5FIP | pdb_00005fip

Discovery and characterization of a novel thermostable and highly halotolerant GH5 cellulase from an Icelandic hot spring isolate

• PDB DOI: https://doi.org/10.2210/pdb5FIP/pdb

• Classification: HYDROLASE
• Organism(s): unidentified
• Mutation(s): No 


• Deposited: 2015-10-01 Released: 2016-01-20 
• Deposition Author(s): Zarafeta, D., Kissas, D., Sayer, C., Gudbergsdottir, S.R., Ladoukakis, E., Isupov, M.N., Chatziioannou, A., Peng, X., Littlechild, J.A., Skretas, G., Kolisis, F.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Discovery and Characterization of a Thermostable and Highly Halotolerant Gh5 Cellulase from an Icelandic Hot Spring Isolate.

Zarafeta, D., Kissas, D., Sayer, C., Gudbergsdottir, S.R., Ladoukakis, E., Isupov, M.N., Chatziioannou, A., Peng, X., Littlechild, J.A., Skretas, G., Kolisis, F.N.

(2016) PLoS One 11: 46454

• PubMed: 26741138 
• DOI: https://doi.org/10.1371/journal.pone.0146454
• Primary Citation Related Structures: 
  5FIP


• PubMed Abstract: 
  

  With the ultimate goal of identifying robust cellulases for industrial biocatalytic conversions, we have isolated and characterized a new thermostable and very halotolerant GH5 cellulase. This new enzyme, termed CelDZ1, was identified by bioinformatic analysis from the genome of a polysaccharide-enrichment culture isolate, initiated from material collected from an Icelandic hot spring. Biochemical characterization of CelDZ1 revealed that it is a glycoside hydrolase with optimal activity at 70°C and pH 5.0 that exhibits good thermostability, high halotolerance at near-saturating salt concentrations, and resistance towards metal ions and other denaturing agents. X-ray crystallography of the new enzyme showed that CelDZ1 is the first reported cellulase structure that lacks the defined sugar-binding 2 subsite and revealed structural features which provide potential explanations of its biochemical characteristics.

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Organizational Affiliation: 
• Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.
Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom.
Danish Archaea Centre, Department of Biology, Copenhagen University, Copenhagen, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 153.43 kDa 
• Atom Count: 11,615 
• Modeled Residue Count: 1,322 
• Deposited Residue Count: 1,336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH5 CELLULASE	A, B, C, D	334	unidentified	Mutation(s): 0  EC: 3.2.1.4
UniProt
Find proteins for I3VS73 (Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485)) Explore I3VS73  Go to UniProtKB:  I3VS73

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG6	HA [auth B]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C12 H26 O6 DMDPGPKXQDIQQG-UHFFFAOYSA-N
PG4	BB [auth D]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	L [auth A], M [auth A], RA [auth C], Y [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], QA [auth C], VA [auth D], W [auth B], X [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	AA [auth B], AB [auth D], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A], SA [auth C], WA [auth D], XA [auth D], YA [auth D], Z [auth B], ZA [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	CB [auth D], DB [auth D], EB [auth D], FB [auth D], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], R [auth A], S [auth A], TA [auth C]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL	GB [auth D], OA [auth B], PA [auth B], T [auth A], U [auth A], UA [auth C], V [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.34	α = 90
b = 137.45	β = 114.44
c = 121.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Zarafeta, D., Kissas, D., Sayer, C., Gudbergsdottir, S.R., Ladoukakis, E., Isupov, M.N., Chatziioannou, A., Peng, X., Littlechild, J.A., Skretas, G., Kolisis, F.N.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description