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(-) Description

Title :  CARBOHYDRATE-BINDING MODULE CBM3B FROM THE CELLULOSOMAL CELLOBIOHYDROLASE 9A FROM CLOSTRIDIUM THERMOCELLUM
 
Authors :  O. Yaniv, S. Petkun, L. J. W. Shimon, E. A. Bayer, R. Lamed, F. Frolow
Date :  02 Jun 11  (Deposition) - 25 Apr 12  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Hydrolase, Cellulose Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Yaniv, S. Petkun, L. J. W. Shimon, E. A. Bayer, R. Lamed, F. Frolow
A Single Mutation Reforms The Binding Activity Of An Adhesion-Deficient Family 3 Carbohydrate-Binding Module
Acta Crystallogr. , Sect. D V. 68 819 2012
PubMed-ID: 22751667  |  Reference-DOI: 10.1107/S0907444912013133

(-) Compounds

Molecule 1 - CELLULOSE 1,4-BETA-CELLOBIOSIDASE
    Atcc: 27405
    Chains: A, B, C, D
    EC Number: 3.2.1.91
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: RIL
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: FAMILY 3B CARBOHYDRATE BINDING MODULE, RESIDUES 1004-1147
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2YLK)

(-) Sites  (0, 0)

(no "Site" information available for 2YLK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:73 -Asp A:74
2Gly B:73 -Asp B:74
3Gly C:73 -Asp C:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YLK)

(-) 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:145
 aligned with Q59325_CLOTM | Q59325 from UniProtKB/TrEMBL  Length:1230

    Alignment length:145
                                  1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142     
        Q59325_CLOTM   1003 RDVKVQYLCENTQTSTQEIKGKFNIVNTGNRDYSLKDIVLRYYFTKEHNSQLQFICYYTPIGSGNLIPSFGGSGDEHYLQLEFKDVKLPAGGQTGEIQFVIRYADNSFHDQSNDYSFDPTIKAFQDYGKVTLYKNGELVWGTPPG 1147
               SCOP domains d2ylka_ A: automated matches                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....ee.eeeeeeeeee.....ee...eeeeee........eeee......hhh.eeeeee......eeeeee...ee....eeeeeeeeeee.....ee.hhh..........ee...eeeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ylk A    0 MDVKVQYLCENTQTSQQEIKGKFNIVNTGNRDYSLKDIVLRYYFTKEHNSQLQFICYYTPIGSGNLIPSFGGSGDEHYLQLEFKDVKLPAGGQTGEIQFVIRYADNSFHDQSNDYSFDPTIKAFQDYGKVTLYKNGELVWGTPPG  144
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139     


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with Q59325_CLOTM | Q59325 from UniProtKB/TrEMBL  Length:1230

    Alignment length:144
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143    
        Q59325_CLOTM   1004 DVKVQYLCENTQTSTQEIKGKFNIVNTGNRDYSLKDIVLRYYFTKEHNSQLQFICYYTPIGSGNLIPSFGGSGDEHYLQLEFKDVKLPAGGQTGEIQFVIRYADNSFHDQSNDYSFDPTIKAFQDYGKVTLYKNGELVWGTPPG 1147
               SCOP domains d2ylkb_ B: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.....ee..eeeeeeeee.....ee...eeeeee........eeee......hhh.eeeeee......eeeeee...ee....eeeeeeeeeee.....ee.hhh..........ee...eeeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ylk B    1 DVKVQYLCENTQTSQQEIKGKFNIVNTGNRDYSLKDIVLRYYFTKEHNSQLQFICYYTPIGSGNLIPSFGGSGDEHYLQLEFKDVKLPAGGQTGEIQFVIRYADNSFHDQSNDYSFDPTIKAFQDYGKVTLYKNGELVWGTPPG  144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain C from PDB  Type:PROTEIN  Length:144
 aligned with Q59325_CLOTM | Q59325 from UniProtKB/TrEMBL  Length:1230

    Alignment length:144
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143    
        Q59325_CLOTM   1004 DVKVQYLCENTQTSTQEIKGKFNIVNTGNRDYSLKDIVLRYYFTKEHNSQLQFICYYTPIGSGNLIPSFGGSGDEHYLQLEFKDVKLPAGGQTGEIQFVIRYADNSFHDQSNDYSFDPTIKAFQDYGKVTLYKNGELVWGTPPG 1147
               SCOP domains d2ylkc_ C: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.....ee..eeeeeeeee.....ee...eeeeeee.......eeee......hhh.eeeeeee....eeeeeee...ee........eeeeeee.....ee.hhh..........ee...eeeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ylk C    1 DVKVQYLCENTQTSQQEIKGKFNIVNTGNRDYSLKDIVLRYYFTKEHNSQLQFICYYTPIGSGNLIPSFGGSGDEHYLQLEFKDVKLPAGGQTGEIQFVIRYADNSFHDQSNDYSFDPTIKAFQDYGKVTLYKNGELVWGTPPG  144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain D from PDB  Type:PROTEIN  Length:144
 aligned with Q59325_CLOTM | Q59325 from UniProtKB/TrEMBL  Length:1230

    Alignment length:144
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143    
        Q59325_CLOTM   1004 DVKVQYLCENTQTSTQEIKGKFNIVNTGNRDYSLKDIVLRYYFTKEHNSQLQFICYYTPIGSGNLIPSFGGSGDEHYLQLEFKDVKLPAGGQTGEIQFVIRYADNSFHDQSNDYSFDPTIKAFQDYGKVTLYKNGELVWGTPPG 1147
               SCOP domains d2ylkd_ D: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.....ee.eeeeeeeeee.....ee...eeeeee........eeee......hhh.eeeeee.hhhh.eeeeee...ee........eeeeeee.....ee.hhh..........ee...eeeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ylk D    1 DVKVQYLCENTQTSQQEIKGKFNIVNTGNRDYSLKDIVLRYYFTKEHNSQLQFICYYTPIGSGNLIPSFGGSGDEHYLQLEFKDVKLPAGGQTGEIQFVIRYADNSFHDQSNDYSFDPTIKAFQDYGKVTLYKNGELVWGTPPG  144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q59325_CLOTM | Q59325)
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:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
    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: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.

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  Cis Peptide Bonds
    Gly A:73 - Asp A:74   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q59325_CLOTM | Q59325: 1rq5 3zqx 4c8x

(-) Related Entries Specified in the PDB File

3zqx CARBOHYDRATE-BINDING MODULE CBM3B FROM THE CELLULOSOMAL CELLOBIOHYDROLASE 9A FROM CLOSTRIDIUM THERMOCELLUM