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(-) Description

Title :  COMPUTATIONALLY DESIGNED ENDO-1,4-BETA-XYLANASE
 
Authors :  A. Morin, J. M. Harp
Date :  01 Apr 10  (Deposition) - 10 Nov 10  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptide Binding, Jelly-Role, Family 11, Thumb, Glycosidase, Hydrolase, Xylan Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Morin, K. W. Kaufmann, C. Fortenberry, J. M. Harp, L. S. Mizoue, J. Meiler
Computational Design Of An Endo-1, 4-{Beta}-Xylanase Ligand Binding Site.
Protein Eng. Des. Sel. V. 24 503 2011
PubMed-ID: 21349882  |  Reference-DOI: 10.1093/PROTEIN/GZR006

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE
    Chains: A
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 44-234
    Gene: XYN11A
    Mutation: YES
    Organism Scientific: THERMOPOLYSPORA FLEXUOSA
    Organism Taxid: 103836

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:5 , THR A:6 , GLN A:7 , GLN A:9 , HOH A:320 , HOH A:380BINDING SITE FOR RESIDUE SO4 A 193
2AC2SOFTWAREARG A:145 , THR A:146 , HOH A:246 , HOH A:276 , HOH A:317BINDING SITE FOR RESIDUE SO4 A 194
3AC3SOFTWAREARG A:43 , ASN A:44 , PRO A:85 , LEU A:86 , ARG A:132 , HOH A:199 , HOH A:249 , HOH A:353BINDING SITE FOR RESIDUE SO4 A 195

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MF9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:84 -Pro A:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MF9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MF9)

(-) Exons   (0, 0)

(no "Exon" information available for 3MF9)

(-) 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:193
 aligned with Q8GMV7_9ACTN | Q8GMV7 from UniProtKB/TrEMBL  Length:344

    Alignment length:196
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228      
         Q8GMV7_9ACTN    39 GTAHADTTITQNQTGYDNGYFYSFWTDAPGTVSMTLHSGGSYSTSWRNTGNFVAGKGWSTGGRRTVTYNASFNPSGNAYLTLYGWTRNPLVEYYIVESWGTYRPTGTYKGTVTTDGGTYDIYETWRYNAPSIEGTRTFQQFWSVRQQKRTSGTITIGNHFDAWARAGMNLGSHDYQIMATEGYQSSGSSTVSISEG 234
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---..eee...eeeee..eeeeeee.....eeeee....eeeeee....eeeeeeee......eeeeeeeeeeeeeeeeeeeeeee...eeeeeeeee.......eeeeeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeeehhhhhhhhhhh.....eeeeeeeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mf9 A   0 G---SDTTITQNQTGYDNGYFYSFRTDAPGTVSMTLHSGGSYSTSWRNTGLFVAGKGWSTGGRRTVTYNASFNPSGNARLTLYGWTRNPLVSYHIVESWGTYRPTGTYKGTVTTDGGTYDIYETWRYNAPSIEGTRTYQQFWSVRQQKRTSGTITIGNHFDAWARAGMNLGSHDYQIMATEGYQSSGSSTVSISEG 192
                            |   |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186      
                            |   1                                                                                                                                                                                               
                            0
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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 3MF9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MF9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MF9)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8GMV7_9ACTN | Q8GMV7)
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.
    GO:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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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 Related Entries

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

UniProtKB/TrEMBL
        Q8GMV7_9ACTN | Q8GMV7: 1m4w 3b5l 3mf6 3mfa 3mfc

(-) Related Entries Specified in the PDB File

1m4w 3mf6 3mfa 3mfc