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(-) Description

Title :  NATIVE XYLANASE10C FROM CELLVIBRIO JAPONICUS
 
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) - 27 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 PRECURSOR
    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)
    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  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NA2Ligand/IonSODIUM ION
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:369 , GLU A:372 , ALA A:423 , HOH A:2132 , HOH A:2370 , HOH A:2374 , HOH A:2449BINDING SITE FOR RESIDUE NA A1609
2AC2SOFTWAREASN A:290 , HOH A:2045 , HOH A:2046 , HOH A:2316BINDING SITE FOR RESIDUE NA A1610
3AC3SOFTWARELYS A:299 , HIS A:332 , TRP A:336 , ASN A:384 , GLU A:385 , GLN A:466 , GLU A:497 , TRP A:552 , TRP A:560 , HOH A:2387 , HOH A:2680BINDING SITE FOR RESIDUE TRS A1608
4AC4SOFTWAREALA A:264 , VAL A:265 , SER A:266 , GLY A:295 , GLY A:553 , ASN A:558 , HOH A:2138 , HOH A:2610 , HOH A:2678 , HOH A:2679BINDING SITE FOR RESIDUE GOL A1607

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (5, 5)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1US3)

(-) 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 1US3)

(-) 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:482
 aligned with XY10C_CELJA | Q59675 from UniProtKB/Swiss-Prot  Length:606

    Alignment length:509
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597         
          XY10C_CELJA    98 DMANGWRGNASGSTSHSGITYSADGVTFAALGDGVGAVFDIARPTTLEDAVIAMVVNVSAEFKASEANLQIFAQLKEDWSKGEWDCLAASSELTADTDLTLTCTIDEDDDKFNQTARDVQVGIQAKGTPAGTITIKSVTITLAQEAYSANVDHLRDLAPSDFPIGVAVSNTDSATYNLLTNSREQAVVKKHFNHLTAGNIMKMSYMQPTEGNFNFTNADAFVDWATENNMTVHGHALVWHSDYQVPNFMKNWAGSAEDFLAALDTHITTIVDHYEAKGNLVSWDVVNEAIDDNSPANFRTTDSAFYVKSGNSSVYIERAFQTARAADPAVILYYNDYNIEQNNAKTTKMVDMVKDFQARSIPIDGVGFQMHVCMNYPSIANISAAMKKVVDLGLLVKITELDVAVNQPHCDAYPANKINPLTEAAQLAQKKRYCDVVKAYLDTVPVNQRGGISVWGTTDANTWLDGLYREQFEDEKISWPLLFDNNYNDKPALRGFADALIGTQCTNTH 606
               SCOP domains d1us3a1 A:98-238 Xylan-binding module fro           m xylanase 10c                                                                               d1us3a2 A:243-606 Xylanase 10c                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1us3A01 A:98-238 Galactose-binding domain           -like                                                                                        -1us3A02 A:244-606 Glycosidases                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.........eee..eeeee.....eeeeeee-----------.eeeeehhhhhhhh.eeeeeeee......-......hhhhh.---.eee...------.....--.eeeeeeee.....eeeeeee...----.......hhhhhh.....eeeee............hhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...............hhhhhhh...hhhhhhhhhhhhhhh...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
                 1us3 A  98 DMANGWRGNASGSTSHSGITYSADGVTFAALGDGVGAVFDI-----------AMVVNVSAEFKASEANLQIFAQLKEDWSK-EWDCLAASSELT---DLTLTCT------KFNQT--DVQVGIQAKGTPAGTITIKSVTIT----AYSANVDHLRDLAPSDFPIGVAVSNTDSATYNLLTNSREQAVVKKHFNHLTAGNIMKMSYMQPTEGNFNFTNADAFVDWATENNMTVHGHALVWHSDYQVPNFMKNWAGSAEDFLAALDTHITTIVDHYEAKGNLVSWDVVNEAIDDNSPANFRTTDSAFYVKSGNSSVYIERAFQTARAADPAVILYYNDYNIEQNNAKTTKMVDMVKDFQARSIPIDGVGFQMHVCMNYPSIANISAAMKKVVDLGLLVKITELDVAVNQPHCDAYPANKINPLTEAAQLAQKKRYCDVVKAYLDTVPVNQRGGISVWGTTDANTWLDGLYREQFEDEKISWPLLFDNNYNDKPALRGFADALIGTQCTNTH 606
                                   107       117       127       137|        -  |    157       167       177| |    187   |   197   |     -|   |  217       227       237|    | 247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597         
                                                                  138         150                         178 |        191 195   201    208 212  |                    238  243                                                                                                                                                                                                                                                                                                                                                                           
                                                                                                            180                                215
   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  (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 1US3)

(-) 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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  1us3
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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 1us2

(-) Related Entries Specified in the PDB File

1gny XYLAN-BINDING MODULE CBM15
1us2 XYLANASE10C (MUTANT E385A) FROM CELLVIBRIO JAPONICUS IN COMPLEX WITH XYLOPENTAOSE