5T3B

Crystal structure of BpGH50

PDB DOI: https://doi.org/10.2210/pdb5T3B/pdb

Classification: HYDROLASE
Organism(s): Phocaeicola plebeius
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-25 Released: 2016-10-12
Deposition Author(s): Giles, K., Pluvinage, B., Boraston, A.B.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.145
R-Value Work: 0.106
R-Value Observed: 0.108

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure of a glycoside hydrolase family 50 enzyme from a subfamily that is enriched in human gut microbiome bacteroidetes.

Giles, K., Pluvinage, B., Boraston, A.B.

(2017) Proteins 85: 182-187

PubMed: 27756110 Search on PubMed
DOI: https://doi.org/10.1002/prot.25189
Primary Citation of Related Structures:
5T3B

PubMed Abstract:
The polysaccharide utilization locus in Bacteroides plebeius that confers the ability to catabolize porphyran contains a putative GH50 β-agarase (BACPLE_01683, BpGH50). BpGH50 did not show any clear activity on agarose or on the related algal galactans porphyran and carrageenan. However, the 1.4 Å resolution X-ray crystal structure of BpGH50 confirmed its possession of the core (α/β) ₈ barrel fold found in GH50 enzymes as well as the structural conservation of the catalytic residues and some substrate binding residues. Examination of the structure supports assignment of this protein as a β-galactosidase but suggests that it may utilize a different, possibly hybrid, algal galactan substrate. Proteins 2016; 85:182-187. © 2016 Wiley Periodicals, Inc.

Organizational Affiliation

Biochemistry & Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada.

Macromolecule Content

Total Structure Weight: 110.5 kDa
Atom Count: 8,756
Modelled Residue Count: 915
Deposited Residue Count: 962
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside Hydrolase	A, B	481	Phocaeicola plebeius	Mutation(s): 0 Gene Names: BACPLE_01683
UniProt
Find proteins for B5CY86 (Phocaeicola plebeius (strain DSM 17135 / JCM 12973 / CCUG 54634 / M2)) Explore B5CY86 Go to UniProtKB: B5CY86
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5CY86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] 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 J [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [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 J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [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 J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [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], P [auth A], Q [auth B], R [auth B], S [auth B], T [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] 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] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] 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] Focus chain P [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]