6PSM

Crystal structure of PsS1_19B C77S in complex with kappa-neocarrabiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.3 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
exo-4S-kappa carrageenan S1 sulfataseA, B, C, D, E, F469Pseudoalteromonas fuligineaMutation(s): 0 
Gene Names: EU509_08890
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4S (Subject of Investigation/LOI)
Query on G4S

Download Ideal Coordinates CCD File 
BA [auth D], H [auth A], IA [auth E], NA [auth F], P [auth B], U [auth C]4-O-sulfo-beta-D-galactopyranose
C6 H12 O9 S
LOTQRUGOUKUSEY-DGPNFKTASA-N
 Ligand Interaction
9RN (Subject of Investigation/LOI)
Query on 9RN

Download Ideal Coordinates CCD File 
CA [auth D], I [auth A], JA [auth E], OA [auth F], Q [auth B], V [auth C]3,6-anhydro-D-galactose
C6 H10 O5
DCQFFOLNJVGHLW-RDQKPOQOSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FA [auth E], GA [auth E], K [auth A], L [auth A], Y [auth D], Z [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D], HA [auth E], M [auth A], MA [auth F], T [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
DA [auth E], G [auth A], KA [auth F], N [auth B], R [auth C], W [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth E], J [auth A], LA [auth F], O [auth B], S [auth C], X [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.05α = 90
b = 93.05β = 90
c = 300.21γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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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