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PDBsum entry 1gmm

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protein ligands metals links
Xylanase PDB id
1gmm
Jmol
Contents
Protein chain
126 a.a. *
Ligands
SO4
Metals
_CA
_NA
Waters ×180
* Residue conservation analysis
PDB id:
1gmm
Name: Xylanase
Title: Carbohydrate binding module cbm6 from xylanase u clostridium thermocellum
Structure: Cbm6. Chain: a. Fragment: xylan binding module (domain), residue 248-380. Engineered: yes
Source: Clostridium thermocellum. Organism_taxid: 1515. Strain: f1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.0Å     R-factor:   0.208     R-free:   0.215
Authors: M.Czjzek,A.Mosbah,D.Bolam,J.Allouch,V.Zamboni,B.Henrissat, H.J.Gilbert
Key ref:
M.Czjzek et al. (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. PubMed id: 11673472 DOI: 10.1074/jbc.M109142200
Date:
19-Sep-01     Release date:   28-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O52780  (O52780_CLOTM) -  Xylanase U
Seq:
Struc:
 
Seq:
Struc:
683 a.a.
126 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     carbohydrate binding     1 term  

 

 
DOI no: 10.1074/jbc.M109142200 J Biol Chem 276:48580-48587 (2001)
PubMed id: 11673472  
 
 
The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved.
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, H.J.Gilbert.
 
  ABSTRACT  
 
Polysaccharide-degrading enzymes are generally modular proteins that contain non-catalytic carbohydrate-binding modules (CBMs), which potentiate the activity of the catalytic module. CBMs have been grouped into sequence-based families, and three-dimensional structural data are available for half of these families. Clostridium thermocellum xylanase 11A is a modular enzyme that contains a CBM from family 6 (CBM6), for which no structural data are available. We have determined the crystal structure of this module to a resolution of 2.1 A. The protein is a beta-sandwich that contains two potential ligand-binding clefts designated cleft A and B. The CBM interacts primarily with xylan, and NMR spectroscopy coupled with site-directed mutagenesis identified cleft A, containing Trp-92, Tyr-34, and Asn-120, as the ligand-binding site. The overall fold of CBM6 is similar to proteins in CBM families 4 and 22, although surprisingly the ligand-binding site in CBM4 and CBM22 is equivalent to cleft B in CBM6. These structural data define a superfamily of CBMs, comprising CBM4, CBM6, and CBM22, and demonstrate that, although CBMs have evolved from a relatively small number of ancestors, the structural elements involved in ligand recognition have been assembled at different locations on the ancestral scaffold.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Electron density map at 2.1 Å and the final structural model represented as sticks. a, final electron density map, contoured at a 1 level, in the region of Tyr-34 and Trp-92, also showing the putative sodium ion. b, electron density map (1 level) showing the presence of a structural calcium ion bridging the N- and C-terminal ends. The figures were produced using the program TURBO-FRODO (26).
Figure 2.
Fig. 2. Ribbon and surface representations of CBM6. a, view showing the ligand-binding cleft (cleft A) formed by the loops between the two -sheets of the sandwich fold. b, surface representation of CBM6 in the same orientation as in a. The shallow binding cleft on top of the globular molecule is formed by Tyr-34 and Trp-92. c, ribbon representation of CBM6 in a perpendicular view with respect to a, showing the second possible cleft (cleft B), which is obstructed by a short loop in CBM6, situated on the concave face of the -sheet sandwich. a and c were produced with Molscript (45) and Raster3D (46), whereas b was produced using GRASP (47).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 48580-48587) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20944224 A.P.Yeh, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, X.Cai, D.Carlton, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, K.Ellrott, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, W.W.Lam, D.Marciano, D.McMullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, C.Puckett, R.Reyes, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1287-1296.
PDB code: 3hbz
19897648 S.Yoshida, R.I.Mackie, and I.K.Cann (2010).
Biochemical and domain analyses of FSUAxe6B, a modular acetyl xylan esterase, identify a unique carbohydrate binding module in Fibrobacter succinogenes S85.
  J Bacteriol, 192, 483-493.  
19218457 C.Montanier, A.L.van Bueren, C.Dumon, J.E.Flint, M.A.Correia, J.A.Prates, S.J.Firbank, R.J.Lewis, G.G.Grondin, M.G.Ghinet, T.M.Gloster, C.Herve, J.P.Knox, B.G.Talbot, J.P.Turkenburg, J.Kerovuo, R.Brzezinski, C.M.Fontes, G.J.Davies, A.B.Boraston, and H.J.Gilbert (2009).
Evidence that family 35 carbohydrate binding modules display conserved specificity but divergent function.
  Proc Natl Acad Sci U S A, 106, 3065-3070.
PDB codes: 2vzp 2vzq 2vzr 2w1w 2w3j 2w46 2w47 2w87
19422833 E.Ficko-Blean, and A.B.Boraston (2009).
N-acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH.
  J Mol Biol, 390, 208-220.
PDB codes: 2w1q 2w1s 2w1u 2wdb
18516288 R.M.Weiner, L.E.Taylor, B.Henrissat, L.Hauser, M.Land, P.M.Coutinho, C.Rancurel, E.H.Saunders, A.G.Longmire, H.Zhang, E.A.Bayer, H.J.Gilbert, F.Larimer, I.B.Zhulin, N.A.Ekborg, R.Lamed, P.M.Richardson, I.Borovok, and S.Hutcheson (2008).
Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T.
  PLoS Genet, 4, e1000087.  
  17671370 E.Vandermarliere, T.M.Bourgois, S.Van Campenhout, S.V.Strelkov, G.Volckaert, J.A.Delcour, C.M.Courtin, and A.Rabijns (2007).
Crystallization and preliminary X-ray analysis of an arabinoxylan arabinofuranohydrolase from Bacillus subtilis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 692-694.  
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.  
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.  
16621834 P.Boonserm, M.Mo, C.Angsuthanasombat, and J.Lescar (2006).
Structure of the functional form of the mosquito larvicidal Cry4Aa toxin from Bacillus thuringiensis at a 2.8-angstrom resolution.
  J Bacteriol, 188, 3391-3401.
PDB code: 2c9k
16333341 D.K.Kam, H.S.Jun, J.K.Ha, G.D.Inglis, and C.W.Forsberg (2005).
Characteristics of adjacent family 6 acetylxylan esterases from Fibrobacter succinogenes and the interaction with the Xyn10E xylanase in hydrolysis of acetylated xylan.
  Can J Microbiol, 51, 821-832.  
15242594 S.Jamal-Talabani, A.B.Boraston, J.P.Turkenburg, N.Tarbouriech, V.M.Ducros, and G.J.Davies (2004).
Ab initio structure determination and functional characterization of CBM36; a new family of calcium-dependent carbohydrate binding modules.
  Structure, 12, 1177-1187.
PDB codes: 1ux7 1w0n
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.  
12831897 D.Shallom, and Y.Shoham (2003).
Microbial hemicellulases.
  Curr Opin Microbiol, 6, 219-228.  
12729009 K.Sakka, M.Nakanishi, M.Sogabe, T.Arai, H.Ohara, A.Tanaka, T.Kimura, and K.Ohmiya (2003).
Isothermal titration calorimetric studies on the binding of a family 6 carbohydrate-binding module of Clostridium thermocellum xynA with xlylooligosaccharides.
  Biosci Biotechnol Biochem, 67, 406-409.  
12391332 S.J.Charnock, D.N.Bolam, D.Nurizzo, L.Szabó, V.A.McKie, H.J.Gilbert, and G.J.Davies (2002).
Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello- and mannohexaose.
  Proc Natl Acad Sci U S A, 99, 14077-14082.
PDB codes: 1gwk 1gwl 1gwm
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.