PDBsum entry 1h6y

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protein metals links
Hydrolase PDB id
Protein chains
157 a.a. *
_CA ×2
Waters ×296
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: The role of conserved amino acids in the cleft of the c-terminal family 22 carbohydrate binding module of clostridium thermocellum xyn10b in ligand binding
Structure: Endo-1,4-beta-xylanase y. Chain: a, b. Fragment: xylan binding domain residue 560-720. Synonym: cbm22-2,xylanase y, xyly, 1,4-beta-d-xylan xylanohydrolase y. Engineered: yes. Mutation: yes
Source: Clostridium thermocellum. Organism_taxid: 1515. Strain: ys. Expressed in: escherichia coli. Expression_system_taxid: 511693.
2.12Å     R-factor:   0.194     R-free:   0.228
Authors: H.Xie,D.N.Bolam,S.J.Charnock,G.J.Davies,M.P.Williamson, P.J.Simpson,C.M.G.A.Fontes,L.M.A.Ferreira,H.J.Gilbert
Key ref:
H.Xie et al. (2001). Clostridium thermocellum Xyn10B carbohydrate-binding module 22-2: the role of conserved amino acids in ligand binding. Biochemistry, 40, 9167-9176. PubMed id: 11478884 DOI: 10.1021/bi0106742
29-Jun-01     Release date:   27-Jun-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P51584  (XYNY_CLOTM) -  Endo-1,4-beta-xylanase Y
1077 a.a.
157 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.  - 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!
  Biochemical function     hydrolase activity, acting on glycosyl bonds     1 term  


DOI no: 10.1021/bi0106742 Biochemistry 40:9167-9176 (2001)
PubMed id: 11478884  
Clostridium thermocellum Xyn10B carbohydrate-binding module 22-2: the role of conserved amino acids in ligand binding.
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, D.N.Bolam.
The majority of plant cell wall hydrolases are modular enzymes which, in addition to a catalytic module, possess one or more carbohydrate-binding modules (CBMs). These carbohydrate-active enzymes and their constituent modules have been classified into a number of families based upon amino acid sequence similarity. The Clostridium thermocellum xylanase, Xyn10B, contains two CBMs that belong to family 22 (CBM22). The crystal structure of the C-terminal CBM22 (CBM22-2) was determined in a previous study [Charnock, S. J., et al. (2000) Biochemistry 39, 5013--5021] and revealed a surface cleft which presents several conserved residues that are implicated in ligand binding. These amino acids have been substituted and the structure and biochemical properties of the mutants analyzed. The data show that R25A, W53A, Y103A, Y136A, and E138A exhibit greatly reduced affinity for xylotetraose relative to that of the wild-type protein. Conversely, mutations Y103F and Y136F have little effect on ligand binding. Using thermodynamic, X-ray, and NMR measurements on the mutants, we show that the cleft of CBM22-2 does indeed form the ligand-binding site. Trp 53 and Tyr 103 most likely participate in hydrophobic stacking interactions with the ligand, while Glu 138 makes one or more important hydrogen bonds with the tetrasaccharide. Although Arg 25 and Tyr 136 are likely to form hydrogen bonds with the ligand, they are also shown to play a critical role in maintaining the structural integrity of the binding cleft.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20721621 D.Schouppe, P.Rougé, Y.Lasanajak, A.Barre, D.F.Smith, P.Proost, and E.J.Van Damme (2010).
Mutational analysis of the carbohydrate binding activity of the tobacco lectin.
  Glycoconj J, 27, 613-623.  
20936681 H.Hwang, T.Vreven, B.G.Pierce, J.H.Hung, and Z.Weng (2010).
Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.
  Proteins, 78, 3104-3110.  
20237675 J.van Ameijde, A.J.Poot, L.T.van Wandelen, A.E.Wammes, R.Ruijtenbeek, D.T.Rijkers, and R.M.Liskamp (2010).
Preparation of novel alkylated arginine derivatives suitable for click-cycloaddition chemistry and their incorporation into pseudosubstrate- and bisubstrate-based kinase inhibitors.
  Org Biomol Chem, 8, 1629-1639.  
20466650 T.Schallus, K.Fehér, U.Sternberg, V.Rybin, and C.Muhle-Goll (2010).
Analysis of the specific interactions between the lectin domain of malectin and diglucosides.
  Glycobiology, 20, 1010-1020.
PDB code: 2kr2
19682075 C.Christiansen, M.Abou Hachem, S.Janecek, A.Viksø-Nielsen, A.Blennow, and B.Svensson (2009).
The carbohydrate-binding module family 20--diversity, structure, and function.
  FEBS J, 276, 5006-5029.  
19389758 I.A.Dvortsov, N.A.Lunina, L.A.Chekanovskaya, W.H.Schwarz, V.V.Zverlov, and G.A.Velikodvorskaya (2009).
Carbohydrate-binding properties of a separately folding protein module from {beta}-1,3-glucanase Lic16A of Clostridium thermocellum.
  Microbiology, 155, 2442-2449.  
18422658 A.Viegas, N.F.Brás, N.M.Cerqueira, P.A.Fernandes, J.A.Prates, C.M.Fontes, M.Bruix, M.J.Romão, A.L.Carvalho, M.J.Ramos, A.L.Macedo, and E.J.Cabrita (2008).
Molecular determinants of ligand specificity in family 11 carbohydrate binding modules: an NMR, X-ray crystallography and computational chemistry approach.
  FEBS J, 275, 2524-2535.  
17985396 C.Junkes, A.Wessolowski, S.Farnaud, R.W.Evans, L.Good, M.Bienert, and M.Dathe (2008).
The interaction of arginine- and tryptophan-rich cyclic hexapeptides with Escherichia coli membranes.
  J Pept Sci, 14, 535-543.  
18784084 M.E.Caines, H.Zhu, M.Vuckovic, L.M.Willis, S.G.Withers, W.W.Wakarchuk, and N.C.Strynadka (2008).
The Structural Basis for T-antigen Hydrolysis by Streptococcus pneumoniae: A TARGET FOR STRUCTURE-BASED VACCINE DESIGN.
  J Biol Chem, 283, 31279-31283.
PDB code: 3ecq
  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.  
16431911 E.J.Taylor, T.M.Gloster, J.P.Turkenburg, F.Vincent, A.M.Brzozowski, C.Dupont, F.Shareck, M.S.Centeno, J.A.Prates, V.Puchart, L.M.Ferreira, C.M.Fontes, P.Biely, and G.J.Davies (2006).
Structure and activity of two metal ion-dependent acetylxylan esterases involved in plant cell wall degradation reveals a close similarity to peptidoglycan deacetylases.
  J Biol Chem, 281, 10968-10975.
PDB codes: 2c71 2c79 2cc0
16461704 F.J.Stjohn, J.D.Rice, and J.F.Preston (2006).
Paenibacillus sp. strain JDR-2 and XynA1: a novel system for methylglucuronoxylan utilization.
  Appl Environ Microbiol, 72, 1496-1506.  
16550304 J.Kleine, and W.Liebl (2006).
Comparative characterization of deletion derivatives of the modular xylanase XynA of Thermotoga maritima.
  Extremophiles, 10, 373-381.  
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.  
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
15665481 E.Ali, G.Zhao, M.Sakka, T.Kimura, K.Ohmiya, and K.Sakka (2005).
Functions of family-22 carbohydrate-binding module in Clostridium thermocellum Xyn10C.
  Biosci Biotechnol Biochem, 69, 160-165.  
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
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.  
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.  
15184164 Y.Brennan, W.N.Callen, L.Christoffersen, P.Dupree, F.Goubet, S.Healey, M.Hernández, M.Keller, K.Li, N.Palackal, A.Sittenfeld, G.Tamayo, S.Wells, G.P.Hazlewood, E.J.Mathur, J.M.Short, D.E.Robertson, and B.A.Steer (2004).
Unusual microbial xylanases from insect guts.
  Appl Environ Microbiol, 70, 3609-3617.  
12842048 A.Varrot, T.P.Frandsen, I.von Ossowski, V.Boyer, S.Cottaz, H.Driguez, M.Schülein, and G.J.Davies (2003).
Structural basis for ligand binding and processivity in cellobiohydrolase Cel6A from Humicola insolens.
  Structure, 11, 855-864.
PDB codes: 1oc5 1oc6 1oc7 1ocb 1ocj
12833544 D.J.Rigden, and M.J.Jedrzejas (2003).
Genome-based identification of a carbohydrate binding module in Streptococcus pneumoniae hyaluronate lyase.
  Proteins, 52, 203-211.  
14660338 Y.Ito, T.Tomita, N.Roy, A.Nakano, N.Sugawara-Tomita, S.Watanabe, N.Okai, N.Abe, and Y.Kamio (2003).
Cloning, expression, and cell surface localization of Paenibacillus sp. strain W-61 xylanase 5, a multidomain xylanase.
  Appl Environ Microbiol, 69, 6969-6978.  
11980475 P.J.Simpson, S.J.Jamieson, M.Abou-Hachem, E.N.Karlsson, H.J.Gilbert, O.Holst, and M.P.Williamson (2002).
The solution structure of the CBM4-2 carbohydrate binding module from a thermostable Rhodothermus marinus xylanase.
  Biochemistry, 41, 5712-5719.
PDB codes: 1k42 1k45
11738044 J.A.Prates, N.Tarbouriech, S.J.Charnock, C.M.Fontes, L.M.Ferreira, and G.J.Davies (2001).
The structure of the feruloyl esterase module of xylanase 10B from Clostridium thermocellum provides insights into substrate recognition.
  Structure, 9, 1183-1190.
PDB codes: 1gkk 1gkl
  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
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.