5FIP

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.234
R-Value Work: 0.193
R-Value Observed: 0.195

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0146454
Primary Citation of 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.

Organizational Affiliation

Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3VS73
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 Download Ideal Coordinates CCD File SDF format, chain HA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain HA [auth B]	HA [auth B]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Interactions & Density Focus chain HA [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain BB [auth D] MOL2 format, chain BB [auth D] mmCIF format, chain BB [auth D]	BB [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Interactions & Density Focus chain BB [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain RA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain RA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain RA [auth C]	L [auth A], M [auth A], RA [auth C], Y [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain RA [auth C] Focus chain Y [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain RA [auth C] Focus chain Y [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain E [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain QA [auth C] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain QA [auth C] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain QA [auth C] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain SA [auth C] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain N [auth A] SDF format, chain Q [auth A] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	AA [auth B] AB [auth D] BA [auth B] CA [auth B] DA [auth B] 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		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain SA [auth C] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain SA [auth C] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain DB [auth D] SDF format, chain JA [auth B] SDF format, chain R [auth A] SDF format, chain CB [auth D] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain IA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain S [auth A] SDF format, chain TA [auth C] MOL2 format, chain DB [auth D] MOL2 format, chain JA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain CB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth C] mmCIF format, chain DB [auth D] mmCIF format, chain JA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain CB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain FB [auth D] mmCIF format, chain IA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain TA [auth C]	CB [auth D] DB [auth D] EB [auth D] FB [auth D] IA [auth B] 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		Interactions Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth C] Interactions & Density Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain GB [auth D] SDF format, chain UA [auth C] SDF format, chain V [auth A] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain UA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A]	GB [auth D] OA [auth B] PA [auth B] T [auth A] U [auth A] 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		Interactions Focus chain GB [auth D] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Interactions & Density Focus chain GB [auth D] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.234
R-Value Work: 0.193
R-Value Observed: 0.195
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-01-20

Deposition Author(s):

Revision History (Full details and data files)

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