spacer
spacer

PDBsum entry 1daq

Go to PDB code: 
protein metals links
Hydrolase PDB id
1daq
Jmol
Contents
Protein chain
71 a.a. *
Metals
_CA ×2
* Residue conservation analysis
PDB id:
1daq
Name: Hydrolase
Title: Solution structure of the type i dockerin domain from the clostridium thermocellum cellulosome (minimized average structure)
Structure: Endoglucanase ss. Chain: a. Fragment: type i dockerin domain (residues 673-741). Synonym: cels. Engineered: yes
Source: Clostridium thermocellum. Organism_taxid: 1515. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 1 models
Authors: B.L.Lytle,B.F.Volkman,W.M.Westler,M.P.Heckman,J.H.D.Wu
Key ref:
B.L.Lytle et al. (2001). Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain. J Mol Biol, 307, 745-753. PubMed id: 11273698 DOI: 10.1006/jmbi.2001.4522
Date:
31-Oct-99     Release date:   04-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0C2S5  (GUNS_CLOTM) -  Cellulose 1,4-beta-cellobiosidase (reducing end) CelS
Seq:
Struc:
 
Seq:
Struc:
741 a.a.
71 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.176  - Cellulose 1,4-beta-cellobiosidase (reducing end).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  

 

 
DOI no: 10.1006/jmbi.2001.4522 J Mol Biol 307:745-753 (2001)
PubMed id: 11273698  
 
 
Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain.
B.L.Lytle, B.F.Volkman, W.M.Westler, M.P.Heckman, J.H.Wu.
 
  ABSTRACT  
 
The type I dockerin domain is responsible for incorporating its associated glycosyl hydrolase into the bacterial cellulosome, a multienzyme cellulolytic complex, via its interaction with a receptor domain (cohesin domain) of the cellulosomal scaffolding subunit. The highly conserved dockerin domain is characterized by two Ca(2+)-binding sites with sequence similarity to the EF-hand motif. Here, we present the three-dimensional solution structure of the 69 residue dockerin domain of Clostridium thermocellum cellobiohydrolase CelS. Torsion angle dynamics calculations utilizing a total of 728 NOE-derived distance constraints and 79 torsion angle restraints yielded an ensemble of 20 structures with an average backbone r.m.s.d. for residues 5 to 29 and 32 to 66 of 0.54 A from the mean structure. The structure consists of two Ca(2+)-binding loop-helix motifs connected by a linker; the E helices entering each loop of the classical EF-hand motif are absent from the dockerin domain. Each dockerin Ca(2+)-binding subdomain is stabilized by a cluster of buried hydrophobic side-chains. Structural comparisons reveal that, in its non-complexed state, the dockerin fold displays a dramatic departure from that of Ca(2+)-bound EF-hand domains. A putative cohesin-binding surface, comprised of conserved hydrophobic and basic residues, is proposed, providing new insight into cellulosome assembly.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. (a) Superposition of the backbone atoms (N, C^a and C') of the selected 20 Ct-Doc structures. The structures are superimposed against the mean structure using residues 5 to 29 and 32 to 66. The a-helices are shown in cyan and the turn of 3[10] helix is highlighted green. Calcium ions are shown as yellow spheres. (b) Ribbon diagram of the energy-minimized averaged structure. (c) Side-view of Ct-Doc (ribbon representation), with the interacting hydrophobic side-chains comprising the two clusters shown in red and green, and the conserved Val15 and Val47 (loop position 8) shown in yellow. All structural representations were generated with the program MOLMOL. [43]
Figure 3.
Figure 3. Comparison of the topology of (a) Ct-Doc and (b) C-terminal domain of cardiac muscle troponin C (PDB code 3CTN).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 745-753) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
18979459 A.Karpol, L.Kantorovich, A.Demishtein, Y.Barak, E.Morag, R.Lamed, and E.A.Bayer (2009).
Engineering a reversible, high-affinity system for efficient protein purification based on the cohesin-dockerin interaction.
  J Mol Recognit, 22, 91-98.  
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.  
19384997 J.Xu, M.F.Crowley, and J.C.Smith (2009).
Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation.
  Protein Sci, 18, 949-959.  
17367380 H.J.Gilbert (2007).
Cellulosomes: microbial nanomachines that display plasticity in quaternary structure.
  Mol Microbiol, 63, 1568-1576.  
17360424 M.Newcomb, C.Y.Chen, and J.H.Wu (2007).
Induction of the celC operon of Clostridium thermocellum by laminaribiose.
  Proc Natl Acad Sci U S A, 104, 3747-3752.  
16672498 H.Ichinose, A.Kuno, T.Kotake, M.Yoshida, K.Sakka, J.Hirabayashi, Y.Tsumuraya, and S.Kaneko (2006).
Characterization of an exo-beta-1,3-galactanase from Clostridium thermocellum.
  Appl Environ Microbiol, 72, 3515-3523.  
16384918 J.J.Adams, G.Pal, Z.Jia, and S.P.Smith (2006).
Mechanism of bacterial cell-surface attachment revealed by the structure of cellulosomal type II cohesin-dockerin complex.
  Proc Natl Acad Sci U S A, 103, 305-310.
PDB code: 2b59
16981205 Y.Zhou, W.Yang, M.Kirberger, H.W.Lee, G.Ayalasomayajula, and J.J.Yang (2006).
Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins.
  Proteins, 65, 643-655.  
15755956 A.L.Demain, M.Newcomb, and J.H.Wu (2005).
Cellulase, clostridia, and ethanol.
  Microbiol Mol Biol Rev, 69, 124-154.  
15802647 C.Wang, O.Schueler-Furman, and D.Baker (2005).
Improved side-chain modeling for protein-protein docking.
  Protein Sci, 14, 1328-1339.  
15981255 C.Zhang, S.Liu, and Y.Zhou (2005).
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function.
  Proteins, 60, 314-318.  
15981272 D.Mustard, and D.W.Ritchie (2005).
Docking essential dynamics eigenstructures.
  Proteins, 60, 269-274.  
15981268 E.Ben-Zeev, N.Kowalsman, A.Ben-Shimon, D.Segal, T.Atarot, O.Noivirt, T.Shay, and M.Eisenstein (2005).
Docking to single-domain and multiple-domain proteins: old and new challenges.
  Proteins, 60, 195-201.  
  16508087 J.J.Adams, G.Pal, K.Yam, H.L.Spencer, Z.Jia, and S.P.Smith (2005).
Purification and crystallization of a trimodular complex comprising the type II cohesin-dockerin interaction from the cellulosome of Clostridium thermocellum.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 46-48.  
15981262 M.D.Daily, D.Masica, A.Sivasubramanian, S.Somarouthu, and J.J.Gray (2005).
CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock.
  Proteins, 60, 181-186.  
15981249 O.Schueler-Furman, C.Wang, and D.Baker (2005).
Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
  Proteins, 60, 187-194.  
15981271 P.Carter, V.I.Lesk, S.A.Islam, and M.J.Sternberg (2005).
Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI.
  Proteins, 60, 281-288.  
15981260 X.H.Ma, C.H.Li, L.Z.Shen, X.Q.Gong, W.Z.Chen, and C.X.Wang (2005).
Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition.
  Proteins, 60, 319-323.  
16167300 Y.Barak, T.Handelsman, D.Nakar, A.Mechaly, R.Lamed, Y.Shoham, and E.A.Bayer (2005).
Matching fusion protein systems for affinity analysis of two interacting families of proteins: the cohesin-dockerin interaction.
  J Mol Recognit, 18, 491-501.  
15292269 D.Nakar, T.Handelsman, Y.Shoham, H.P.Fierobe, J.P.Belaich, E.Morag, R.Lamed, and E.A.Bayer (2004).
Pinpoint mapping of recognition residues on the cohesin surface by progressive homologue swapping.
  J Biol Chem, 279, 42881-42888.  
15487947 E.A.Bayer, J.P.Belaich, Y.Shoham, and R.Lamed (2004).
The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides.
  Annu Rev Microbiol, 58, 521-554.  
15604820 L.Hildén, and G.Johansson (2004).
Recent developments on cellulases and carbohydrate-binding modules with cellulose affinity.
  Biotechnol Lett, 26, 1683-1693.  
15502162 M.Hammel, H.P.Fierobe, M.Czjzek, S.Finet, and V.Receveur-Bréchot (2004).
Structural insights into the mechanism of formation of cellulosomes probed by small angle X-ray scattering.
  J Biol Chem, 279, 55985-55994.  
14761991 Q.Xu, E.A.Bayer, M.Goldman, R.Kenig, Y.Shoham, and R.Lamed (2004).
Architecture of the Bacteroides cellulosolvens cellulosome: description of a cell surface-anchoring scaffoldin and a family 48 cellulase.
  J Bacteriol, 186, 968-977.  
14623971 A.L.Carvalho, F.M.Dias, J.A.Prates, T.Nagy, H.J.Gilbert, G.J.Davies, L.M.Ferreira, M.J.Romão, and C.M.Fontes (2003).
Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex.
  Proc Natl Acad Sci U S A, 100, 13809-13814.
PDB code: 1ohz
12694917 D.J.Rigden, M.J.Jedrzejas, and M.Y.Galperin (2003).
An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands.
  FEMS Microbiol Lett, 221, 103-110.  
12875810 D.J.Rigden, M.J.Jedrzejas, O.V.Moroz, and M.Y.Galperin (2003).
Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands?
  Trends Microbiol, 11, 295-297.  
12925809 I.Noach, R.Lamed, Q.Xu, S.Rosenheck, L.J.Shimon, E.A.Bayer, and F.Frolow (2003).
Preliminary X-ray characterization and phasing of a type II cohesin domain from the cellulosome of Acetivibrio cellulolyticus.
  Acta Crystallogr D Biol Crystallogr, 59, 1670-1673.  
12644701 J.T.Welch, W.R.Kearney, and S.J.Franklin (2003).
Lanthanide-binding helix-turn-helix peptides: solution structure of a designed metallonuclease.
  Proc Natl Acad Sci U S A, 100, 3725-3730.  
  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.  
11841200 F.Schaeffer, M.Matuschek, G.Guglielmi, I.Miras, P.M.Alzari, and P.Béguin (2002).
Duplicated dockerin subdomains of Clostridium thermocellum endoglucanase CelD bind to a cohesin domain of the scaffolding protein CipA with distinct thermodynamic parameters and a negative cooperativity.
  Biochemistry, 41, 2106-2114.  
11841201 I.Miras, F.Schaeffer, P.Béguin, and P.M.Alzari (2002).
Mapping by site-directed mutagenesis of the region responsible for cohesin-dockerin interaction on the surface of the seventh cohesin domain of Clostridium thermocellum CipA.
  Biochemistry, 41, 2115-2119.  
11980476 M.Abou-Hachem, E.N.Karlsson, P.J.Simpson, S.Linse, P.Sellers, M.P.Williamson, S.J.Jamieson, H.J.Gilbert, D.N.Bolam, and O.Holst (2002).
Calcium binding and thermostability of carbohydrate binding module CBM4-2 of Xyn10A from Rhodothermus marinus.
  Biochemistry, 41, 5720-5729.  
11524680 S.Raghothama, R.Y.Eberhardt, P.Simpson, D.Wigelsworth, P.White, G.P.Hazlewood, T.Nagy, H.J.Gilbert, and M.P.Williamson (2001).
Characterization of a cellulosome dockerin domain from the anaerobic fungus Piromyces equi.
  Nat Struct Biol, 8, 775-778.
PDB codes: 1e8p 1e8q
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. Where a reference describes a PDB structure, the PDB code is shown on the right.