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PDBsum entry 1e8r

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protein links
Hydrolase PDB id
1e8r
Jmol
Contents
Protein chain
50 a.a. *
* Residue conservation analysis
PDB id:
1e8r
Name: Hydrolase
Title: Solution structure of type x cbd
Structure: Endo-1,4-beta-xylanase. Chain: a. Fragment: type x cellulose binding domain (cbdx). Engineered: yes
Source: Pseudomonas fluorescens. Organism_taxid: 294. Plasmid: bl21. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 5 models
Authors: S.Raghothama,P.J.Simpson,H.J.Gilbert,M.P.Williamson
Key ref:
S.Raghothama et al. (2000). Solution structure of the CBM10 cellulose binding module from Pseudomonas xylanase A. Biochemistry, 39, 978-984. PubMed id: 10653641 DOI: 10.1021/bi992163+
Date:
28-Sep-00     Release date:   03-Oct-00    
Supersedes: 1ct7
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P14768  (XYNA_CELJU) -  Endo-1,4-beta-xylanase A
Seq:
Struc:
 
Seq:
Struc:
611 a.a.
50 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.3.2.1.8  - 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   1 term 
  Biochemical function     cellulose binding     1 term  

 

 
DOI no: 10.1021/bi992163+ Biochemistry 39:978-984 (2000)
PubMed id: 10653641  
 
 
Solution structure of the CBM10 cellulose binding module from Pseudomonas xylanase A.
S.Raghothama, P.J.Simpson, L.Szabó, T.Nagy, H.J.Gilbert, M.P.Williamson.
 
  ABSTRACT  
 
Plant cell wall hydrolases generally have a modular structure consisting of a catalytic domain linked to one or more noncatalytic carbohydrate-binding modules (CBMs), whose common function is to attach the enzyme to the polymeric substrate. Xylanase A from Pseudomonas fluorescens subsp. cellulosa (Pf Xyn10A) consists of a family 10 catalytic domain, an N-terminal family IIa cellulose-binding module, and an internal family 10 cellulose-binding module. The structure of the 45-residue family 10 CBM has been determined in solution using NMR. It consists of two antiparallel beta-sheets, one with two strands and one with three, with a short alpha-helix across one face of the three-stranded sheet. There is a high density of aromatic residues on one side of the protein, including three aromatic residues (Tyr8, Trp22, and Trp24), which are exposed and form a flat surface on one face, in a classical polysaccharide-binding arrangement. The fold is closely similar to that of the oligonucleotide/oligosaccharide-binding (OB) fold, but appears to have arisen by convergent evolution, because there is no sequence similarity, and the presumed binding sites are on different faces.
 

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.  
20178562 V.Arantes, and J.N.Saddler (2010).
Access to cellulose limits the efficiency of enzymatic hydrolysis: the role of amorphogenesis.
  Biotechnol Biofuels, 3, 4.  
18415096 J.R.Liu, C.H.Duan, X.Zhao, J.T.Tzen, K.J.Cheng, and C.K.Pai (2008).
Cloning of a rumen fungal xylanase gene and purification of the recombinant enzyme via artificial oil bodies.
  Appl Microbiol Biotechnol, 79, 225-233.  
18214952 R.Minai, Y.Matsuo, H.Onuki, and H.Hirota (2008).
Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions.
  Proteins, 72, 367-381.  
17201922 A.Malik, and S.Ahmad (2007).
Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network.
  BMC Struct Biol, 7, 1.  
17103163 N.Palackal, C.S.Lyon, S.Zaidi, P.Luginbühl, P.Dupree, F.Goubet, J.L.Macomber, J.M.Short, G.P.Hazlewood, D.E.Robertson, and B.A.Steer (2007).
A multifunctional hybrid glycosyl hydrolase discovered in an uncultured microbial consortium from ruminant gut.
  Appl Microbiol Biotechnol, 74, 113-124.  
16844685 A.W.Blake, L.McCartney, J.E.Flint, D.N.Bolam, A.B.Boraston, H.J.Gilbert, and J.P.Knox (2006).
Understanding the biological rationale for the diversity of cellulose-directed carbohydrate-binding modules in prokaryotic enzymes.
  J Biol Chem, 281, 29321-29329.  
17005007 M.S.Centeno, A.Goyal, J.A.Prates, L.M.Ferreira, H.J.Gilbert, and C.M.Fontes (2006).
Novel modular enzymes encoded by a cellulase gene cluster in Cellvibrio mixtus.
  FEMS Microbiol Lett, 265, 26-34.  
16314409 S.Najmudin, C.I.Guerreiro, A.L.Carvalho, J.A.Prates, M.A.Correia, V.D.Alves, L.M.Ferreira, M.J.Romão, H.J.Gilbert, D.N.Bolam, and C.M.Fontes (2006).
Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains.
  J Biol Chem, 281, 8815-8828.
PDB codes: 2c24 2c26 2c4x
15784618 J.Flint, D.N.Bolam, D.Nurizzo, E.J.Taylor, M.P.Williamson, C.Walters, G.J.Davies, and H.J.Gilbert (2005).
Probing the mechanism of ligand recognition in family 29 carbohydrate-binding modules.
  J Biol Chem, 280, 23718-23726.
PDB codes: 1w8t 1w8u 1w8w 1w8z 1w90 1w9f 1wcu
15192099 A.L.Carvalho, A.Goyal, J.A.Prates, D.N.Bolam, H.J.Gilbert, V.M.Pires, L.M.Ferreira, A.Planas, M.J.Romão, and C.M.Fontes (2004).
The family 11 carbohydrate-binding module of Clostridium thermocellum Lic26A-Cel5E accommodates beta-1,4- and beta-1,3-1,4-mixed linked glucans at a single binding site.
  J Biol Chem, 279, 34785-34793.
PDB code: 1v0a
15340925 D.M.Standley, H.Toh, and H.Nakamura (2004).
Detecting local structural similarity in proteins by maximizing number of equivalent residues.
  Proteins, 57, 381-391.  
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.  
14738848 I.Levy, T.Paldi, and O.Shoseyov (2004).
Engineering a bifunctional starch-cellulose cross-bridge protein.
  Biomaterials, 25, 1841-1849.  
15004011 J.L.Henshaw, D.N.Bolam, V.M.Pires, M.Czjzek, B.Henrissat, L.M.Ferreira, C.M.Fontes, and H.J.Gilbert (2004).
The family 6 carbohydrate binding module CmCBM6-2 contains two ligand-binding sites with distinct specificities.
  J Biol Chem, 279, 21552-21559.  
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.  
11327868 D.N.Bolam, H.Xie, P.White, P.J.Simpson, S.M.Hancock, M.P.Williamson, and H.J.Gilbert (2001).
Evidence for synergy between family 2b carbohydrate binding modules in Cellulomonas fimi xylanase 11A.
  Biochemistry, 40, 2468-2477.
PDB codes: 1heh 1hej
11478884 H.Xie, H.J.Gilbert, S.J.Charnock, G.J.Davies, M.P.Williamson, P.J.Simpson, S.Raghothama, C.M.Fontes, F.M.Dias, L.M.Ferreira, and D.N.Bolam (2001).
Clostridium thermocellum Xyn10B carbohydrate-binding module 22-2: the role of conserved amino acids in ligand binding.
  Biochemistry, 40, 9167-9176.
PDB codes: 1h6x 1h6y
  11673472 M.Czjzek, D.N.Bolam, A.Mosbah, J.Allouch, C.M.Fontes, L.M.Ferreira, O.Bornet, V.Zamboni, H.Darbon, N.L.Smith, G.W.Black, B.Henrissat, and H.J.Gilbert (2001).
The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved.
  J Biol Chem, 276, 48580-48587.
PDB code: 1gmm
11371186 V.Notenboom, A.B.Boraston, D.G.Kilburn, and D.R.Rose (2001).
Crystal structures of the family 9 carbohydrate-binding module from Thermotoga maritima xylanase 10A in native and ligand-bound forms.
  Biochemistry, 40, 6248-6256.
PDB codes: 1i82 1i8a 1i8u
11785761 Y.Bourne, and B.Henrissat (2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
  Curr Opin Struct Biol, 11, 593-600.  
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.