6JQ9

Crystal structure of a lyase from Alteromonas sp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Biochemical characterization and structural analysis of ulvan lyase from marine Alteromonas sp. reveals the basis for its salt tolerance.

Qin, H.M.Gao, D.Zhu, M.Li, C.Zhu, Z.Wang, H.Liu, W.Tanokura, M.Lu, F.

(2020) Int J Biol Macromol 147: 1309-1317

  • DOI: 10.1016/j.ijbiomac.2019.10.095
  • Primary Citation of Related Structures:  
    6JQ9

  • PubMed Abstract: 
  • Marine macroalgae have gained considerable attention as renewable biomass sources. Ulvan is a water-soluble anionic polysaccharide, and its depolymerization into fermentable monosaccharides has great potential for the production of bioethanol or high-value food additives ...

    Marine macroalgae have gained considerable attention as renewable biomass sources. Ulvan is a water-soluble anionic polysaccharide, and its depolymerization into fermentable monosaccharides has great potential for the production of bioethanol or high-value food additives. Ulvan lyase from Alteromonas sp. (AsPL) utilizes a β-elimination mechanism to cleave the glycosidic bond between rhamnose 3-sulfate and glucuronic acid, forming an unsaturated uronic acid at the non-reducing end. AsPL was active in the temperature range of 30-50 °C and pH values ranging from 7.5 to 9.5. Furthermore, AsPL was found to be halophilic, showing high activity and stability in the presence of up to 2.5 M NaCl. The apparent K m and k cat values of AsPL are 3.19 ± 0.37 mg mL -1 and 4.19 ± 0.21 s -1 , respectively. Crystal structure analysis revealed that AsPL adopts a β-propeller fold with four anti-parallel β-strands in each of the seven propeller blades. The acid residues at the protein surface and two Ca 2+ coordination sites contribute to its salt tolerance. The research on ulvan lyase has potential commercial value in the utilization of algal resources for biofuel production to relieve the environmental burden of petrochemicals.


    Organizational Affiliation

    Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, PR China. Electronic address: lfp@tust.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Short ulvan lyaseA, B483Alteromonas sp. LORMutation(s): 0 
Gene Names: LOR_107
EC: 4.2.2
UniProt
Find proteins for A0A109PTH9 (Alteromonas sp. (strain LOR))
Explore A0A109PTH9 
Go to UniProtKB:  A0A109PTH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A109PTH9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.048α = 90
b = 121.768β = 90
c = 124.304γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2021-10-20
    Changes: Database references, Derived calculations