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(-) Description

Title :  TYPE II COHESIN-DOCKERIN DOMAIN FROM BACTEROIDES CELLOLOSOLVENS
 
Authors :  A. Viegas, A. L. Carvalho, M. J. Romao, J. A. M. Prates, C. M. G. A. Fontes
Date :  22 Dec 10  (Deposition) - 11 Jan 12  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Structrual Protein-Hydrolase Complex, Cellulosome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Viegas, A. L. Carvalho, J. A. M. Prates, M. J. Romao, C. M. G. A. Fontes
Type Ii Cohesin-Dockerin Domain From Bacteroides Cellolosolvens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CELLULOSOMAL SCAFFOLDIN
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPET21A
    Expression System Vector TypePLASMID
    FragmentRESIDUES 2073-2242
    Organism ScientificBACTEROIDES CELLULOSOLVENS
    Organism Taxid35825
    SynonymTYPE II COHESIN-DOCKERIN
 
Molecule 2 - CELLULOSOMAL FAMILY-48 PROCESSIVE GLYCOSIDE HYDROLASE
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPET21A
    Expression System Vector TypePLASMID
    FragmentRESIDUES 683-752
    Organism ScientificBACTEROIDES CELLULOSOLVENS
    Organism Taxid35825
    SynonymTYPE II COHESIN-DOCKERIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)  CD
Biological Unit 2 (1x)AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/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

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:41 , ASN B:43 , ASP B:45 , VAL B:47 , ASP B:52 , HOH B:2032BINDING SITE FOR RESIDUE CA B1067
2AC2SOFTWAREASP B:8 , ASN B:10 , ASP B:12 , VAL B:14 , ASP B:19 , HOH B:2016BINDING SITE FOR RESIDUE CA B1068
3AC3SOFTWAREASP D:8 , ASN D:10 , ASP D:12 , VAL D:14 , ASP D:19 , HOH D:2010BINDING SITE FOR RESIDUE CA D1065
4AC4SOFTWAREASP D:45 , VAL D:47 , ASP D:52 , HOH D:2014BINDING SITE FOR RESIDUE CA D1066

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y3N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y3N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y3N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y3N)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y3N)

(-) 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:173
 aligned with Q9FDJ9_9FIRM | Q9FDJ9 from UniProtKB/TrEMBL  Length:2319

    Alignment length:173
                                  2081      2091      2101      2111      2121      2131      2141      2151      2161      2171      2181      2191      2201      2211      2221      2231      2241   
        Q9FDJ9_9FIRM   2072 DGSVLTAIDNDKVAVGDKVTLTINVDKITNFSGYQFNIKYNTTYLQPWDTIADEAYTDSTMPDYGTLLQGRFNATDMSKHNLSQGVLNFGRLYMNLSAYRASGKPESTGAVAKVTFKVIKEIPAEGIKLATFENGSSMNNAVDGTMLFDWDGNMYSSSAYKVVQPGLIYPKGT 2244
               SCOP domains d2y3na_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...ee....eeeeeeeee....eeeeeeeee.....eeeee....ee.......ee.........eeeee.......eeeeeeee.hhhhhhhhh.....eeeeeeeeee........ee..ee............eeeee......hhh.eee....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2y3n A    3 SGSVLTAIDNDKVAVGDKVTLTINVDKITNFSGYQFNIKYNTTYLQPWDTIADEAYTDSTMPDYGTLLQGRFNATDMSKHNLSQGVLNFGRLYMNLSAYRASGKPESTGAVAKVTFKVIKEIPAEGIKLATFENGSSMNNAVDGTMLFDWDGNMYSSSAYKVVQPGLIYPKLE  175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172   

Chain B from PDB  Type:PROTEIN  Length:60
 aligned with Q6UB36_9FIRM | Q6UB36 from UniProtKB/TrEMBL  Length:752

    Alignment length:86
                                   671       681       691       701       711       721       731       741      
        Q6UB36_9FIRM    662 MGAFAILFPNDVPPPPITPTPFVKLKGDLNGDGVINMADVMILAQSFGKAIGNPGVNEKADLNNDGVINMADAIILAQYFGKTKSA  747
               SCOP domains d                    2y3nb_ B: automated matches                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------------------..............hhhhhhhhhhh.....------...........hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                2y3n B    1 M--------------------FVKLKGDLNGDGVINMADVMILAQSFGKAI------EKADLNNDGVINSDDAIILAQYFGKTKSA   66
                            |        -         - |      10        20        30|      |40        50        60      
                            |                    2                           31     38                            
                            1                                                                                     

Chain C from PDB  Type:PROTEIN  Length:171
 aligned with Q9FDJ9_9FIRM | Q9FDJ9 from UniProtKB/TrEMBL  Length:2319

    Alignment length:171
                                  2081      2091      2101      2111      2121      2131      2141      2151      2161      2171      2181      2191      2201      2211      2221      2231      2241 
        Q9FDJ9_9FIRM   2072 DGSVLTAIDNDKVAVGDKVTLTINVDKITNFSGYQFNIKYNTTYLQPWDTIADEAYTDSTMPDYGTLLQGRFNATDMSKHNLSQGVLNFGRLYMNLSAYRASGKPESTGAVAKVTFKVIKEIPAEGIKLATFENGSSMNNAVDGTMLFDWDGNMYSSSAYKVVQPGLIYPK 2242
               SCOP domains d2y3nc_ C: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...ee....eeeeeeeee....eeeeeeeee.....eeeee....ee.......ee.........eeeee...hhh.eeeeeeee.hhhhhhhh......eeeeeeeeee........ee..ee..hhhhh.....eeeee....ee....eee....eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2y3n C    3 SGSVLTAIDNDKVAVGDKVTLTINVDKITNFSGYQFNIKYNTTYLQPWDTIADEAYTDSTMPDYGTLLQGRFNATDMSKHNLSQGVLNFGRLYMNLSAYRASGKPESTGAVAKVTFKVIKEIPAEGIKLATFENGSSMNNAVDGTMLFDWDGNMYSSSAYKVVQPGLIYPK  173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 

Chain D from PDB  Type:PROTEIN  Length:49
 aligned with Q6UB36_9FIRM | Q6UB36 from UniProtKB/TrEMBL  Length:752

    Alignment length:84
                                   671       681       691       701       711       721       731       741    
        Q6UB36_9FIRM    662 MGAFAILFPNDVPPPPITPTPFVKLKGDLNGDGVINMADVMILAQSFGKAIGNPGVNEKADLNNDGVINMADAIILAQYFGKTK  745
               SCOP domains d                    2y3nd_ D: automated matches                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .--------------------..............hhhhhhhhhhhh..---------------....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                2y3n D    1 M--------------------FVKLKGDLNGDGVINMADVMILAQSFGK---------------DGVINSDDAIILAQYFGKTK   64
                            |        -         - |      10        20        |-         -    |   50        60    
                            1                    2                         29              45                   

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y3N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y3N)

(-) Gene Ontology  (13, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (Q9FDJ9_9FIRM | Q9FDJ9)
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:0030248    cellulose binding    Interacting selectively and non-covalently with cellulose.
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.

Chain B,D   (Q6UB36_9FIRM | Q6UB36)
molecular function
    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: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: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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9FDJ9_9FIRM | Q9FDJ91tyj 2xbt

(-) Related Entries Specified in the PDB File

1tyj CRYSTAL STRUCTURE ANALYSIS OF TYPE II COHESIN A11 FROMBACTEROIDES CELLULOSOLVENS
2xbt STRUCTURE OF A SCAFFOLDIN CARBOHYDRATE-BINDING MODULE FAMILY 3B FROM THE CELLULOSOME OF BACTEROIDES CELLULOSOLVENS: STRUCTURAL DIVERSITY AND IMPLICATIONS FOR CARBOHYDRATE BINDING