3QHO

Crystal analysis of the complex structure, Y299F-cellotetraose, of endocellulase from pyrococcus horikoshii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Functional analysis of hyperthermophilic endocellulase from Pyrococcus horikoshii by crystallographic snapshots

Kim, H.-W.Ishikawa, K.

(2011) Biochem.J. 437: 223-230

  • DOI: 10.1042/BJ20110292
  • Primary Citation of Related Structures:  3AXX, 3QHM, 3QHN

  • PubMed Abstract: 
  • A hyperthermophilic membrane-related β-1,4-endoglucanase (family 5, cellulase) of the archaeon Pyrococcus horikoshii was found to be capable of hydrolysing cellulose at high temperatures. The hyperthermophilic cellulase has promise for applications i ...

    A hyperthermophilic membrane-related β-1,4-endoglucanase (family 5, cellulase) of the archaeon Pyrococcus horikoshii was found to be capable of hydrolysing cellulose at high temperatures. The hyperthermophilic cellulase has promise for applications in biomass utilization. To clarify its detailed function, we determined the crystal structures of mutants of the enzyme in complex with either the substrate or product ligands. We were able to resolve different kinds of complex structures at 1.65-2.01 Å (1 Å=0.1 nm). The structural analysis of various mutant enzymes yielded a sequence of crystallographic snapshots, which could be used to explain the catalytic process of the enzyme. The substrate position is fixed by the alignment of one cellobiose unit between the two aromatic amino acid residues at subsites +1 and +2. During the enzyme reaction, the glucose structure of cellulose substrates is distorted at subsite -1, and the β-1,4-glucoside bond between glucose moieties is twisted between subsites -1 and +1. Subsite -2 specifically recognizes the glucose residue, but recognition by subsites +1 and +2 is loose during the enzyme reaction. This type of recognition is important for creation of the distorted boat form of the substrate at subsite -1. A rare enzyme-substrate complex was observed within the low-activity mutant Y299F, which suggested the existence of a trapped ligand structure before the formation by covalent bonding of the proposed intermediate structure. Analysis of the enzyme-substrate structure suggested that an incoming water molecule, essential for hydrolysis during the retention process, might be introduced to the cleavage position after the cellobiose product at subsites +1 and +2 was released from the active site.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of endoglucanase from Pyrococcus horikoshii
      Kim, H.-W.,Mino, K.,Ishikawa, K.
      (2008) Acta Crystallogr.,Sect.F 64: 1169
    • Structure of hyperthermophilic endocellulase from Pyrococcus horikoshii
      Kim, H.-W.,Ishikawa, K.
      (2010) Proteins 78: 496


    Organizational Affiliation

    National Institute of Advanced Industrial Science and Technology (AIST), Health Research Institute, Ikeda, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
458aa long hypothetical endo-1,4-beta-glucanase
A, B, C
458Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)N/A
Find proteins for O58925 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O58925
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CTT
Query on CTT

Download SDF File 
Download CCD File 
A, B, C
beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranose
CELLOTETRAOSE
C24 H42 O21
LUEWUZLMQUOBSB-HGDSAIHNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 161.164α = 90.00
b = 58.528β = 109.24
c = 138.317γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description