMVVNVSAEFKASEANLQIFAQLKEDWSKGEWDCLAASSELTADTDLTLTCTIDEDDDKFNQTARDVQVGIQAKGTPAGTITIKSVTITLAQEAYSANVDHLRDLAPSDFPIGVAVSNTDSATYNLLTNSREQAVVKKHFNHLTAGNIMKMSYMQPTEGNFNFTNADAFVDWATENNMTVHGHALVWHSDYQVPNFMKNWAGSAEDFLAALDTHITTIVDHYEAKGNLVSWDVVNEAIDDNSPANFRTTDSAFYVKSGNSSVYIERAFQTARAADPAVILYYNDYNIEQNNAKTTKMVDMVKDFQARSIPIDGVGFQMHVCMNYPSIANISAAMKKVVDLGLLVKITELDVAVNQPHCDAYPANKINPLTEAAQLAQKKRYCDVVKAYLDTVPVNQRGGISVWGTTDANTWLDGLYREQFEDEKISWPLLFDNNYNDKPALRGFADALIGTQCTNTH 606
               SCOP domains d1us2a1 A:95-239 Xylan-binding module from xylanase 10c                                                                                             d1us2a2 A:243-606 Xylanase 10c                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1us2A01 A:95-239 Galactose-binding domain-like                                                                                                      -1us2A02 A:244-606 Glycosidases                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.........ee....eeee.....eeeeeee...ee....eeeeeeeehhhhhhh..eeeeeeee..eeeeee.....hhhhh.--..eeeeee........ee....eeeeeeee.....eeeeeeeeee.---.......hhhhhh.....eeeee............hhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...............hhhhhhh....hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhh...eeeeeeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhh.....................hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------------------------GH10_2  PDB: A:245-596 UniProt: 245-596                                                                                                                                                                                                                                                                                                                         ---------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ---------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1us2 A  95 IEVDMANGWRGNASGSTSHSGITYSADGVTFAALGDGVGAVFDIARPTTLEDAVIAMVVNVSAEFKASEANLQIFAQLKEDWSKGEWDCLAASSELT--TDLTLTCTIDEDDDKFNQTARDVQVGIQAKGTPAGTITIKSVTITL---AYSANVDHLRDLAPSDFPIGVAVSNTDSATYNLLTNSREQAVVKKHFNHLTAGNIMKMSYMQPTEGNFNFTNADAFVDWATENNMTVHGHALVWHSDYQVPNFMKNWAGSAEDFLAALDTHITTIVDHYEAKGNLVSWDVVNAAIDDNSPANFRTTDSAFYVKSGNSSVYIERAFQTARAADPAVILYYNDYNIEQNNAKTTKMVDMVKDFQARSIPIDGVGFQMHVCMNYPSIANISAAMKKVVDLGLLVKITELDVAVNQPHCDAYPANKINPLTEAAQLAQKKRYCDVVKAYLDTVPVNQRGGISVWGTTDANTWLDGLYREQFEDEKISWPLLFDNNYNDKPALRGFADALIGTQCTNTH 606
                                   104       114       124       134       144       154       164       174       184      |194       204       214       224       234    |  244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604  
                                                                                                                          191  |                                          239 243                                                                                                                                                                                                                                                                                                                                                                           
                                                                                                                             194
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1US2)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XY10C_CELJA | Q59675)
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:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  1us2
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  XY10C_CELJA | Q59675
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 Related Entries

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

UniProtKB/Swiss-Prot
        XY10C_CELJA | Q59675: 1gny 1us3

(-) Related Entries Specified in the PDB File

1gny XYLAN-BINDING MODULE CBM15
1us3 NATIVE XYLANASE10C FROM CELLVIBRIO JAPONICUS