Summary: Dockerin type I repeat
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Dockerin Edit Wikipedia article
Structure of the Dockerin type I domain from C. thermocellum cellulosome.
Dockerin is a protein domain found in the cellulosome cellular structure of anaerobic bacteria. It is found on many endoglucanase enzymes. The dockerin's binding partner is the cohesin domain, located on the scaffoldin protein. This interaction between the dockerin domains of the enzyme constituents of the cellulosome and the cohesin domains of the scaffoldin protein is essential to the construction of the cellulosome complex. The Dockerin domain has two in-tandem repeats of a non-EF hand calcium binding motif. Each motif is characterized by a loop-helix structure. The three-dimensional structure of dockerin has been determined in solution, as well as in complex with Cohesin.
There are three types of Dockerin domains: I, II and III which bind to Cohesin Type I, Cohesin Type II and Cohesin Type III respectively. A type I dockerin domain is 65-70 residues long. The binding specificity of Type I interaction was well studied by structural and mutagenesis studies. Type II interaction is less well characterized.
- Ding SY, Rincon MT, Lamed R, Martin JC, McCrae SI, Aurilia V, et al. (2001). "Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens.". J Bacteriol. 183 (6): 1945–53. doi:10.1128/JB.183.6.1945-1953.2001. PMC . PMID 11222592.
- SCOP 63447
- doi:10.1006/jmbi.2001.4522. PMID 11273698.; Lytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH (March 2001). "Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain". J. Mol. Biol. 307 (3): 745–53.
- Gilbert, H. J.; Davies, G. J.; Ferreira, L. M. A.; Romao, M. J.; Fontes, C. M. G. A. (2003). "Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex". Proceedings of the National Academy of Sciences. 100 (24): 13809–13814. doi:10.1073/pnas.1936124100. PMC . PMID 14623971.; Carvalho, A. L.; Dias, F. M. V.; Prates, J. A. M.; Nagy, T.;
- InterPro: InterPro: IPR016134
- Adams JJ, Webb BA, Spencer HL, Smith SP (February 2005). "Structural characterization of type II dockerin module from the cellulosome of Clostridium thermocellum: calcium-induced effects on conformation and target recognition". Biochemistry. 44 (6): 2173–82. doi:10.1021/bi048039u. PMID 15697243.
- Lytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH (2001). "Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain". J Mol Biol. 307 (3): 745–753. doi:10.1006/jmbi.2001.4522. PMID 11273698.
- Bayer EA, Shimon LJ, Shoham Y, Lamed R (1998). "Cellulosomes-structure and ultrastructure". J Struct Biol. 124 (2–3): 221–234. doi:10.1006/jsbi.1998.4065. PMID 10049808.
- Haimovitz R, Barak Y, Morag E, Voronov-Goldman M, Shoham Y, Lamed R, Bayer EA (2008). "Cohesin-dockerin microarray: Diverse specificities between two complementary families of interacting protein modules". Proteomics. 8 (5): 968–979. doi:10.1002/pmic.200700486. PMID 18219699.
- Adams JJ, Webb BA, Spencer HL, Smith SP (2005). "Structural characterization of type II dockerin module from the cellulosome of Clostridium thermocellum: calcium-induced effects on conformation and target recognition". Biochemistry. 44 (6): 2173–2182. doi:10.1021/bi048039u. PMID 15697243.
- Jindou S, Soda A, Karita S, Kajino T, Béguin P, Wu JH, Inagaki M, Kimura T, Sakka K, Ohmiya K (2004). "Cohesin-dockerin interactions within and between Clostridium josui and Clostridium thermocellum: binding selectivity between cognate dockerin and cohesin domains and species specificity". J Biol Chem. 279 (11): 9867–9874. doi:10.1074/jbc.M308673200. PMID 14688277.
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Dockerin type I repeat Provide feedback
The dockerin repeat is the binding partner of the cohesin domain PF00963. The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome . The dockerin repeats, each bearing homology to the EF-hand calcium-binding loop bind calcium .
Shoham Y, Lamed R, Bayer EA; , Trends Microbiol 1999;7:275-281.: The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides [In Process Citation] PUBMED:10390637 EPMC:10390637
Lytle BL, Volkman BF, Westler WM, Wu JH; , Arch Biochem Biophys 2000;379:237-244.: Secondary structure and calcium-induced folding of the Clostridium thermocellum dockerin domain determined by NMR spectroscopy. PUBMED:10898940 EPMC:10898940
Internal database links
|Similarity to PfamA using HHSearch:||EF-hand_5|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002105
Gram-positive, thermophilic anaerobes such as Clostridium thermocellum or Clostridium cellulolyticum secretes a highly active and thermostable cellulase complex (cellulosome) responsible for the degradation of crystalline cellulose [PUBMED:2252383, PUBMED:1478480]. The cellulosome contains at least 30 polypeptides, the majority of the enzymes are endoglucanases (EC), but there are also some xylanases (EC), beta-glucosidases (EC) and endo-beta-1,3-1,4-glucanases (EC).
Complete sequence data for many of these enzymes has been obtained. A majority of these proteins contain a highly conserved type I dockerin domain of about 65 to 70 residues, which is generally (but not always) located in the C terminus. The dockerin domain is the binding partner of the cohesin domain (see INTERPRO). The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome [PUBMED:10390637]. The dockerin domain contains a tandem repeat of two calcium-binding loop-helix motifs (distinct from EF-hand Ca-binding motifs). These motifs are about 24 amino acids in length. This entry represents these repeated Ca-binding motifs.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|
|Biological process||polysaccharide catabolic process (GO:0000272)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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The EF hand is a calcium binding domain found in a wide variety of proteins .
The clan contains the following 23 members:Ca_chan_IQ Caleosin Cbl_N2 DAG_kinase_N Dockerin_1 EF-hand_1 EF-hand_10 EF-hand_11 EF-hand_2 EF-hand_3 EF-hand_4 EF-hand_5 EF-hand_6 EF-hand_7 EF-hand_8 EF-hand_9 EF-hand_like EFhand_Ca_insen IQ IQCJ-SCHIP1 p25-alpha S_100 SPARC_Ca_bdg
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Number in seed:||99|
|Number in full:||845|
|Average length of the domain:||20.90 aa|
|Average identity of full alignment:||45 %|
|Average coverage of the sequence by the domain:||3.97 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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There are 4 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Dockerin_1 domain has been found. There are 29 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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