3VGI | pdb_00003vgi

The crystal structure of hyperthermophilic family 12 endocellulase from Pyrococcus furiosus

PDB DOI: https://doi.org/10.2210/pdb3VGI/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-08-11 Released: 2012-09-12
Deposition Author(s): Kataoka, M., Kim, H.-W., Ishikawa, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.07 ?
R-Value Free:
0.158 (Depositor), 0.160 (DCC)
R-Value Work:
0.127 (Depositor), 0.130 (DCC)
R-Value Observed:
0.129 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Atomic resolution of the crystal structure of the hyperthermophilic family 12 endocellulase and stabilizing role of the DxDxDG calcium-binding motif in Pyrococcus furiosus.

Kim, H.-W., Kataoka, M., Ishikawa, K.

(2012) FEBS Lett 586: 1009-1013

PubMed: 22569255 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2012.02.029
Primary Citation of Related Structures:
3VGI

PubMed Abstract:
Hyperthermophilic glycoside hydrolase family 12 endocellulase (EGPf) from the archaeon Pyrococcus furiosus catalyzes the hydrolytic cleavage of β-1,4-glucosidic linkage in β-glucan cellulose. A truncated EGPf (EGPfΔN30) mutant lacking the proline and hydroxyl-residue rich region at the N terminus was constructed, and its crystal structure was resolved at an atomic resolution of 1.07 ?. Our results indicate that the structure of EGPf, which consists of a β-jelly roll, exhibits structural similarity with the endocellulase of Thermotoga maritima. Additionally, we further determined that the thermostability of EGPf is maintained in part by the binding of Ca?? in a DxDxDG Ca??-binding motif, atypical of most archaeal proteins.

Organizational Affiliation

National Institute of Advanced Industrial Science and Technology, Biomass Technology Research Center, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.

Macromolecule Content

Total Structure Weight: 37.48 kDa
Atom Count: 2,657
Modelled Residue Count: 270
Deposited Residue Count: 319
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase A	A	319	Pyrococcus furiosus	Mutation(s): 0 Gene Names: eglA
UniProt
Find proteins for Q9V2T0 (Pyrococcus furiosus) Explore Q9V2T0 Go to UniProtKB: Q9V2T0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9V2T0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NHE Query on NHE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] 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 J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain E [auth A] 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 J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain E [auth A] 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 J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	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], L [auth A], M [auth A], N [auth A], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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 L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] 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 L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]