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PDBsum entry 2nlr

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protein ligands links
Hydrolase PDB id
2nlr
Jmol
Contents
Protein chain
222 a.a. *
Ligands
BGC-BGC-G2F-SHG
Waters ×306
* Residue conservation analysis
PDB id:
2nlr
Name: Hydrolase
Title: Streptomyces lividans endoglucanase (ec: 3.2.1.4) complex wi modified glucose trimer
Structure: Protein (endoglucanase . Chain: a. Fragment: catalytic domain. Synonym: celb. Engineered: yes
Source: Streptomyces lividans. Organism_taxid: 1916. Strain: 66. Gene: celb. Expressed in: streptomyces lividans. Expression_system_taxid: 1916.
Resolution:
1.20Å     R-factor:   0.112     R-free:   0.142
Authors: G.Sulzenbacher,C.Dupont,G.J.Davies
Key ref:
G.Sulzenbacher et al. (1999). The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution. Biochemistry, 38, 4826-4833. PubMed id: 10200171 DOI: 10.1021/bi982648i
Date:
02-Nov-98     Release date:   10-Nov-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q54331  (Q54331_STRLI) -  Cellulase B
Seq:
Struc:
381 a.a.
222 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     polysaccharide catabolic process   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     2 terms  

 

 
DOI no: 10.1021/bi982648i Biochemistry 38:4826-4833 (1999)
PubMed id: 10200171  
 
 
The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution.
G.Sulzenbacher, L.F.Mackenzie, K.S.Wilson, S.G.Withers, C.Dupont, G.J.Davies.
 
  ABSTRACT  
 
Glycoside hydrolases have been classified into over 66 families on the basis of amino acid sequence. Recently a number of these families have been grouped into "clans" which share a common fold and catalytic mechanism [Henrissat, B., and Bairoch, A. (1996) Biochem. J. 316, 695-696]. Glycoside hydrolase Clan GH-C groups family 11 xylanases and family 12 cellulases, which share the same jellyroll topology, with two predominantly antiparallel beta-sheets forming a long substrate-binding cleft, and act with net retention of anomeric configuration. Here we present the three-dimensional structure of a family 12 endoglucanase, Streptomyces lividans CelB2, in complex with a 2-deoxy-2-fluorocellotrioside. Atomic resolution (1.2 A) data allow clear identification of two distinct species in the crystal. One is the glycosyl-enzyme intermediate, with the mechanism-based inhibitor covalently linked to the nucleophile Glu 120, and the other a complex with the reaction product, 2-deoxy-2-fluoro-beta-D-cellotriose. The active site architecture of the complex provides insight into the double-displacement mechanism of retaining glycoside hydrolases and also sheds light on the basis of the differences in specificity between family 12 cellulases and family 11 xylanases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17266375 D.Crich, and L.Li (2007).
4,6-O-benzylidene-directed beta-mannopyranosylation and alpha-glucopyranosylation: the 2-deoxy-2-fluoro and 3-deoxy-3-fluoro series of donors and the importance of the O2-C2-C3-O3 interaction.
  J Org Chem, 72, 1681-1690.  
17376777 T.M.Gloster, F.M.Ibatullin, K.Macauley, J.M.Eklöf, S.Roberts, J.P.Turkenburg, M.E.Bjørnvad, P.L.Jørgensen, S.Danielsen, K.S.Johansen, T.V.Borchert, K.S.Wilson, H.Brumer, and G.J.Davies (2007).
Characterization and three-dimensional structures of two distinct bacterial xyloglucanases from families GH5 and GH12.
  J Biol Chem, 282, 19177-19189.
PDB codes: 2jem 2jen 2jep 2jeq
15853815 J.Jänis, J.Hakanpää, N.Hakulinen, F.M.Ibatullin, A.Hoxha, P.J.Derrick, J.Rouvinen, and P.Vainiotalo (2005).
Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography.
  FEBS J, 272, 2317-2333.
PDB code: 1xnk
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
14715651 G.Sulzenbacher, C.Bignon, T.Nishimura, C.A.Tarling, S.G.Withers, B.Henrissat, and Y.Bourne (2004).
Crystal structure of Thermotoga maritima alpha-L-fucosidase. Insights into the catalytic mechanism and the molecular basis for fucosidosis.
  J Biol Chem, 279, 13119-13128.
PDB codes: 1hl8 1hl9 1odu
12649442 M.Sandgren, P.J.Gualfetti, A.Shaw, L.S.Gross, M.Saldajeno, A.G.Day, T.A.Jones, and C.Mitchinson (2003).
Comparison of family 12 glycoside hydrolases and recruited substitutions important for thermal stability.
  Protein Sci, 12, 848-860.
PDB codes: 1oa2 1oa3 1oa4
11914491 S.Khademi, D.Zhang, S.M.Swanson, A.Wartenberg, K.Witte, and E.F.Meyer (2002).
Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride.
  Acta Crystallogr D Biol Crystallogr, 58, 660-667.
PDB codes: 1ks4 1ks5
11526340 E.Sabini, K.S.Wilson, S.Danielsen, M.Schülein, and G.J.Davies (2001).
Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display (2,5)B conformations at the active centre.
  Acta Crystallogr D Biol Crystallogr, 57, 1344-1347.
PDB codes: 1h4g 1h4h
10679381 G.A.Petsko, and D.Ringe (2000).
Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.
  Curr Opin Chem Biol, 4, 89-94.  
10824094 S.Zhang, D.C.Irwin, and D.B.Wilson (2000).
Site-directed mutation of noncatalytic residues of Thermobifida fusca exocellulase Cel6B.
  Eur J Biochem, 267, 3101-3115.  
11042447 U.M.Unligil, and J.M.Rini (2000).
Glycosyltransferase structure and mechanism.
  Curr Opin Struct Biol, 10, 510-517.  
11032794 U.M.Unligil, S.Zhou, S.Yuwaraj, M.Sarkar, H.Schachter, and J.M.Rini (2000).
X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.
  EMBO J, 19, 5269-5280.
PDB codes: 1fo8 1fo9 1foa
10381409 E.Sabini, G.Sulzenbacher, M.Dauter, Z.Dauter, P.L.Jørgensen, M.Schülein, C.Dupont, G.J.Davies, and K.S.Wilson (1999).
Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.
  Chem Biol, 6, 483-492.
PDB codes: 1h4g 1h4h 1qh6 1qh7
10508763 J.Jiménez-Barbero, J.L.Asensio, F.J.Cañada, and A.Poveda (1999).
Free and protein-bound carbohydrate structures.
  Curr Opin Struct Biol, 9, 549-555.  
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.