6BYT

Complex structure of LOR107 mutant (R320) with tetrasaccharide substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism.

Ulaganathan, T.Helbert, W.Kopel, M.Banin, E.Cygler, M.

(2018) J. Biol. Chem. 293: 4026-4036

  • DOI: 10.1074/jbc.RA117.001642
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ulvan is a major cell wall component of green algae of the genus Ulva and some marine bacteria encode enzymes that can degrade this polysaccharide. The first ulvan degrading lyases have been recently characterized and several putative ulvan lyases ha ...

    Ulvan is a major cell wall component of green algae of the genus Ulva and some marine bacteria encode enzymes that can degrade this polysaccharide. The first ulvan degrading lyases have been recently characterized and several putative ulvan lyases have been recombinantly expressed, confirmed as ulvan lyases and partially characterized. Two families of ulvan degrading lyases, PL24 and PL25, have recently been established. The PL24 lyase LOR_107 from the bacterial Alteromonadales sp. strain LOR degrades ulvan endolytically, cleaving the bond at the C4 of a glucuronic acid. However, the mechanism and LOR_107 structural features involved are unknown. We present here the crystal structure of LOR_107, representing the first PL24 family structure. We found that LOR_107 adopts a seven-bladed β-propeller fold with a deep canyon on one side of the protein. Comparative sequence analysis revealed a cluster of conserved residues within this canyon, and site-directed mutagenesis disclosed several residues essential for catalysis. We also found that LOR_107 uses the His/Tyr catalytic mechanism, common to several PL families. We captured a tetrasaccharide substrate in the structures of two inactive mutants, which indicated a two-step binding event, with the first substrate interaction near the top of the canyon coordinated by Arg-320, followed by sliding of the substrate into the canyon toward the active-site residues. Surprisingly, the LOR_107 structure was very similar to that of PL25 family PLSV_3936, despite only ~14% sequence identity between the two enzymes. On the basis of our structural and mutational analyses, we propose a catalytic mechanism for LOR_107 that differs from the typical His/Tyr mechanism.


    Organizational Affiliation

    University of Saskatchewan, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Short ulvan lyase
A, B
506Alteromonas sp. LORMutation(s): 1 
Find proteins for A0A109PTH9 (Alteromonas sp. LOR)
Go to UniProtKB:  A0A109PTH9
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GCB
Query on GCB

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Download CCD File 
A, B
D-SACCHARIC ACID 1,5-LACTONE
D-GLUCARO-1,5-LACTONE
C6 H8 O7
YLKFQNUGXOLRNI-QDQPNEQZSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
83Y
Query on 83Y

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Download CCD File 
A, B
6-deoxy-3-O-sulfo-alpha-L-mannopyranose
L-rhamnose-3-sulphate
C6 H12 O8 S
PHTKRPBOKDCSPW-HGVZOGFYSA-N
 Ligand Interaction
GCD
Query on GCD

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Download CCD File 
A, B
4,5-DEHYDRO-D-GLUCURONIC ACID
C6 H8 O6
IAKKJSVSFCTLRY-YKKSOZKNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.220α = 90.00
b = 120.660β = 90.00
c = 127.090γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Cootmodel building
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canada--

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Database references
  • Version 1.2: 2018-05-02
    Type: Data collection, Database references