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(-) Description

Title :  THE CLOSTRIDIUM CELLULOLYTICUM DOCKERIN DISPLAYS A DUAL BINDING MODE FOR ITS COHESIN PARTNER
 
Authors :  B. A. Pinheiro, J. A. M. Prates, M. R. Proctor, H. J. Gilbert, G. J. Davies, V. A. Money, C. Martinez-Fleites, E. A. Bayer, C. M. G. A. Fontes, H. P. Fierobe
Date :  31 Jan 08  (Deposition) - 13 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Adhesion, Carbohydrate Metabolism, Polysaccharide Degradation, Hydrolase, Glycosidase, Cellulose Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Pinheiro, M. R. Proctor, C. Martinez-Fleites, J. A. M. Prates, V. A. Money, G. J. Davies, E. A. Bayer, C. M. G. A. Fontes, H. P. Fierobe, H. J. Gilbert
The Clostridium Cellulolyticum Dockerin Displays A Dual Binding Mode For Its Cohesin Partner.
J. Biol. Chem. V. 283 18422 2008
PubMed-ID: 18445585  |  Reference-DOI: 10.1074/JBC.M801533200

(-) Compounds

Molecule 1 - SCAFFOLDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET22B
    Fragment: RESIDUES 277-427
    Organism Scientific: CLOSTRIDIUM CELLULOLYTICUM
    Organism Taxid: 1521
    Synonym: COHESIN
 
Molecule 2 - ENDOGLUCANASE A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET22B
    Fragment: RESIDUES 410-473
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM CELLULOLYTICUM
    Organism Taxid: 1521
    Synonym: DOCKERIN, ENDO-1,4-BETA-GLUCANASE A, EGCCA, CELLULASE A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:38 , ASN B:40 , ASP B:42 , GLU B:44 , ASP B:49 , HOH B:2069BINDING SITE FOR RESIDUE CA B1066
2AC2SOFTWAREASP B:7 , ASN B:9 , ASP B:11 , ASN B:13 , ASP B:18 , HOH B:2030BINDING SITE FOR RESIDUE CA B1067

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VN6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VN6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VN6)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CLOS_CELLULOSOME_RPTPS00448 Clostridium cellulosome enzymes repeated domain signature.GUNA_CLOCE415-434
446-465		  2B:7-26
B:38-57
2EF_HAND_1PS00018 EF-hand calcium-binding domain.GUNA_CLOCE415-427  1B:7-19

(-) Exons   (0, 0)

(no "Exon" information available for 2VN6)

(-) 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
(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:151
 aligned with Q45996_9FIRM | Q45996 from UniProtKB/TrEMBL  Length:1546

    Alignment length:151
                                   286       296       306       316       326       336       346       356       366       376       386       396       406       416       426 
         Q45996_9FIRM   277 TVLPKDIPGDSLKVTVGTANGKPGDTVTVPVTFADVAKMKNVGTCNFYLGYDASLLEVVSVDAGPIVKNAAVNFSSSASNGTISFLFLDNTITDELITADGVFANIKFKLKSVTAKTTTPVTFKDGGAFGDGTMSKIASVTKTNGSVTIDP 427
               SCOP domains d2vn6a_ A: Cohesin domain                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....eeeee.eeee....eeeeeeeee.........eeeeeee.....eeeeeeee.....hhhhheeeeee..eeeeeee............eeeeeeeeee......eeeeeeeeeeeeee.........eeee.eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vn6 A   2 TVLPKDIPGDSLKVTVGTANGKPGDTVTVPVTFADVAKMKNVGTCNFYLGYDASLLEVVSVDAGPIVKNAAVNFSSSASNGTISFLFLDNTITDELITADGVFANIKFKLKSVTAKTTTPVTFKDGGAFGDGTMSKIASVTKTNGSVTIDP 152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 


Chain B from PDB  Type:PROTEIN  Length:64
 aligned with GUNA_CLOCE | P17901 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:64
                                   419       429       439       449       459       469    
           GUNA_CLOCE   410 VIVYGDYNNDGNVDALDFAGLKKYIMAADHAYVKNLDVNLDNEVNAFDLAILKKYLLGMVSKLP 473
               SCOP domains d2vn6b_ B: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------Dockerin_1-2vn6B01   ------- Pfam domains (1)
           Pfam domains (2) ------------------------------------Dockerin_1-2vn6B02   ------- Pfam domains (2)
         Sec.struct. author .............hhhhhhhhhhhhhh.....hhhhh.......hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----CLOS_CELLULOSOME_RPT-----------CLOS_CELLULOSOME_RPT-------- PROSITE (1)
                PROSITE (2) -----EF_HAND_1    ---------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------- Transcript
                 2vn6 B   2 VIVYGDYNNDGNVDSTDFAGLKKYIMAADHAYVKNLDVNLDNEVNAFDLAILKKYLLGMVSKLE  65
                                    11        21        31        41        51        61
   Legend:   → Mismatch (orange background)
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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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VN6)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (11, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q45996_9FIRM | Q45996)
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.
    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.

Chain B   (GUNA_CLOCE | P17901)
molecular function
    GO:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
    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.
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: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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  2vn6
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  Q45996_9FIRM | Q45996
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 Related Entries

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

UniProtKB/Swiss-Prot
        GUNA_CLOCE | P17901: 1edg 2vn5
UniProtKB/TrEMBL
        Q45996_9FIRM | Q45996: 1ehx 1g1k 1g43 2vn5

(-) Related Entries Specified in the PDB File

1edg SINGLE CRYSTAL STRUCTURE DETERMINATION OF THE CATALYTIC DOMAIN OF CELCCA CARRIED OUT AT 15 DEGREE C
1ehx NMR SOLUTION STRUCTURE OF THE LAST UNKNOWN MODULE OF THECELLULOSOMAL SCAFFOLDIN PROTEIN CIPC OF CLOSTRIDUMCELLULOLYTICUM
1g1k COHESIN MODULE FROM THE CELLULOSOME OF CLOSTRIDIUMCELLULOLYTICUM
1g43 CRYSTAL STRUCTURE OF A FAMILY IIIA CBD FROM CLOSTRIDIUMCELLULOLYTICUM
2vn5 THE CLOSTRIDIUM CELLULOLYTICUM DOCKERIN DISPLAYS A DUAL BINDING MODE FOR ITS COHESIN PARTNER