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(-) Description

Title :  3B' CARBOHYDRATE-BINDING MODULE FROM THE CEL9V GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM THERMOCELLUM, IN-HOUSE DATA
 
Authors :  S. Petkun, S. Jindou, L. J. W. Shimon, E. A. Bayer, R. Lamed, F. Frolow
Date :  21 Jul 09  (Deposition) - 29 Dec 09  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Cellulose Degradation, Hydrolase, Glycoside Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Petkun, S. Jindou, L. J. W. Shimon, E. A. Bayer, R. Lamed, F. Frolow
Structure Of A Family 3B' Carbohydrate-Binding Module From The Cel9V Glycoside Hydrolase From Clostridium Thermocellum: Structural Diversity And Implications For Carbohydrate Binding
Acta Crystallogr. , Sect. D V. 66 33 2010
PubMed-ID: 20057047  |  Reference-DOI: 10.1107/S0907444909043030
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCOSIDE HYDROLASE, FAMILY 9
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET-28A
    Expression System Vector TypePLASMID
    FragmentCARBOHYDRATE-BINDING MODULE3B', RESIDUES 731-888
    Organism ScientificCLOSTRIDIUM THERMOCELLUM
    Organism Taxid1515
    SynonymCEL9V GLYCOSIDE HYDROLASE

 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
2CL1Ligand/IonCHLORIDE ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:55 , ASP A:57 , ASP A:125 , ASP A:128 , ASP A:129 , HOH A:2166BINDING SITE FOR RESIDUE CA A1163
2AC2SOFTWARELYS A:22 , ASP A:23 , GLY A:24 , THR A:25 , LYS A:26 , ASN A:27 , THR A:28 , ARG A:30 , HOH A:2035 , HOH A:2209 , HOH A:2210BINDING SITE FOR RESIDUE SO4 A1164
3AC3SOFTWARELYS A:77 , GLU A:100BINDING SITE FOR RESIDUE CL A1165

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WO4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WO4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:PROTEIN  Length:159
 aligned with A3DJ30_CLOTH | A3DJ30 from UniProtKB/TrEMBL  Length:961

    Alignment length:159
                                   742       752       762       772       782       792       802       812       822       832       842       852       862       872       882         
         A3DJ30_CLOTH   733 SQTPDANASISVSYKCGVKDGTKNTIRATINIKNTGTTPVNLSDIKVRYWFTSDGNEQNNFVCDYAAFGTDKVKGIVKKIENSVPGADTYCEISFTEDAGRLAPGGSTGTIPFRIEGAAEYDQTDDYSYNSEMSDDFGDNTKITAYIKDKLKYGVEPVT 891
               SCOP domains d2wo4a_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------CBM_3-2wo4A01 A:15-97                                                              ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.eeeeeee........eeeeeeeeee.....ee...eeeeeee.......eeeee.....hhh.eeeeeeeeeeee..eeeeeeeee.....ee........eeeeeee..........................eeee..eeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wo4 A   4 SQTPDANASISVSYKCGVKDGTKNTIRATINIKNTGTTPVNLSDIKVRYWFTSDGNEQNNFVCDYAAFGTDKVKGIVKKIENSVPGADTYCEISFTEDAGRLAPGGSTGTIPFRIEGAAEYDQTDDYSYNSEMSDDFGDNTKITAYIKDKLKYGVEAAA 162
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153         

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  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  (0, 0)

(no "CATH Domain" information available for 2WO4)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: CBD (21)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A3DJ30_CLOTH | A3DJ30)
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:0030248    cellulose binding    Interacting selectively and non-covalently with cellulose.
    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: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: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/TrEMBL
        A3DJ30_CLOTH | A3DJ302wnx 2wob

(-) Related Entries Specified in the PDB File

2wnx 3B' CARBOHYDRATE-BINDING MODULE FROM THE CEL9V GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM THERMOCELLUM
2wob 3B' CARBOHYDRATE-BINDING MODULE FROM THE CEL9V GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM THERMOCELLUM. ORTHORHOMBIC STRUCTURE