5Y33 | pdb_00005y33

Crystal structure of alginate lyase from Flavobacterium sp. UMI-01 reveals polymannuronate specificity

• PDB DOI: https://doi.org/10.2210/pdb5Y33/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Flavobacterium sp. UMI-01
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-07-27 Released: 2018-07-04 
• Deposition Author(s): Qin, H.-M., Miyakawa, T., Nakamura, A., Tanokura, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Structural basis for controlling the enzymatic properties of polymannuronate preferred alginate lyase FlAlyA from the PL-7 family.

Qin, H.M., Miyakawa, T., Inoue, A., Nishiyama, R., Nakamura, A., Asano, A., Ojima, T., Tanokura, M.

(2018) Chem Commun (Camb) 54: 555-558

• PubMed: 29292806 
• DOI: https://doi.org/10.1039/c7cc06523j
• Primary Citation of Related Structures:  
  5Y33


• PubMed Abstract: 
  

  FlAlyA is an endolytic enzyme with a preference for polymannuronate. The crystal structure and mutagenesis studies elucidated that the structural variations at outer uronate-binding subsites +2, +3 and -2 control the enzymatic properties of PL-7 family enzymes. Lys158 mutations changed the pH dependency and enhanced the production of mono- and disaccharides.

---

Organizational Affiliation: 
• Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.9 kDa 
• Atom Count: 2,446 
• Modeled Residue Count: 260 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate lyase	A	260	Flavobacterium sp. UMI-01	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.75	α = 90
b = 71.75	β = 90
c = 50.88	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	data reduction
PHENIX	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-04 
Deposition Author(s): Qin, H.-M., Miyakawa, T., Nakamura, A., Tanokura, M.

Revision History  

• Version 1.0: 2018-07-04
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references