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(-) Description

Title :  CARBOHYDRATE BINDING MODULE CBM6 FROM XYLANASE U CLOSTRIDIUM THERMOCELLUM
 
Authors :  M. Czjzek, A. Mosbah, D. Bolam, J. Allouch, V. Zamboni, B. Henrissat, H. J. Gilbert
Date :  19 Sep 01  (Deposition) - 28 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Xylanase, Carbohydrate Binding Module, Cbm Family 6, Xylan Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Czjzek, D. Bolam, A. Mosbah, J. Allouch, C. M. Fontes, L. M. Ferreira, O. Bornet, V. Zamboni, H. Darbon, N. L. Smith, G. W. Black, B. Henrissat, H. J. Gilbert
The Location Of The Ligand-Binding Site Of Carbohydrate-Binding Modules That Have Evolved From A Common Sequence Is Not Conserved.
J. Biol. Chem. V. 276 48580 2001
PubMed-ID: 11673472  |  Reference-DOI: 10.1074/JBC.M109142200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CBM6
    ChainsA
    EC Number3.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET21A
    FragmentXYLAN BINDING MODULE (DOMAIN), RESIDUE 248-380
    Organism ScientificCLOSTRIDIUM THERMOCELLUM
    Organism Taxid1515
    StrainF1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2NA1Ligand/IonSODIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:91 , TRP A:92 , ASN A:93 , SER A:101 , HOH A:2178 , HOH A:2179 , HOH A:2180BINDING SITE FOR RESIDUE SO4 A1130
2AC2SOFTWARETYR A:34 , ILE A:35 , ASP A:64 , PRO A:118 , VAL A:119 , ASN A:120BINDING SITE FOR RESIDUE NA A1131
3AC3SOFTWAREGLU A:8 , GLU A:10 , SER A:30 , ASP A:122 , HOH A:2019BINDING SITE FOR RESIDUE CA A1132

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GMM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GMM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GMM)

(-) Exons   (0, 0)

(no "Exon" information available for 1GMM)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:126
 aligned with O52780_CLOTM | O52780 from UniProtKB/TrEMBL  Length:683

    Alignment length:126
                                   260       270       280       290       300       310       320       330       340       350       360       370      
         O52780_CLOTM   251 FSKIESEEYNSLKSSTIQTIGTSDGGSGIGYIESGDYLVFNKINFGNGANSFKARVASGADTPTNIQLRLGSPTGTLIGTLTVASTGGWNNYEEKSCSITNTTGQHDLYLVFSGPVNIDYFIFDSN 376
               SCOP domains d1gmma_ A: Carbohydrate binding module from xylanase U                                                                         SCOP domains
               CATH domains 1gmmA00 A:4-129 Galactose-binding domain-like                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee.hhh.eee....eeee.....eeee......eeeeeeee....eeeeeeeeee.....eeeeeee.....eeeeeeee....eeeeeeeeeeeeeee..eeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gmm A   4 FSKIESEEYNSLKSSTIQTIGTSDGGSGIGYIESGDYLVFNKINFGNGANSFKARVASGADTPTNIQLRLGSPTGTLIGTLTVASTGGWNNYEEKSCSITNTTGQHDLYLVFSGPVNIDYFIFDSN 129
                                    13        23        33        43        53        63        73        83        93       103       113       123      

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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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GMM)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O52780_CLOTM | O52780)
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: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:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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

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        O52780_CLOTM | O527801uxx

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