6ITG

a new alginate lyase (PL6) from Vibrio splendidus OU02


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into a novel Ca2+-independent PL-6 alginate lyase from Vibrio OU02 identify the possible subsites responsible for product distribution.

Lyu, Q.Zhang, K.Shi, Y.Li, W.Diao, X.Liu, W.

(2019) Biochim Biophys Acta Gen Subj 1863: 1167-1176

  • DOI: 10.1016/j.bbagen.2019.04.013
  • Primary Citation of Related Structures:  
    6ITG, 5Z9T, 6A40

  • PubMed Abstract: 
  • Alginate lyases have a wide range of industrial applications, such as oligosaccharide preparation, medical treatment, and bioconversion. Therefore, the discovery and characterization of novel alginate lyases are extremely important. PL-6 alginate lyases are classified into two groups: those with a single domain or two domains ...

    Alginate lyases have a wide range of industrial applications, such as oligosaccharide preparation, medical treatment, and bioconversion. Therefore, the discovery and characterization of novel alginate lyases are extremely important. PL-6 alginate lyases are classified into two groups: those with a single domain or two domains. However, only one structure of a two-domain alginate lyase has been determined to date. In this study, we characterized a novel single-domain PL-6 alginate lyase (named AlyF). According to the biochemical analysis, AlyF possesses unique features compared with other PL-6 enzymes, including (1) a Ca 2+ -independent catalytic mechanism and (2) a PolyG-specific cleavage specificity that predominantly produces trisaccharides. The structures of AlyF and its complexes described here reveal the structural basis for these unique features and substrate binding mechanisms, which were further confirmed using mutagenesis. More importantly, we determined the possible subsites specifying the predominantly trisaccharide products of AlyF, which may facilitate the rational design of AlyF for potential applications in preparing a single alginate oligomer.


    Organizational Affiliation

    MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China. Electronic address: liuweizhi@ouc.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alginate lyaseA, B536Vibrio splendidusMutation(s): 0 
Gene Names: BTO12_02510
UniProt
Find proteins for A0A2S7V3I3 (Vibrio splendidus)
Explore A0A2S7V3I3 
Go to UniProtKB:  A0A2S7V3I3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download Ideal Coordinates CCD File 
E [auth A], G [auth B]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], F [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.327α = 90
b = 106.327β = 90
c = 100.575γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-11-23 
  • Released Date: 2019-05-01 
  • Deposition Author(s): Liu, W.Z., Lyu, Q.Q.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina41706151

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references