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PDBsum entry 1ohz

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protein ligands metals Protein-protein interface(s) links
Cell adhesion PDB id
1ohz
Jmol
Contents
Protein chains
140 a.a. *
56 a.a. *
Ligands
NO3 ×2
EDO
Metals
_CL
_CA ×2
Waters ×115
* Residue conservation analysis
PDB id:
1ohz
Name: Cell adhesion
Title: Cohesin-dockerin complex from the cellulosome of clostridium thermocellum
Structure: Cellulosomal scaffolding protein a. Chain: a. Fragment: residues 181-340. Synonym: cellulosomal glycoprotein s1/sl, cellulose integrating protein a, cohesin. Engineered: yes. Endo-1,4-beta-xylanase y. Chain: b. Fragment: residues 733-791.
Source: Clostridium thermocellum. Organism_taxid: 1515. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Hexamer (from PDB file)
Resolution:
2.20Å     R-factor:   0.211     R-free:   0.241
Authors: A.L.Carvalho,F.M.V.Dias,J.A.M.Prates,L.M.A.Ferreira, H.J.Gilbert,G.J.Davies,M.J.Romao,C.M.G.A.Fontes
Key ref:
A.L.Carvalho et al. (2003). Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex. Proc Natl Acad Sci U S A, 100, 13809-13814. PubMed id: 14623971 DOI: 10.1073/pnas.1936124100
Date:
04-Jun-03     Release date:   20-Nov-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q06851  (CIPA_CLOTH) -  Cellulosomal-scaffolding protein A
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1853 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P51584  (XYNY_CLOTM) -  Endo-1,4-beta-xylanase Y
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1077 a.a.
56 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain B: E.C.3.2.1.8  - Endo-1,4-beta-xylanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     carbohydrate binding     2 terms  

 

 
DOI no: 10.1073/pnas.1936124100 Proc Natl Acad Sci U S A 100:13809-13814 (2003)
PubMed id: 14623971  
 
 
Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex.
A.L.Carvalho, F.M.Dias, J.A.Prates, T.Nagy, H.J.Gilbert, G.J.Davies, L.M.Ferreira, M.J.Romão, C.M.Fontes.
 
  ABSTRACT  
 
The utilization of organized supramolecular assemblies to exploit the synergistic interactions afforded by close proximity, both for enzymatic synthesis and for the degradation of recalcitrant substrates, is an emerging theme in cellular biology. Anaerobic bacteria harness a multiprotein complex, termed the "cellulosome," for efficient degradation of the plant cell wall. This megadalton catalytic machine organizes an enzymatic consortium on a multifaceted molecular scaffold whose "cohesin" domains interact with corresponding "dockerin" domains of the enzymes. Here we report the structure of the cohesin-dockerin complex from Clostridium thermocellum at 2.2-A resolution. The data show that the beta-sheet cohesin domain interacts predominantly with one of the helices of the dockerin. Whereas the structure of the cohesin remains essentially unchanged, the loop-helix-helix-loop-helix motif of the dockerin undergoes conformational change and ordering compared with its solution structure, although the classical 12-residue EF-hand coordination to two calcium ions is maintained. Significantly, internal sequence duplication within the dockerin is manifested in near-perfect internal twofold symmetry, suggesting that both "halves" of the dockerin may interact with cohesins in a similar manner, thus providing a higher level of structure to the cellulosome and possibly explaining the presence of "polycellulosomes." The structure provides an explanation for the lack of cross-species recognition between cohesin-dockerin pairs and thus provides a blueprint for the rational design, construction, and exploitation of these catalytic assemblies.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Structure of the type I Coh-Doc complex. (a) The complex is formed between a cohesin 2 molecule (red) and a Ca^2+-bound dockerin (green). The residues involved in domain contacts are shown as stick models. The two Ca^2+-binding sites of the dockerin domain are represented as orange spheres. (b) C representation of the Coh-Doc structure with every 10th residue labeled. (c) Ca^2+ coordination in the dockerin domain. The Ca^2+-bound residues are shown as stick models with green labels.
Figure 3.
Fig. 3. Stereo picture of the cohesin (red)-dockerin (yellow) complex. The dockerin solution structure (1DAQ [PDB] ) is overlaid in blue and reveals the movement of -helix 3 away from the cohesin.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21168322 G.T.Beckham, Y.J.Bomble, E.A.Bayer, M.E.Himmel, and M.F.Crowley (2011).
Applications of computational science for understanding enzymatic deconstruction of cellulose.
  Curr Opin Biotechnol, 22, 231-238.  
21054503 K.Sakka, Y.Sugihara, S.Jindou, M.Sakka, M.Inagaki, K.Sakka, and T.Kimura (2011).
Analysis of cohesin-dockerin interactions using mutant dockerin proteins.
  FEMS Microbiol Lett, 314, 75-80.  
21038354 A.Demishtein, A.Karpol, Y.Barak, R.Lamed, and E.A.Bayer (2010).
Characterization of a dockerin-based affinity tag: application for purification of a broad variety of target proteins.
  J Mol Recognit, 23, 525-535.  
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.  
  20802784 C.Yanyi, X.Shenghui, Z.Yubin, and Y.J.Jie (2010).
Calciomics: prediction and analysis of EF-hand calcium binding proteins by protein engineering.
  Sci China Chem, 53, 52-60.  
20725658 J.Janin (2010).
Protein-protein docking tested in blind predictions: the CAPRI experiment.
  Mol Biosyst, 6, 2351-2362.  
20682763 J.Xu, and J.C.Smith (2010).
Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin-dockerin complex and its variants.
  Protein Eng Des Sel, 23, 759-768.  
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.  
19758121 B.A.Pinheiro, H.J.Gilbert, K.Sakka, K.Sakka, V.O.Fernandes, J.A.Prates, V.D.Alves, D.N.Bolam, L.M.Ferreira, and C.M.Fontes (2009).
Functional insights into the role of novel type I cohesin and dockerin domains from Clostridium thermocellum.
  Biochem J, 424, 375-384.  
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.  
19384998 K.Usui, T.Maki, F.Ito, A.Suenaga, S.Kidoaki, M.Itoh, M.Taiji, T.Matsuda, Y.Hayashizaki, and H.Suzuki (2009).
Nanoscale elongating control of the self-assembled protein filament with the cysteine-introduced building blocks.
  Protein Sci, 18, 960-969.  
19452551 N.Kowalsman, and M.Eisenstein (2009).
Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models.
  Proteins, 77, 297-318.  
19116695 R.E.Nordon, S.J.Craig, and F.C.Foong (2009).
Molecular engineering of the cellulosome complex for affinity and bioenergy applications.
  Biotechnol Lett, 31, 465-476.  
  18097105 I.Noach, O.Alber, E.A.Bayer, R.Lamed, M.Levy-Assaraf, L.J.Shimon, and F.Frolow (2008).
Crystallization and preliminary X-ray analysis of Acetivibrio cellulolyticus cellulosomal type II cohesin module: two versions having different linker lengths.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 58-61.  
18716000 J.J.Adams, K.Gregg, E.A.Bayer, A.B.Boraston, and S.P.Smith (2008).
Structural basis of Clostridium perfringens toxin complex formation.
  Proc Natl Acad Sci U S A, 105, 12194-12199.
PDB codes: 2ozn 2vo8
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.  
  18259053 O.Alber, I.Noach, R.Lamed, L.J.Shimon, E.A.Bayer, and F.Frolow (2008).
Preliminary X-ray characterization of a novel type of anchoring cohesin from the cellulosome of Ruminococcus flavefaciens.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 77-80.  
18219699 R.Haimovitz, Y.Barak, E.Morag, M.Voronov-Goldman, Y.Shoham, R.Lamed, and E.A.Bayer (2008).
Cohesin-dockerin microarray: Diverse specificities between two complementary families of interacting protein modules.
  Proteomics, 8, 968-979.  
  18678939 S.Najmudin, B.A.Pinheiro, M.J.Romão, J.A.Prates, and C.M.Fontes (2008).
Purification, crystallization and crystallographic analysis of Clostridium thermocellum endo-1,4-beta-D-xylanase 10B in complex with xylohexaose.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 715-718.  
17360613 A.L.Carvalho, F.M.Dias, T.Nagy, J.A.Prates, M.R.Proctor, N.Smith, E.A.Bayer, G.J.Davies, L.M.Ferreira, M.J.Romão, C.M.Fontes, and H.J.Gilbert (2007).
Evidence for a dual binding mode of dockerin modules to cohesins.
  Proc Natl Acad Sci U S A, 104, 3089-3094.
PDB code: 2ccl
17905885 F.Mingardon, A.Chanal, C.Tardif, E.A.Bayer, and H.P.Fierobe (2007).
Exploration of new geometries in cellulosome-like chimeras.
  Appl Environ Microbiol, 73, 7138-7149.  
17367380 H.J.Gilbert (2007).
Cellulosomes: microbial nanomachines that display plasticity in quaternary structure.
  Mol Microbiol, 63, 1568-1576.  
17394030 M.Brylinski, M.Kochanczyk, E.Broniatowska, and I.Roterman (2007).
Localization of ligand binding site in proteins identified in silico.
  J Mol Model, 13, 665-675.  
17803233 N.London, and O.Schueler-Furman (2007).
Assessing the energy landscape of CAPRI targets by FunHunt.
  Proteins, 69, 809-815.  
17803234 S.J.de Vries, A.D.van Dijk, M.Krzeminski, M.van Dijk, A.Thureau, V.Hsu, T.Wassenaar, and A.M.Bonvin (2007).
HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets.
  Proteins, 69, 726-733.  
17444519 T.M.Cheng, T.L.Blundell, and J.Fernandez-Recio (2007).
pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking.
  Proteins, 68, 503-515.  
17803223 X.Q.Gong, S.Chang, Q.H.Zhang, C.H.Li, L.Z.Shen, X.H.Ma, M.H.Wang, B.Liu, H.Q.He, W.Z.Chen, and C.X.Wang (2007).
A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI.
  Proteins, 69, 859-865.  
16899489 A.D.van Dijk, and A.M.Bonvin (2006).
Solvated docking: introducing water into the modelling of biomolecular complexes.
  Bioinformatics, 22, 2340-2347.  
16506242 C.J.Camacho, H.Ma, and P.C.Champ (2006).
Scoring a diverse set of high-quality docked conformations: a metascore based on electrostatic and desolvation interactions.
  Proteins, 63, 868-877.  
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
16487313 M.Desvaux, E.Dumas, I.Chafsey, and M.Hébraud (2006).
Protein cell surface display in Gram-positive bacteria: from single protein to macromolecular protein structure.
  FEMS Microbiol Lett, 256, 1.  
17022659 M.Desvaux (2006).
Unravelling carbon metabolism in anaerobic cellulolytic bacteria.
  Biotechnol Prog, 22, 1229-1238.  
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.  
15981252 A.D.van Dijk, S.J.de Vries, C.Dominguez, H.Chen, H.X.Zhou, and A.M.Bonvin (2005).
Data-driven docking: HADDOCK's adventures in CAPRI.
  Proteins, 60, 232-238.  
15755956 A.L.Demain, M.Newcomb, and J.H.Wu (2005).
Cellulase, clostridia, and ethanol.
  Microbiol Mol Biol Rev, 69, 124-154.  
15981253 C.J.Camacho (2005).
Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets.
  Proteins, 60, 245-251.  
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.  
15981246 D.Law, M.Hotchko, and L.Ten Eyck (2005).
Progress in computation and amide hydrogen exchange for prediction of protein-protein complexes.
  Proteins, 60, 302-307.  
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.  
15981258 G.R.Smith, P.W.Fitzjohn, C.S.Page, and P.A.Bates (2005).
Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI.
  Proteins, 60, 263-268.  
15981245 G.Terashi, M.Takeda-Shitaka, D.Takaya, K.Komatsu, and H.Umeyama (2005).
Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues.
  Proteins, 60, 289-295.  
16080151 H.Chen, and H.X.Zhou (2005).
Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data.
  Proteins, 61, 21-35.  
15981266 J.Fernández-Recio, R.Abagyan, and M.Totrov (2005).
Improving CAPRI predictions: optimized desolvation for rigid-body docking.
  Proteins, 60, 308-313.  
  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.  
15981267 J.Janin (2005).
The targets of CAPRI rounds 3-5.
  Proteins, 60, 170-175.  
15981263 K.Wiehe, B.Pierce, J.Mintseris, W.W.Tong, R.Anderson, R.Chen, and Z.Weng (2005).
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5.
  Proteins, 60, 207-213.  
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.  
16102601 M.Desvaux (2005).
Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia.
  FEMS Microbiol Rev, 29, 741-764.  
15950297 M.Desvaux, A.Khan, A.Scott-Tucker, R.R.Chaudhuri, M.J.Pallen, and I.R.Henderson (2005).
Genomic analysis of the protein secretion systems in Clostridium acetobutylicum ATCC 824.
  Biochim Biophys Acta, 1745, 223-253.  
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.  
15981265 S.R.Comeau, S.Vajda, and C.J.Camacho (2005).
Performance of the first protein docking server ClusPro in CAPRI rounds 3-5.
  Proteins, 60, 239-244.  
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.  
15981251 Y.Inbar, D.Schneidman-Duhovny, I.Halperin, A.Oron, R.Nussinov, and H.J.Wolfson (2005).
Approaching the CAPRI challenge with an efficient geometry-based docking.
  Proteins, 60, 217-223.  
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.  
15197390 R.H.Doi, and A.Kosugi (2004).
Cellulosomes: plant-cell-wall-degrading enzyme complexes.
  Nat Rev Microbiol, 2, 541-551.  
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 codes are shown on the right.