PDBsum entry 1e8p

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protein links
Cellulose docking domain PDB id
Protein chain
46 a.a. *
* Residue conservation analysis
PDB id:
Name: Cellulose docking domain
Title: Characterisation of the cellulose docking domain from piromyces equi
Structure: Endoglucanase. Chain: a. Fragment: cellulose docking domain. Synonym: dockerin. Engineered: yes
Source: Piromyces equi. Organism_taxid: 99929. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 1 models
Authors: S.Raghothama,R.Y.Eberhardt,P.White,G.P.Hazlewood, H.J.Gilbert,P.J.Simpson,M.P.Williamson
Key ref:
S.Raghothama et al. (2001). Characterization of a cellulosome dockerin domain from the anaerobic fungus Piromyces equi. Nat Struct Biol, 8, 775-778. PubMed id: 11524680 DOI: 10.1038/nsb0901-775
28-Sep-00     Release date:   07-Sep-01    
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Protein chain
Pfam   ArchSchema ?
Q9P868  (Q9P868_PIREQ) -  Endoglucanase 45A
410 a.a.
46 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)


DOI no: 10.1038/nsb0901-775 Nat Struct Biol 8:775-778 (2001)
PubMed id: 11524680  
Characterization of a cellulosome dockerin domain from the anaerobic fungus Piromyces equi.
S.Raghothama, R.Y.Eberhardt, P.Simpson, D.Wigelsworth, P.White, G.P.Hazlewood, T.Nagy, H.J.Gilbert, M.P.Williamson.
The recycling of photosynthetically fixed carbon in plant cell walls is a key microbial process. In anaerobes, the degradation is carried out by a high molecular weight multifunctional complex termed the cellulosome. This consists of a number of independent enzyme components, each of which contains a conserved dockerin domain, which functions to bind the enzyme to a cohesin domain within the protein scaffoldin protein. Here we describe the first three-dimensional structure of a fungal dockerin, the N-terminal dockerin of Cel45A from the anaerobic fungus Piromyces equi. The structure contains a novel fold of 42 residues. The ligand binding site consists of residues Trp 35, Tyr 8 and Asp 23, which are conserved in all fungal dockerins. The binding site is on the opposite side of the N- and C-termini of the molecule, implying that tandem dockerin domains, seen in the majority of anaerobic fungal plant cell wall degrading enzymes, could present multiple simultaneous binding sites and, therefore, permit tailoring of binding to catalytic demands.
  Selected figure(s)  
Figure 2.
Figure 2. Solution structure of the P. equi dockerin. a, Stereo view of the ensemble of 34 structures, colored from red at the N-terminus to blue at the C-terminus. b, Stereo MOLSCRIPT27 diagram of the dockerin structure, showing the locations of disulfide bridges and the binding site residues discussed in the text. The protein present in the sample consisted of 52 residues -- that is, the 38-residue 'core' sequence that is highly conserved in fungal dockerins, plus all 12 residues C-terminal of the core sequence prior to the start of the second dockerin domain, and two N-terminal residues from the GST-tag. The figure shows only the ordered residues -2 -44. c, Surface of the protein, in the same orientation as (b). Side chains of residues Tyr 8 and Trp 35 are in purple, and Asp 23 in light lilac. Acidic residues are in red, basic in dark blue and hydrophobic in yellow.
Figure 3.
Figure 3. 15N T[2] values for backbone nitrogens. Values (ms) are plotted against residue number.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 775-778) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20410935 A.S.Liggenstoffer, N.H.Youssef, M.B.Couger, and M.S.Elshahed (2010).
Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores.
  ISME J, 4, 1225-1235.  
19690850 C.K.Pai, Z.Y.Wu, M.J.Chen, Y.F.Zeng, J.W.Chen, C.H.Duan, M.L.Li, and J.R.Liu (2010).
Molecular cloning and characterization of a bifunctional xylanolytic enzyme from Neocallimastix patriciarum.
  Appl Microbiol Biotechnol, 85, 1451-1462.  
20373916 C.M.Fontes, and H.J.Gilbert (2010).
Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates.
  Annu Rev Biochem, 79, 655-681.  
19025568 A.Peer, S.P.Smith, E.A.Bayer, R.Lamed, and I.Borovok (2009).
Noncellulosomal cohesin- and dockerin-like modules in the three domains of life.
  FEMS Microbiol Lett, 291, 1.  
18378601 L.G.Ljungdahl (2008).
The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use.
  Ann N Y Acad Sci, 1125, 308-321.  
17468286 F.Mingardon, A.Chanal, A.M.López-Contreras, C.Dray, E.A.Bayer, and H.P.Fierobe (2007).
Incorporation of fungal cellulases in bacterial minicellulosomes yields viable, synergistically acting cellulolytic complexes.
  Appl Environ Microbiol, 73, 3822-3832.  
17225100 X.L.Li, C.D.Skory, E.A.Ximenes, D.B.Jordan, B.S.Dien, S.R.Hughes, and M.A.Cotta (2007).
Expression of an AT-rich xylanase gene from the anaerobic fungus Orpinomyces sp. strain PC-2 in and secretion of the heterologous enzyme by Hypocrea jecorina.
  Appl Microbiol Biotechnol, 74, 1264-1275.  
16267281 M.T.Rincon, T.Cepeljnik, J.C.Martin, R.Lamed, Y.Barak, E.A.Bayer, and H.J.Flint (2005).
Unconventional mode of attachment of the Ruminococcus flavefaciens cellulosome to the cell surface.
  J Bacteriol, 187, 7569-7578.  
  16233456 K.Ohmiya, K.Sakka, T.Kimura, and K.Morimoto (2003).
Application of microbial genes to recalcitrant biomass utilization and environmental conservation.
  J Biosci Bioeng, 95, 549-561.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.