6PSO

Crystal structure of PsS1_19B C77S in complex with iota-neocarratetraose

• PDB DOI:  https://doi.org/10.2210/pdb6PSO/pdb

• Classification: HYDROLASE
• Organism(s): Pseudoalteromonas fuliginea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-07-13 Released: 2019-09-25 
• Deposition Author(s): Hettle, A.G., Boraston, A.B.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.231 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies.

Hettle, A.G., Hobbs, J.K., Pluvinage, B., Vickers, C., Abe, K.T., Salama-Alber, O., McGuire, B.E., Hehemann, J.H., Hui, J.P.M., Berrue, F., Banskota, A., Zhang, J., Bottos, E.M., Van Hamme, J., Boraston, A.B.

(2019) Commun Biol 2: 474-474

• PubMed: 31886414 
• DOI: https://doi.org/10.1038/s42003-019-0721-y
• Primary Citation of Related Structures:  
  6PNU, 6POP, 6PRM, 6PSM, 6PSO, 6PT4, 6PT6, 6PT9, 6PTK, 6PTM


• PubMed Abstract: 
  

Pseudoalteromonas is a globally distributed marine-associated genus that can be found in a broad range of aquatic environments, including in association with macroalgal surfaces where they may take advantage of these rich sources of polysaccharides. The metabolic systems that confer the ability to metabolize this abundant form of photosynthetically fixed carbon, however, are not yet fully understood. Through genomics, transcriptomics, microbiology, and specific structure-function studies of pathway components we address the capacity of newly isolated marine pseudoalteromonads to metabolize the red algal galactan carrageenan. The results reveal that the κ/ι-carrageenan specific polysaccharide utilization locus (CarPUL) enables isolates possessing this locus the ability to grow on this substrate. Biochemical and structural analysis of the enzymatic components of the CarPUL promoted the development of a detailed model of the κ/ι-carrageenan metabolic pathway deployed by pseudoalteromonads, thus furthering our understanding of how these microbes have adapted to a unique environmental niche.

---

Organizational Affiliation: 

1Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 108.16 kDa 
• Atom Count: 7,555 
• Modelled Residue Count: 894 
• Deposited Residue Count: 938 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
exo-4S-kappa carrageenan S1 sulfatase	A [auth B], B [auth A]	469	Pseudoalteromonas fuliginea	Mutation(s): 0  Gene Names: EU509_08890

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose	C, D	4		N/A
Glycosylation Resources
GlyTouCan:  G24165XP GlyCosmos:  G24165XP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth B], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth B], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.231 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.264	α = 90
b = 93.995	β = 90
c = 170.547	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Hettle, A.G., Boraston, A.B.

---

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2020-01-15
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary