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(-) Description

Title :  THE COMPLEX STRUCTURE OF CDBFV E109A WITH XYLOTRIOSE
 
Authors :  Y. S. Cheng, C. C. Chen, C. H. Huang, T. Y. Huang, T. P. Ko, J. W. Huang, T. H. J. R. Liu, R. T. Guo
Date :  09 Jan 14  (Deposition) - 19 Mar 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym./Biol. Unit :  A
Keywords :  Xylanase, Regulatory N-Terminal Region, Disulfide Bond, Industrial Enzyme, Beta-Jellyroll Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. S. Cheng, C. C. Chen, C. H. Huang, T. P. Ko, W. Luo, J. W. Huang, J. R. Liu R. T. Guo
Structural Analysis Of A Glycoside Hydrolase Family 11 Xylanase From Neocallimastix Patriciarum: Insights Into The Molecular Basis Of A Thermophilic Enzyme
J. Biol. Chem. 2014
PubMed: search  |  Reference-DOI: 10.1074/JBC.M114.550905

(-) Compounds

Molecule 1 - CDBFV
    Chains: A
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Plasmid: PPICZALPHAA
    Expression System Strain: X33
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Organism Scientific: NEOCALLIMASTIX PATRICIARUM
    Organism Taxid: 4758
    Synonym: XYLANASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BXP1Ligand/Ion4-O-BETA-D-XYLOPYRANOSYL-BETA-D-XYLOPYRANOSE
2XYP3Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:30 , TRP A:32 , LEU A:59 , ARG A:61 , TYR A:100 , TRP A:102 , PRO A:151 , SER A:152 , ILE A:153 , HOH A:645 , HOH A:657 , HOH A:713 , HOH A:782 , HOH A:848BINDING SITE FOR RESIDUE BXP A 501
2AC2SOFTWAREGLN A:12 , GLY A:25 , GLY A:26 , SER A:44 , ASP A:57 , GLY A:93 , TYR A:94 , TYR A:96 , TYR A:111 , TRP A:125 , ARG A:148 , GLN A:161 , GLU A:202 , VAL A:206 , HOH A:626 , HOH A:645 , HOH A:671 , HOH A:740 , HOH A:817 , HOH A:840BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 502 TO 504

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:172
2A:50 -A:60

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:105 -Pro A:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WP6)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH11_3PS51761 Glycosyl hydrolases family 11 (GH11) domain profile.XYNC_NEOPA34-234  1A:15-215
2GH11_1PS00776 Glycosyl hydrolases family 11 (GH11) active site signature 1.XYNC_NEOPA125-135  1A:106-116

(-) Exons   (0, 0)

(no "Exon" information available for 3WP6)

(-) 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:228
 aligned with XYNC_NEOPA | Q9UV68 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:228
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236        
           XYNC_NEOPA    17 TLAQSFCSSASHSGQSVKETGNKVGTIGGVGYELWADSGNNSATFYSDGSFSCTFQNAGDYLCRSGLSFDSTKTPSQIGRMKADFKLVKQNISNVGYSYVGVYGWTRSPLVEYYIVDNWLSPSPPGDWVGNKKHGSFTIDGAQYTVYENTRTGPSIDGNTTFKQYFSIRQQARDCGTIDISAHFDQWEKLGMTMGKLHEAKVLGEAGNGNGGVSGTADFPYAKVYIGD 244
               SCOP domains d3wp6a_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhh.....eeee...eeeee..eeeeeee.....eeeee....eeeeeeee.eeeeeeeee.....hhhhhh.eeeeeeeeeeeee...eeeeeeeeeee...eeeeeeee.......hhhhh.eeeeeeee..eeeeeeeeeeee......eeeeeeeeee.....eeeeehhhhhhhhhhh.....ee.eeeeeeeee.....eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------GH11_3  PDB: A:15-215 UniProt: 34-234                                                                                                                                                                    ---------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------GH11_1     ------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wp6 A  -3 AEFQSFCSSASHSGQSVKVTGNKVGTIGGVGYELWADSGNNSATFYSDGSFSCTFQNAGDYLCRSGLSFDSTKTPSQIGRMKADFKLVKQNSSNVGYSYVGVYGWTRSPLVAYYIVDNWLSPFPPGDWVGNKKHGSFTIDGAQYTVYENTRTGPSIDGDTTFNQYFSIRQQARDCGTIDISAHFDQWEKLGMTMGKLHEAKVLGEAGNVNGGASGTADFPYAKVYIGD 225
                              ||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217        
                             -1|                                                                                                                                                                                                                                
                               1
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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  (0, 0)

(no "CATH Domain" information available for 3WP6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WP6)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYNC_NEOPA | Q9UV68)
molecular function
    GO:0030248    cellulose binding    Interacting selectively and non-covalently with cellulose.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNC_NEOPA | Q9UV68: 3wp4 3wp5

(-) Related Entries Specified in the PDB File

3wp4
3wp5 THE COMPLEX STRUCTURE OF THE SAME PROTEIN WITH XYLOTRIOSE