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(-) Description

Title :  CRYSTAL STRUCTURE OF A GLYCOSIDE HYDROLASE FAMILY 11 XYLANASE FROM ASPERGILLUS NIGER IN COMPLEX WITH XYLOPENTAOSE
 
Authors :  E. Vandermarliere, S. Rombouts, S. V. Strelkov, J. A. Delcour, C. M. Courtin, A. Rabijns
Date :  16 Aug 07  (Deposition) - 25 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycoside Hydrolase, Xylanase, Glycosidase, Xylan Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Vandermarliere, T. M. Bourgois, S. Rombouts, S. Van Campenhout, G. Volckaert, S. V. Strelkov, J. A. Delcour, A. Rabijns, C. M. Courtin
Crystallographic Analysis Shows Substrate Binding At The -3 To +1 Active-Site Subsites And At The Surface Of Glycoside Hydrolase Family 11 Endo-1, 4-Beta-Xylanases.
Biochem. J. V. 410 71 2008
PubMed-ID: 17983355  |  Reference-DOI: 10.1042/BJ20071128
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE I
    Chains: A
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Mutation: YES
    Organism Scientific: ASPERGILLUS NIGER
    Organism Taxid: 5061
    Synonym: XYLANASE I, 1,4- BETA-D-XYLAN XYLANOHYDROLASE I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2XYP6Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:8 , TYR A:70 , PRO A:119 , SER A:120 , TYR A:164 , XYP A:1136BINDING SITE FOR RESIDUE XYP A 1135
2AC2SOFTWAREASP A:37 , TYR A:70 , GLU A:79 , TYR A:81 , PRO A:119 , GLN A:129 , XYP A:1135BINDING SITE FOR RESIDUE XYP A 1136
3AC3SOFTWAREASN A:13 , LEU A:14 , GLY A:15 , TYR A:102 , XYP A:1138BINDING SITE FOR RESIDUE XYP A 1137
4AC4SOFTWARETYR A:29 , TRP A:30 , GLU A:31 , ASP A:32 , XYP A:1137 , XYP A:1139BINDING SITE FOR RESIDUE XYP A 1138
5AC5SOFTWAREASP A:16 , GLU A:31 , XYP A:1138 , XYP A:1140BINDING SITE FOR RESIDUE XYP A 1139
6AC6SOFTWAREXYP A:1139BINDING SITE FOR RESIDUE XYP A 1140
7AC7SOFTWARETHR A:53 , SER A:183 , HOH A:1157BINDING SITE FOR RESIDUE NA A 1141

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:92 -A:111

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:1 -Ala A:2
2Ala A:2 -Gly A:3
3Tyr A:75 -Pro A:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QZ2)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH11_1PS00776 Glycosyl hydrolases family 11 (GH11) active site signature 1.XYNA_ASPNG103-113  1A:76-86
2GH11_2PS00777 Glycosyl hydrolases family 11 (GH11) active site signature 2.XYNA_ASPNG194-205  1A:168-178

(-) Exons   (0, 0)

(no "Exon" information available for 2QZ2)

(-) 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    
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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:183
 aligned with XYNA_ASPNG | P55329 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:183
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207   
           XYNA_ASPNG    28 SAGINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSKAITYSAEYSASGSSSYLAVYGWVNYPQAEYYIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAQHGFGNSDFNYQVMAVEAWSGAGSASVTIS 210
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qz2A00 A:1-183  [code=2.60.120.180, no name defined]                                                                                                                                   CATH domains
               Pfam domains Glyco_hydro_11-2qz2A01 A:1-182                                                                                                                                                        - Pfam domains
         Sec.struct. author .....eeeeehhhhheeeee....eeeeee.......eeeeeee.......eeeeeeee...eeeeeeeeeee....eeeeeeeee...hhhhh.eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeee.....eeeehhhhhhhhhhhhh.....eeeeeeeeeeeee.eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------GH11_1     --------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qz2 A   1 SAGINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSNAITYSAEYSASGSSSYLAVYGWVNYPQAEYYIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAQHGFGNSDFNYQVVAVAAWSGAGSASVTIS 183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
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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  (0, 0)

(no "SCOP Domain" information available for 2QZ2)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYNA_ASPNG | P55329)
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: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)

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        XYNA_ASPNG | P55329: 1t6g 1ukr

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