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(-) Description

Title :  CELLULOMONAS FIMI XYLANASE/CELLULASE CEX (CF XYN10A) IN COMPLEX WITH SULFUR SUBSTITUTED BETA-1,4 XYLOTETRAOSE
 
Authors :  D. A. Kuntz, M. Saul, D. R. Rose
Date :  16 Apr 08  (Deposition) - 21 Apr 09  (Release) - 21 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Cex, Xylanase, Isofagomine Inhibitor, Tim Barrel, Cellulose Degradation, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. K. Y. Poon, I. D. D'Angelo, D. A. Kuntz, T. Kantner, M. L. Ludkiwzek, C. Tarling, D. R. Rose, M. Saul, L. P. Mcintosh, S. G. Withers
Probing The Binding Sites Of Family 10 And 11 Xylanases With Extended Oligosaccharides
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXO-BETA-1,4-GLUCANASE
    ChainsA
    EC Number3.2.1.91
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC12
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 43-357
    GeneCEX
    Organism ScientificCELLULOMONAS FIMI
    Organism Taxid1708
    SynonymCELLULOMONAS FIMI FAMILY 10 XYLANASE/CELLULASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1X4S1Ligand/IonBETA-D-XYLOPYRANOSYL-(1->4)-4-THIO-BETA-D-XYLOPYRANOSYL-(1->4)-4-THIO-BETA-D-XYLOPYRANOSYL-(1->4)-4-THIO-BETA-D-XYLOPYRANOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:43 , ASN A:44 , LYS A:47 , TRP A:84 , GLN A:87 , GLU A:127 , TYR A:171 , GLN A:203 , HIS A:205 , GLU A:233 , TRP A:273 , TRP A:281 , PHE A:286 , HOH A:435 , HOH A:436 , HOH A:558 , HOH A:588 , HOH A:633 , HOH A:777BINDING SITE FOR RESIDUE X4S A 316

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:167 -A:199
2A:261 -A:267

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:80 -Thr A:81
2Thr A:240 -Pro A:241

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH10_1PS00591 Glycosyl hydrolases family 10 (GH10) active site.GUX_CELFI267-277  1A:226-236

(-) Exons   (0, 0)

(no "Exon" information available for 3CUI)

(-) 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:314
 aligned with GUX_CELFI | P07986 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:314
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351    
            GUX_CELFI    42 ATTLKEAADGAGRDFGFALDPNRLSEAQYKAIADSEFNLVVAENAMKWDATEPSQNSFSFGAGDRVASYAADTGKELYGHTLVWHSQLPDWAKNLNGSAFESAMVNHVTKVADHFEGKVASWDVVNEAFADGDGPPQDSAFQQKLGNGYIETAFRAARAADPTAKLCINDYNVEGINAKSNSLYDLVKDFKARGVPLDCVGFQSHLIVGQVPGDFRQNLQRFADLGVDVRITELDIRMRTPSDATKLATQAADYKKVVQACMQVTRCQGVTVWGITDKYSWVPDVFPGEGAALVWDASYAKKPAYAAVMEAFGA 355
               SCOP domains d3cuia_ A: Xylanase A, catalytic core                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3cuiA00 A:1-314 Glycosidases                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhhh.eeeeeeeee....hhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeeeee............hhhhhhhh.hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhh....eeee..eee......hhhhhhhhhhh...eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhh..ee...........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cui A   1 ATTLKEAADGAGRDFGFALDPNRLSEAQYKAIADSEFNLVVAENAMKWDATEPSQNSFSFGAGDRVASYAADTGKELYGHTLVWHSQLPDWAKNLNGSAFESAMVNHVTKVADHFEGKVASWDVVNEAFADGGGRRQDSAFQQKLGNGYIETAFRAARAADPTAKLCINDYNVEGINAKSNSLYDLVKDFKARGVPLDCVGFQSHLIVGQVPGDFRQNLQRFADLGVDVRITELDIRMRTPSDATKLATQAADYKKVVQACMQVTRCQGVTVWGITDKYSWVPDVFPGEGAALVWDASYAKKPAYAAVMEAFGA 314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310    

Chain A from PDB  Type:PROTEIN  Length:314
 aligned with Q59277_CELFI | Q59277 from UniProtKB/TrEMBL  Length:485

    Alignment length:314
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352    
         Q59277_CELFI    43 ATTLKEAADGAGRDFGFALDPNRLSEAQYKAIADSEFNLVVAENAMKWDATEPSQNSFSFGAGDRVASYAADTGKELYGHTLVWHSQLPDWAKNLNGSAFESAMVNHVTKVADHFEGKVASWDVVNEAFADGGGRRQDSAFQQKLGNGYIETAFRAARAADPTAKLCINDYNVEGINAKSNSLYDLVKDFKARGVPLDCVGFQSHLIVGQVPGDFRQNLQRFADLGVDVRITELDIRMRTPSDATKLATQAADYKKVVQACMQVTRCQGVTVWGITDKYSWVPDVFPGEGAALVWDASYAKKPAYAAVMEAFGA 356
               SCOP domains d3cuia_ A: Xylanase A, catalytic core                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3cuiA00 A:1-314 Glycosidases                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhhh.eeeeeeeee....hhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeeeee............hhhhhhhh.hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhh....eeee..eee......hhhhhhhhhhh...eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhh..ee...........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cui A   1 ATTLKEAADGAGRDFGFALDPNRLSEAQYKAIADSEFNLVVAENAMKWDATEPSQNSFSFGAGDRVASYAADTGKELYGHTLVWHSQLPDWAKNLNGSAFESAMVNHVTKVADHFEGKVASWDVVNEAFADGGGRRQDSAFQQKLGNGYIETAFRAARAADPTAKLCINDYNVEGINAKSNSLYDLVKDFKARGVPLDCVGFQSHLIVGQVPGDFRQNLQRFADLGVDVRITELDIRMRTPSDATKLATQAADYKKVVQACMQVTRCQGVTVWGITDKYSWVPDVFPGEGAALVWDASYAKKPAYAAVMEAFGA 314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310    

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GUX_CELFI | P07986)
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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016162    cellulose 1,4-beta-cellobiosidase activity    Catalysis of the hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains.
    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:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    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.

Chain A   (Q59277_CELFI | Q59277)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GUX_CELFI | P079861exg 1exh 1exp 1fh7 1fh8 1fh9 1fhd 1j01 2exo 2his 2xyl 3cuf 3cug 3cuh 3cuj
        Q59277_CELFI | Q592773cuf 3cug 3cuh 3cuj

(-) Related Entries Specified in the PDB File

1fh7 CEX COMPLEXED WITH XYLOBIOSE DEOXYNOJIRIMYCIN
1fh8 CEX COMPLEXED WITH XYLOBIOSE ISOFAGOMINE
1fh9 CEX COMPLEXED WITH XYLOBIOSE LACTAM OXIME
1fhd CEX COMPLEXED WITH XYLOBIOSE IMIDAZOLE
3cuf CEX COMPLEXED WITH CELLOBIOSE-LIKE IMIDAZOLE
3cug CEX COMPLEXED WITH CELLOTETRAOSE-LIKE IMIDAZOLE
3cuh CEX COMPLEXED WITH CELLOTRIOSE-LIKE IMIDAZOLE
3cuj CEX COMPLEXED WITH THIO-XYLO PENTAOSE