2NLR

STREPTOMYCES LIVIDANS ENDOGLUCANASE (EC: 3.2.1.4) COMPLEX WITH MODIFIED GLUCOSE TRIMER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.142 
  • R-Value Observed: 0.111 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution.

Sulzenbacher, G.Mackenzie, L.F.Wilson, K.S.Withers, S.G.Dupont, C.Davies, G.J.

(1999) Biochemistry 38: 4826-4833

  • DOI: 10.1021/bi982648i
  • Structures With Same Primary Citation

  • PubMed 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. ...

    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.


    Related Citations: 
    • The Streptomyces lividans Family 12 Endoglucanase: Construction of the Catalytic Core, Expression and X-Ray Structure at 1.75 A Resolution
      Sulzenbacher, G., Sharek, F., Morosoli, R., Dupont, C., Davies, G.J.
      (1997) Biochemistry 36: 16032
    • Purification and Characterisation of the Celb Endoglucanase from Streptomyces lividans 66 and DNA Sequence of the Encoding Gene
      Wittmann, S., Shareck, F., Kluepfel, D., Morosoli, R.
      (1994) Appl Environ Microbiol 60: 1701

    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, Y010 5DD, U.K.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ENDOGLUCANASE (E.C.3.2.1.4))
A
234Streptomyces lividansMutation(s): 0 
Gene Names: celB
EC: 3.2.1.4
Find proteins for Q54331 (Streptomyces lividans)
Go to UniProtKB:  Q54331
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SHG
Query on SHG

Download CCD File 
A
2-deoxy-2-fluoro-beta-D-glucopyranose
C6 H11 F O5
ZCXUVYAZINUVJD-QZABAPFNSA-N
 Ligand Interaction
G2F
Query on G2F

Download CCD File 
A
2-deoxy-2-fluoro-alpha-D-glucopyranose
C6 H11 F O5
ZCXUVYAZINUVJD-UKFBFLRUSA-N
 Ligand Interaction
BGC
Query on BGC

Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.142 
  • R-Value Observed: 0.111 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.96α = 90
b = 65.96β = 90
c = 88.741γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXLrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-10
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description