5UAS

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

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 

wwPDB Validation 3D Report Full Report


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


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

  • DOI: 10.1021/acschembio.7b00126
  • Structures With Same Primary Citation

  • 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UlvanLyase-PL25
A, B
473Pseudoalteromonas sp. PLSVMutation(s): 0 
Gene Names: PLSV_3936
EC: 4.2.2
Find proteins for A0A1W2VMZ5 (Pseudoalteromonas sp. (strain PLSV))
Go to UniProtKB:  A0A1W2VMZ5
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
83Y
Query on 83Y
Download CCD File 
A, B
6-deoxy-3-O-sulfo-alpha-L-mannopyranose
C6 H12 O8 S
PHTKRPBOKDCSPW-HGVZOGFYSA-N		 Ligand Interaction
BDP
Query on BDP
Download CCD File 
A, B
BETA-D-GLUCOPYRANURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N		 Ligand Interaction
GCD
Query on GCD
Download CCD File 
A, B
4,5-DEHYDRO-D-GLUCURONIC ACID
C6 H8 O6
IAKKJSVSFCTLRY-YKKSOZKNSA-N		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
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 = 173.62α = 90
b = 71.81β = 122.44
c = 109.27γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references