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(-) Description

Title :  3B' CARBOHYDRATE-BINDING MODULE FROM THE CEL9V GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM THERMOCELLUM. ORTHORHOMBIC STRUCTURE
 
Authors :  S. Petkun, S. Jindou, L. J. W. Shimon, E. A. Bayer, R. Lamed, F. Frolow
Date :  22 Jul 09  (Deposition) - 29 Dec 09  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,C,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Biol. Unit 3:  E  (1x)
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
    Chains: A, C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-28A
    Fragment: CARBOHYDRATE-BINDING MODULE 3B', RESIDUES 731-888
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Synonym: CEL9V GLYCOSIDE HYDROLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ACE
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  C 
Biological Unit 3 (1x):   E

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM 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:2083BINDING SITE FOR RESIDUE CA A 1161
2AC2SOFTWARETHR C:55 , ASP C:57 , ASP C:125 , ASP C:128 , ASP C:129 , HOH C:2069BINDING SITE FOR RESIDUE CA C 1161
3AC3SOFTWARETHR E:55 , ASP E:57 , ASP E:125 , ASP E:128 , ASP E:129 , HOH E:2059BINDING SITE FOR RESIDUE CA E 1161

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:23 -Gly A:24
2Glu C:159 -Ala C:160
3Asp E:23 -Gly E:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WOB)

(-) Exons   (0, 0)

(no "Exon" information available for 2WOB)

(-) Sequences/Alignments

Asymmetric 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:150
 aligned with A3DJ30_CLOTH | A3DJ30 from UniProtKB/TrEMBL  Length:961

    Alignment length:150
                                   749       759       769       779       789       799       809       819       829       839       849       859       869       879       889
         A3DJ30_CLOTH   740 ASISVSYKCGVKDGTKNTIRATINIKNTGTTPVNLSDIKVRYWFTSDGNEQNNFVCDYAAFGTDKVKGIVKKIENSVPGADTYCEISFTEDAGRLAPGGSTGTIPFRIEGAAEYDQTDDYSYNSEMSDDFGDNTKITAYIKDKLKYGVEP 889
               SCOP domains d2woba_ A: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..........eeeeeeeee......hhh.eeeeeee........eeee.........eeeeeee.........eeeeeee...............eeeeee.....hhhhh...hhhhh.........eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wob A  11 ASISVSYKCGVKDGTKNTIRATINIKNTGTTPVNLSDIKVRYWFTSDGNEQNNFVCDYAAFGTDKVKGIVKKIENSVPGADTYCEISFTEDAGRLAPGGSTGTIPFRIEGAAEYDQTDDYSYNSEMSDDFGDNTKITAYIKDKLKYGVEA 160
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160


Chain C from PDB  Type:PROTEIN  Length:153
 aligned with A3DJ30_CLOTH | A3DJ30 from UniProtKB/TrEMBL  Length:961

    Alignment length:153
                                   747       757       767       777       787       797       807       817       827       837       847       857       867       877       887   
         A3DJ30_CLOTH   738 ANASISVSYKCGVKDGTKNTIRATINIKNTGTTPVNLSDIKVRYWFTSDGNEQNNFVCDYAAFGTDKVKGIVKKIENSVPGADTYCEISFTEDAGRLAPGGSTGTIPFRIEGAAEYDQTDDYSYNSEMSDDFGDNTKITAYIKDKLKYGVEPV 890
               SCOP domains d2wobc_ C: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..........eeeeeeeee......hhh.eeeeeee........eeee.........eeeeeee.........eeeeeee...............eeeeee.....hhhhh.................eeee..eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wob C   9 ANASISVSYKCGVKDGTKNTIRATINIKNTGTTPVNLSDIKVRYWFTSDGNEQNNFVCDYAAFGTDKVKGIVKKIENSVPGADTYCEISFTEDAGRLAPGGSTGTIPFRIEGAAEYDQTDDYSYNSEMSDDFGDNTKITAYIKDKLKYGVEAA 161
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158   


Chain E from PDB  Type:PROTEIN  Length:156
 aligned with A3DJ30_CLOTH | A3DJ30 from UniProtKB/TrEMBL  Length:961

    Alignment length:156
                                   746       756       766       776       786       796       806       816       826       836       846       856       866       876       886      
         A3DJ30_CLOTH   737 DANASISVSYKCGVKDGTKNTIRATINIKNTGTTPVNLSDIKVRYWFTSDGNEQNNFVCDYAAFGTDKVKGIVKKIENSVPGADTYCEISFTEDAGRLAPGGSTGTIPFRIEGAAEYDQTDDYSYNSEMSDDFGDNTKITAYIKDKLKYGVEPVTI 892
               SCOP domains d2wobe_ E: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee..........eeeeeeeee......hhh.eeeeeee........eeee.........eeeeeee.........eeeeeee...............eeeeee.....hhhhh...hhhhh.........eeee..eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wob E   8 DANASISVSYKCGVKDGTKNTIRATINIKNTGTTPVNLSDIKVRYWFTSDGNEQNNFVCDYAAFGTDKVKGIVKKIENSVPGADTYCEISFTEDAGRLAPGGSTGTIPFRIEGAAEYDQTDDYSYNSEMSDDFGDNTKITAYIKDKLKYGVEAAAL 163
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157
   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, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WOB)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E   (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 | A3DJ30: 2wnx 2wo4

(-) Related Entries Specified in the PDB File

2wnx 3B' CARBOHYDRATE-BINDING MODULE FROM THE CEL9V GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM THERMOCELLUM
2wo4 3B' CARBOHYDRATE-BINDING MODULE FROM THE CEL9V GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM THERMOCELLUM, IN-HOUSE DATA