6PTK

Crystal structure of the sulfatase PsS1_NC C84A with bound sulfate ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
exo-2S-iota carrageenan S1 sulfatase
A, B, C, D
497Pseudoalteromonas fuligineaMutation(s): 0 
Gene Names: EU509_08820
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G4S
Query on G4S

Download Ideal Coordinates CCD File 
G [auth A],
JA [auth C],
WA [auth D],
Z [auth B]
4-O-sulfo-beta-D-galactopyranose
C6 H12 O9 S
LOTQRUGOUKUSEY-DGPNFKTASA-N
9RN
Query on 9RN

Download Ideal Coordinates CCD File 
F [auth A],
IA [auth C],
VA [auth D],
Y [auth B]
3,6-anhydro-alpha-D-galactopyranose
C6 H10 O5
DCQFFOLNJVGHLW-RDQKPOQOSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C],
E [auth A],
MA [auth D],
S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
K [auth A]
KA [auth C]
L [auth A]
CA [auth C],
DA [auth C],
K [auth A],
KA [auth C],
L [auth A],
Q [auth A],
RA [auth D],
SA [auth D],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth C]
H [auth A]
I [auth A]
J [auth A]
NA [auth D]
BA [auth C],
H [auth A],
I [auth A],
J [auth A],
NA [auth D],
OA [auth D],
PA [auth D],
QA [auth D],
T [auth B],
U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
EA [auth C]
FA [auth C]
GA [auth C]
HA [auth C]
LA [auth C]
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
LA [auth C],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
R [auth A],
TA [auth D],
UA [auth D],
W [auth B],
X [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.83α = 90
b = 110.68β = 105.38
c = 175.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • 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 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary