Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 108.34 kDa 
• Atom Count: 8214 
• Modelled Residue Count: 880 
• Deposited Residue Count: 946 
• Unique protein chains: 1

5UAS

Structure of a new family of Polysaccharide lyase PL25-Ulvanlyase bound to -[GlcA(1-4)Rha3S]-

• DOI: 10.2210/pdb5UAS/pdb

• Classification: LYASE
• Organism(s): Pseudoalteromonas sp. PLSV
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-20 Released: 2017-03-29 
• Deposition Author(s): Ulaganathan, T.S., Cygler, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.212 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Literature

New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture.

Ulaganathan, T., Boniecki, M.T., Foran, E., Buravenkov, V., Mizrachi, N., Banin, E., Helbert, W., Cygler, M.

(2017) ACS Chem Biol 12: 1269-1280

• PubMed: 28290654 
• DOI: 10.1021/acschembio.7b00126
• Primary Citation of Related Structures:  
  5UAS, 5UAM


• PubMed Abstract: 
  

Ulvan is a complex sulfated polysaccharide biosynthesized by green seaweed and contains predominantly rhamnose, xylose, and uronic acid sugars. Ulvan-degrading enzymes have only recently been identified and added to the CAZy ( www.cazy.org ) database as family PL24, but neither their structure nor catalytic mechanism(s) are yet known. Several homologous, new ulvan lyases, have been discovered in Pseudoalteromonas sp. strain PLSV, Alteromonas LOR, and Nonlabens ulvanivorans, defining a new family PL25, with the lyase encoded by the gene PLSV_3936 being one of them. This enzyme cleaves the glycosidic bond between 3-sulfated rhamnose (R3S) and glucuronic acid (GlcA) or iduronic acid (IdoA) via a β-elimination mechanism. We report the crystal structure of PLSV_3936 and its complex with a tetrasaccharide substrate. PLSV_3936 folds into a seven-bladed β-propeller, with each blade consisting of four antiparallel β-strands. Sequence conservation analysis identified a highly conserved region lining at one end of a deep crevice on the protein surface. The putative active site was identified by mutagenesis and activity measurements. Crystal structure of the enzyme with a bound tetrasaccharide substrate confirmed the identity of base and acid residues and allowed determination of the catalytic mechanism and also the identification of residues neutralizing the uronic acid carboxylic group. The PLSV_3936 structure provides an example of a convergent evolution among polysaccharide lyases toward a common active site architecture embedded in distinct folds.

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Organizational Affiliation: 

Department of Biochemistry, McGill University , Montreal, Quebec H3G 0B1, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UlvanLyase-PL25	A, B	473	Pseudoalteromonas sp. PLSV	Mutation(s): 0  Gene Names: PLSV_3936 EC: 4.2.2
UniProt
Find proteins for A0A1W2VMZ5 (Pseudoalteromonas sp. (strain PLSV)) Explore A0A1W2VMZ5  Go to UniProtKB:  A0A1W2VMZ5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose	C, D	4		N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	H [auth A], I [auth A], J [auth A], N [auth B], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	F [auth A], L [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	G [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.212 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.62	α = 90
b = 71.81	β = 122.44
c = 109.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-12-20 
• Released Date: 2017-03-29 
Deposition Author(s): Ulaganathan, T.S., Cygler, M.

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2017-05-31
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary