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(-) Description

Title :  CRYSTAL STRUCTURE OF COH-OLPC(CTHE_0452)-DOC435(CTHE_0435) COMPLEX: A NOVEL TYPE I COHESIN-DOCKERIN COMPLEX FROM CLOSTRIDIUM THERMOCELLUM ATTC 27405
 
Authors :  V. D. Alves, A. L. Carvalho, S. H. Najmudin, J. Bras, J. A. M. Prates, C. M. G. A. Fontes
Date :  27 Jan 12  (Deposition) - 28 Nov 12  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cellulosome, Cohesin, Dockerin, Type I Cohesin-Dockerin, Protein- Protein Interaction, Cell Adhesion, Cell Adhesion-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Bras, V. D. Alves, A. L. Carvalho, S. Najmudin, J. A. Prates, L. M. Ferreira, D. N. Bolam, M. J. Romao, H. J. Gilbert, C. M. Fontes
Novel Clostridium Thermocellum Type I Cohesin-Dockerin Complexes Reveal A Single Binding Mode.
J. Biol. Chem. V. 287 44394 2012
PubMed-ID: 23118225  |  Reference-DOI: 10.1074/JBC.M112.407700

(-) Compounds

Molecule 1 - CELLULOSOME ANCHORING PROTEIN COHESIN REGION
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: TUNER CELLS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 99-257
    Gene: CTHE_0452
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 203119
    Strain: ATCC 27405
 
Molecule 2 - DOCKERIN TYPE 1
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: TUNER CELLS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 32-112
    Gene: CTHE_0435
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 203119
    Strain: ATCC 27405

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2SO49Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:14 , LYS A:147 , HOH A:362 , HOH A:443 , HOH A:455 , SER C:125 , SER C:127 , LYS C:130 , HOH C:310 , HOH C:450BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWAREILE A:82 , VAL A:83 , TYR A:84 , LYS A:85 , HOH A:360 , HOH A:409BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWAREASP A:73 , HOH A:385 , HOH A:413BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWAREASP B:9 , ASN B:11 , ASP B:13 , VAL B:15 , ASP B:20 , HOH B:201BINDING SITE FOR RESIDUE CA B 101
05AC5SOFTWAREASP B:45 , ASN B:47 , ASP B:49 , VAL B:51 , ASP B:56 , HOH B:202BINDING SITE FOR RESIDUE CA B 102
06AC6SOFTWAREASN B:47 , TYR B:59 , HOH B:263BINDING SITE FOR RESIDUE SO4 B 103
07AC7SOFTWAREASN B:58 , ARG B:62 , MET B:67 , HOH B:248BINDING SITE FOR RESIDUE SO4 B 104
08AC8SOFTWAREILE C:82 , VAL C:83 , TYR C:84 , LYS C:85 , HOH C:372 , HOH C:444BINDING SITE FOR RESIDUE SO4 C 201
09AC9SOFTWARETHR C:72 , ASP C:73BINDING SITE FOR RESIDUE SO4 C 202
10BC1SOFTWARELYS C:105 , HOH C:334 , HOH C:400 , HOH C:419BINDING SITE FOR RESIDUE SO4 C 203
11BC2SOFTWARESER A:125 , SER A:127 , LYS A:130 , ASP C:14 , LYS C:147 , HOH C:403 , HOH C:424 , HOH C:458BINDING SITE FOR RESIDUE SO4 C 204
12BC3SOFTWAREASP D:9 , ASN D:11 , ASP D:13 , VAL D:15 , ASP D:20 , HOH D:201BINDING SITE FOR RESIDUE CA D 101
13BC4SOFTWAREASP D:45 , ASN D:47 , ASP D:49 , VAL D:51 , ASP D:56 , HOH D:202BINDING SITE FOR RESIDUE CA D 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DH2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DH2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DH2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DH2)

(-) Exons   (0, 0)

(no "Exon" information available for 4DH2)

(-) 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:158
 aligned with A3DCL1_CLOTH | A3DCL1 from UniProtKB/TrEMBL  Length:257

    Alignment length:158
                                                                                                                                                                                     257  
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     |  
         A3DCL1_CLOTH   102 IHEAETADYILDVLVEGVKAKAGDTVEIPLKFENVPSHGIQSFNLSLYYDSKAIEVLKVEPGSIITDPANNFDYNIVYKDSEIVFLFDDDKQKGEGLIKTDGVFAKLTVRIKPDIFKDSGSTKKYSLITFGESNFCDFDLKPILAVLKEGKVEIEK--   -
               SCOP domains d4dh2a_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.eeeeeee..eeee...eeeeeeeee........eeeeeee.....eeeeeeee.....hhhhheeeeeehhh.eeeeeee.............eeeeeeeeee...........eeeeeeeeeeeeee......eeeeee.eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dh2 A   7 IHEAETADYILDVLVEGVKAKAGDTVEIPLKFENVPSHGIQSFNLSLYYDSKAIEVLKVEPGSIITDPANNFDYNIVYKDSEIVFLFDDDKQKGEGLIKTDGVFAKLTVRIKPDIFKDSGSTKKYSLITFGESNFCDFDLKPILAVLKEGKVEIEKLE 164
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156        


Chain B from PDB  Type:PROTEIN  Length:72
 aligned with A3DCJ4_CLOTH | A3DCJ4 from UniProtKB/TrEMBL  Length:350

    Alignment length:72
                                    44        54        64        74        84        94       104  
         A3DCJ4_CLOTH    35 AVIGDVNADGVVNISDYVLMKRYILRIIADFPADDDMWVGDVNGDNVINDIDCNYLKRYLLHMIREFPKNSY 106
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh.........hhhhhhh.......hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 4dh2 B   5 AVIGDVNADGVVNISDYVLMKRYILRIIADFPADDDMWVGDVNGDNVINDIDCNYLKRYLLHMIREFPKNSY  76
                                    14        24        34        44        54        64        74  


Chain C from PDB  Type:PROTEIN  Length:156
 aligned with A3DCL1_CLOTH | A3DCL1 from UniProtKB/TrEMBL  Length:257

    Alignment length:156
                                                                                                                                                                                    257 
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    | 
         A3DCL1_CLOTH   103 HEAETADYILDVLVEGVKAKAGDTVEIPLKFENVPSHGIQSFNLSLYYDSKAIEVLKVEPGSIITDPANNFDYNIVYKDSEIVFLFDDDKQKGEGLIKTDGVFAKLTVRIKPDIFKDSGSTKKYSLITFGESNFCDFDLKPILAVLKEGKVEIEK-   -
               SCOP domains d4dh2c_ C: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.eeeeeee..eeee...eeeeeeeee........eeeeeee.....eeeeeeee.....hhhhheeeeeehhh.eeeeeee.............eeeeeeeeee...........eeeeeeeeeeeeee.....eeeeeee.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dh2 C   8 HEAETADYILDVLVEGVKAKAGDTVEIPLKFENVPSHGIQSFNLSLYYDSKAIEVLKVEPGSIITDPANNFDYNIVYKDSEIVFLFDDDKQKGEGLIKTDGVFAKLTVRIKPDIFKDSGSTKKYSLITFGESNFCDFDLKPILAVLKEGKVEIEKL 163
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157      


Chain D from PDB  Type:PROTEIN  Length:70
 aligned with A3DCJ4_CLOTH | A3DCJ4 from UniProtKB/TrEMBL  Length:350

    Alignment length:70
                                    44        54        64        74        84        94       104
         A3DCJ4_CLOTH    35 AVIGDVNADGVVNISDYVLMKRYILRIIADFPADDDMWVGDVNGDNVINDIDCNYLKRYLLHMIREFPKN 104
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh.........hhhhhhh.......hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4dh2 D   5 AVIGDVNADGVVNISDYVLMKRYILRIIADFPADDDMWVGDVNGDNVINDIDCNYLKRYLLHMIREFPKN  74
                                    14        24        34        44        54        64        74
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DH2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DH2)

(-) Gene Ontology  (4, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (A3DCL1_CLOTH | A3DCL1)
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.
biological process
    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   (A3DCJ4_CLOTH | A3DCJ4)
molecular function
    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: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 Specified in the PDB File

3ul4 CRYSTAL STRUCTURE OF COH-OLPA(CTHE_3080)-DOC918(CTHE_0918) COMPLEX: A NOVEL TYPE I COHESIN-DOCKERIN COMPLEX FROM CLOSTRIDIUM THERMOCELLUM ATTC 27405