4MGQ

PbXyn10C CBM APO

PDB DOI: 10.2210/pdb4MGQ/pdb

Classification: HYDROLASE
Organism(s): Prevotella bryantii B14
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-08-28 Released: 2014-08-20
Deposition Author(s): Chekan, J.R., Nair, S.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.209
R-Value Work: 0.182
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes.

Zhang, M., Chekan, J.R., Dodd, D., Hong, P.Y., Radlinski, L., Revindran, V., Nair, S.K., Mackie, R.I., Cann, I.

(2014) Proc Natl Acad Sci U S A 111: E3708-E3717

PubMed: 25136124 Search on PubMedSearch on PubMed Central
DOI: 10.1073/pnas.1406156111
Primary Citation of Related Structures:
4MGQ, 4MGS, 4QPW

PubMed Abstract:

Enzymes that degrade dietary and host-derived glycans represent the most abundant functional activities encoded by genes unique to the human gut microbiome. However, the biochemical activities of a vast majority of the glycan-degrading enzymes are poorly understood. Here, we use transcriptome sequencing to understand the diversity of genes expressed by the human gut bacteria Bacteroides intestinalis and Bacteroides ovatus grown in monoculture with the abundant dietary polysaccharide xylan. The most highly induced carbohydrate active genes encode a unique glycoside hydrolase (GH) family 10 endoxylanase (BiXyn10A or BACINT_04215 and BACOVA_04390) that is highly conserved in the Bacteroidetes xylan utilization system. The BiXyn10A modular architecture consists of a GH10 catalytic module disrupted by a 250 amino acid sequence of unknown function. Biochemical analysis of BiXyn10A demonstrated that such insertion sequences encode a new family of carbohydrate-binding modules (CBMs) that binds to xylose-configured oligosaccharide/polysaccharide ligands, the substrate of the BiXyn10A enzymatic activity. The crystal structures of CBM1 from BiXyn10A (1.8 Å), a cocomplex of BiXyn10A CBM1 with xylohexaose (1.14 Å), and the CBM from its homolog in the Prevotella bryantii B14 Xyn10C (1.68 Å) reveal an unanticipated mode for ligand binding. A minimal enzyme mix, composed of the gene products of four of the most highly up-regulated genes during growth on wheat arabinoxylan, depolymerizes the polysaccharide into its component sugars. The combined biochemical and biophysical studies presented here provide a framework for understanding fiber metabolism by an important group within the commensal bacterial population known to influence human health.

Organizational Affiliation:

Energy Biosciences Institute, Institute for Genomic Biology, and Departments of Animal Sciences, Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 icann@illinois.edu s-nair@life.illinois.edu r-mackie@illinois.edu.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 10	A	168	Prevotella bryantii B14	Mutation(s): 0 Gene Names: PBR_0377, SAMN05444375_11828 EC: 3.2.1.8
UniProt
Find proteins for D8DVU6 (Prevotella bryantii B14) Explore D8DVU6 Go to UniProtKB: D8DVU6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D8DVU6
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction