PDBsum entry 1hej

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Hydrolase(xylan degradation) PDB id
Protein chain
88 a.a. *
* Residue conservation analysis
PDB id:
Name: Hydrolase(xylan degradation)
Title: C-terminal xylan binding domain from cellulomonas fimi xylanase 11a
Structure: Endo-1,4-beta-xylanase d. Chain: c. Fragment: xylan binding domain 2. Synonym: xylanase d, cbm2b-2, xbd2. Engineered: yes
Source: Cellulomonas fimi. Organism_taxid: 1708. Strain: jm83. Expressed in: escherichia coli. Expression_system_taxid: 469008.
NMR struc: 5 models
Authors: P.J.Simpson,X.Hefang,D.N.Bolam,P.White,S.M.Hancock, H.J.Gilbert,M.P.Williamson
Key ref:
D.N.Bolam et al. (2001). Evidence for synergy between family 2b carbohydrate binding modules in Cellulomonas fimi xylanase 11A. Biochemistry, 40, 2468-2477. PubMed id: 11327868 DOI: 10.1021/bi002564l
22-Nov-00     Release date:   10-May-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P54865  (XYND_CELFI) -  Bifunctional xylanase/deacetylase
644 a.a.
88 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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   1 term 
  Biochemical function     carbohydrate binding     3 terms  


DOI no: 10.1021/bi002564l Biochemistry 40:2468-2477 (2001)
PubMed id: 11327868  
Evidence for synergy between family 2b carbohydrate binding modules in Cellulomonas fimi xylanase 11A.
D.N.Bolam, H.Xie, P.White, P.J.Simpson, S.M.Hancock, M.P.Williamson, H.J.Gilbert.
Glycoside hydrolases often contain multiple copies of noncatalytic carbohydrate binding modules (CBMs) from the same or different families. Currently, the functional importance of this complex molecular architecture is unclear. To investigate the role of multiple CBMs in plant cell wall hydrolases, we have determined the polysaccharide binding properties of wild type and various derivatives of Cellulomonas fimi xylanase 11A (Cf Xyn11A). This protein, which binds to both cellulose and xylan, contains two family 2b CBMs that exhibit 70% sequence identity, one internal (CBM2b-1), which has previously been shown to bind specifically to xylan and the other at the C-terminus (CBM2b-2). Biochemical characterization of CBM2b-2 showed that the module bound to insoluble and soluble oat spelt xylan and xylohexaose with K(a) values of 5.6 x 10(4), 1.2 x 10(4), and 4.8 x 10(3) M(-1), respectively, but exhibited extremely weak affinity for cellohexaose (<10(2) M(-1)), and its interaction with insoluble cellulose was too weak to quantify. The CBM did not interact with soluble forms of other plant cell wall polysaccharides. The three-dimensional structure of CBM2b-2 was determined by NMR spectroscopy. The module has a twisted "beta-sandwich" architecture, and the two surface exposed tryptophans, Trp 570 and Trp 602, which are in a perpendicular orientation with each other, were shown to be essential for ligand binding. In addition, changing Arg 573 to glycine altered the polysaccharide binding specificity of the module from xylan to cellulose. These data demonstrate that the biochemical properties and tertiary structure of CBM2b-2 and CBM2b-1 are extremely similar. When CBM2b-1 and CBM2b-2 were incorporated into a single polypeptide chain, either in the full-length enzyme or an artificial construct comprising both CBM2bs covalently joined via a flexible linker, there was an approximate 18-20-fold increase in the affinity of the protein for soluble and insoluble xylan, as compared to the individual modules, and a measurable interaction with insoluble acid-swollen cellulose, although the K(a) (approximately 6.0 x 10(4) M(-1)) was still much lower than for insoluble xylan (K(a) = approximately 1.0 x 10(6) M(-1)). These data demonstrate that the two family 2b CBMs of Cf Xyn11A act in synergy to bind acid swollen cellulose and xylan. We propose that the increased affinity of glycoside hydrolases for polysaccharides, through the synergistic interactions of CBMs, provides an explanation for the duplication of CBMs from the same family in some prokaryotic cellulases and xylanases.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21307602 Q.Yin, Y.Teng, Y.Li, M.Ding, and F.Zhao (2011).
Expression and characterization of full-length Ampullaria crossean endoglucanase EG65s and their two functional modules.
  Biosci Biotechnol Biochem, 75, 240-246.  
19787349 A.Sunna (2010).
Modular organisation and functional analysis of dissected modular beta-mannanase CsMan26 from Caldicellulosiruptor Rt8B.4.
  Appl Microbiol Biotechnol, 86, 189-200.  
20696902 C.Hervé, A.Rogowski, A.W.Blake, S.E.Marcus, H.J.Gilbert, and J.P.Knox (2010).
Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects.
  Proc Natl Acad Sci U S A, 107, 15293-15298.  
19144002 C.Hervé, A.Rogowski, H.J.Gilbert, and J.Paul Knox (2009).
Enzymatic treatments reveal differential capacities for xylan recognition and degradation in primary and secondary plant cell walls.
  Plant J, 58, 413-422.  
18025086 B.Bae, S.Ohene-Adjei, S.Kocherginskaya, R.I.Mackie, M.A.Spies, I.K.Cann, and S.K.Nair (2008).
Molecular basis for the selectivity and specificity of ligand recognition by the family 16 carbohydrate-binding modules from Thermoanaerobacterium polysaccharolyticum ManA.
  J Biol Chem, 283, 12415-12425.
PDB codes: 2zew 2zex 2zey 2zez
17468268 D.Guillén, M.Santiago, L.Linares, R.Pérez, J.Morlon, B.Ruiz, S.Sánchez, and R.Rodríguez-Sanoja (2007).
Alpha-amylase starch binding domains: cooperative effects of binding to starch granules of multiple tandemly arranged domains.
  Appl Environ Microbiol, 73, 3833-3837.  
17622484 O.O.Obembe, E.Jacobsen, J.Timmers, H.Gilbert, A.W.Blake, J.P.Knox, R.G.Visser, and J.P.Vincken (2007).
Promiscuous, non-catalytic, tandem carbohydrate-binding modules modulate the cell-wall structure and development of transgenic tobacco (Nicotiana tabacum) plants.
  J Plant Res, 120, 605-617.  
16230347 A.B.Boraston, M.Healey, J.Klassen, E.Ficko-Blean, A.Lammerts van Bueren, and V.Law (2006).
A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition.
  J Biol Chem, 281, 587-598.
PDB codes: 2c3g 2c3h 2c3v 2c3w 2c3x
16601125 J.Henshaw, A.Horne-Bitschy, A.L.van Bueren, V.A.Money, D.N.Bolam, M.Czjzek, N.A.Ekborg, R.M.Weiner, S.W.Hutcheson, G.J.Davies, A.B.Boraston, and H.J.Gilbert (2006).
Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains.
  J Biol Chem, 281, 17099-17107.
PDB codes: 2cdo 2cdp
16537424 L.McCartney, A.W.Blake, J.Flint, D.N.Bolam, A.B.Boraston, H.J.Gilbert, and J.P.Knox (2006).
Differential recognition of plant cell walls by microbial xylan-specific carbohydrate-binding modules.
  Proc Natl Acad Sci U S A, 103, 4765-4770.  
  16511072 T.Nakamura, K.Ishikawa, Y.Hagihara, T.Oku, A.Nakagawa, T.Inoue, M.Ataka, and K.Uegaki (2005).
Crystallization and preliminary X-ray diffraction analysis of a chitin-binding domain of hyperthermophilic chitinase from Pyrococcus furiosus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 476-478.  
15004012 D.N.Bolam, H.Xie, G.Pell, D.Hogg, G.Galbraith, B.Henrissat, and H.J.Gilbert (2004).
X4 modules represent a new family of carbohydrate-binding modules that display novel properties.
  J Biol Chem, 279, 22953-22963.  
15014076 F.M.Dias, F.Vincent, G.Pell, J.A.Prates, M.S.Centeno, L.E.Tailford, L.M.Ferreira, C.M.Fontes, G.J.Davies, and H.J.Gilbert (2004).
Insights into the molecular determinants of substrate specificity in glycoside hydrolase family 5 revealed by the crystal structure and kinetics of Cellvibrio mixtus mannosidase 5A.
  J Biol Chem, 279, 25517-25526.
PDB code: 1uuq
17147616 Q.Ji, R.J.Oomen, J.P.Vincken, D.N.Bolam, H.J.Gilbert, L.C.Suurs, and R.G.Visser (2004).
Reduction of starch granule size by expression of an engineered tandem starch-binding domain in potato plants.
  Plant Biotechnol J, 2, 251-260.  
12427734 A.B.Boraston, E.Kwan, P.Chiu, R.A.Warren, and D.G.Kilburn (2003).
Recognition and hydrolysis of noncrystalline cellulose.
  J Biol Chem, 278, 6120-6127.  
11849546 A.B.Boraston, B.W.McLean, G.Chen, A.Li, R.A.Warren, and D.G.Kilburn (2002).
Co-operative binding of triplicate carbohydrate-binding modules from a thermophilic xylanase.
  Mol Microbiol, 43, 187-194.  
11958335 S.Subramaniyan, and P.Prema (2002).
Biotechnology of microbial xylanases: enzymology, molecular biology, and application.
  Crit Rev Biotechnol, 22, 33-64.  
11560933 A.C.Freelove, D.N.Bolam, P.White, G.P.Hazlewood, and H.J.Gilbert (2001).
A novel carbohydrate-binding protein is a component of the plant cell wall-degrading complex of Piromyces equi.
  J Biol Chem, 276, 43010-43017.  
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.