PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

Related Articles
Signaling: A Platform for Opposing Functions
May 2015
Protein Folding and Misfolding: It's the Journey, Not the Destination
March 2015
Molecular Portraits of the Cell
February 2015
Nuclear Pore Complex: A Flexible Transporter
February 2015
Nuclear Pore Complex: Higher Resolution of Macromolecules
February 2015
Nuclear Pore Complex: Integrative Approach to Probe Nup133
February 2015
Piecing Together the Nuclear Pore Complex
February 2015
Updating ModBase
January 2015
Transmembrane Spans
December 2014
Mining Protein Dynamics
May 2014
Novel Proteins and Networks: Assigning Function
May 2014
Cancer Networks: Predicting Catalytic Residues from 3D Protein Structures
November 2013
The Immune System: A Brotherhood of Immunoglobulins
June 2013
The Immune System: Super Cytokines
June 2013
Infectious Diseases: Targeting Meningitis
May 2013
PDZ Domains
April 2013
Protein Interaction Networks: Adding Structure to Protein Networks
April 2013
Design and Discovery: Flexible Backbone Protein Redesign
February 2013
Pocket changes
July 2012
Predictive protein origami
July 2012
Refining protein structure prediction
March 2012
Metal mates
February 2012
Devil is in the details
January 2012
Playing while you work
November 2011
Docking and rolling
October 2011
Fit to serve
October 2011
Rosetta hone
July 2011
Structure from sequence
July 2011
An easier solution for symmetry
June 2011
Solutions in the solution
June 2011
Regulating nitrogen assimilation
January 2011
Guard cells pick up the SLAC
December 2010
Alpha/Beta Barrels
October 2010
Modeling RNA structures
May 2010
Deducing function from small structural clues
February 2010
Spot the pore
January 2010
Network coverage
November 2009
GPCR modeling: any good?
August 2009
Protein modeling made easy
July 2009
Model proteins in your lunch break
April 2009
Click for cancer-protein interactions
December 2008
Modeling with SAXS
October 2008
Designing activity
September 2008

Technology Topics Modeling

Novel Proteins and Networks: Assigning Function

SBKB [doi:10.1038/sbkb.2014.199]
Featured Article - May 2014
Short description: Structural modeling and docking of substrates identifies a biochemical pathway that is validated experimentally.

Homology modeling of Pro-B in the active site of HpbD (magenta) was confirmed by X-ray crystallography data (cyan). 1

Within high-throughput sequencing and structure data, many proteins have unknown function while others are misannotated. In a previous functional identification effort, researchers analyzed a bacterial protein with a solved three-dimensional (3D) structure, Pelagibaca bermudensis HpbD, by performing in silico docking of a library of metabolites within its active site. Follow-up studies confirmed the activity of pbHpbD with the identified metabolite, proline betaine (Pro-B), which functions as an osmoprotectant in high-osmolarity conditions, or as a source of carbon and nitrogen in others.

Cronan, Gerlt and colleagues (Enzyme Function Initiative) have now extended their previous study by identifying a protein with similar activity in a different species, Paracoccus denitrificans. With a sequence identity of 64%, modeling the structure of pdHpbD on that of pbHpbD allowed docking of Pro-B into the former's active site, using the in-house software Protein Local Optimization. X-ray structures of pdHpbD confirmed the modeling results (PDB 4J1O).

To find other proteins involved in the Pro-B degradation pathway, the authors searched the genomic neighborhood of hpbD for related genes and, based on P. bermudensis data, predicted and validated the Pro-B catalysis pathway for P. denitrificans using genetic complementation and metabolyte analyses. Further, when a deletional analysis implicated HpbR in substrate-mediated transcriptional regulation, a BLAST search using the substrate-binding domain identified a protein with little overall sequence identity, but one that enabled homology modeling of the substrate-binding site and successful docking of Pro-B. Subsequent RT-PCRn analyses confirmed HpbR as a regulator of Pro-B catabolic genes.

The authors advocate this approach for function discovery in bacterial enzymes, combining co-location of genes with in silico metabolite docking into known or modeled 3D structures, in addition to guidance and confirmation using genetic and metabolite analyses.

Irene Kaganman

References

  1. R. Kumar et al. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.
    MBio. 5, e00933-13 (2014). doi:10.1128/mBio.00933-13

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health