6B0K

Crystal structure of Ps i-CgsB C78S in complex with k-carrapentaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

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This is version 1.3 of the entry. See complete history


Literature

The Molecular Basis of Polysaccharide Sulfatase Activity and a Nomenclature for Catalytic Subsites in this Class of Enzyme.

Hettle, A.G.Vickers, C.Robb, C.S.Liu, F.Withers, S.G.Hehemann, J.H.Boraston, A.B.

(2018) Structure 26: 747

  • DOI: 10.1016/j.str.2018.03.012
  • Primary Citation of Related Structures:  
    6B0J, 6B0K, 6B1V, 6BIA

  • PubMed Abstract: 
  • Sulfatases play a biologically important role by cleaving sulfate groups from molecules. They can be identified on the basis of signature sequences within their primary structures, and the largest family, S1, has predictable features that contribute specifically to the recognition and catalytic removal of sulfate groups ...

    Sulfatases play a biologically important role by cleaving sulfate groups from molecules. They can be identified on the basis of signature sequences within their primary structures, and the largest family, S1, has predictable features that contribute specifically to the recognition and catalytic removal of sulfate groups. However, despite advances in the prediction and understanding of S1 sulfatases, a major question regards the molecular determinants that drive substrate recognition beyond the targeted sulfate group. Here, through analysis of an endo-4S-ι-carrageenan sulfatase (PsS1_19A) from Pseudoalteromonas sp. PS47, particularly X-ray crystal structures in complex with intact substrates, we show that specific recognition of the substrate leaving group components, in this case carbohydrate, provides the enzyme with specificity for its substrate. On the basis of these results we propose a catalytic subsite nomenclature that we anticipate will form a general foundation for understanding and describing the molecular basis of substrate recognition by sulfatases.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada. Electronic address: boraston@uvic.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Iota-carrageenan sulfataseA, B, C451PseudoalteromonasMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4S (Subject of Investigation/LOI)
Query on G4S

Download Ideal Coordinates CCD File 
BA [auth C], F [auth A], H [auth A], O [auth B], Q [auth B], S [auth B], X [auth C], Z [auth C]4-O-sulfo-beta-D-galactopyranose
C6 H12 O9 S
LOTQRUGOUKUSEY-DGPNFKTASA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
I [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
ARG (Subject of Investigation/LOI)
Query on ARG

Download Ideal Coordinates CCD File 
J [auth A]ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
9RN (Subject of Investigation/LOI)
Query on 9RN

Download Ideal Coordinates CCD File 
AA [auth C], E [auth A], G [auth A], P [auth B], R [auth B], Y [auth C]3,6-anhydro-D-galactose
C6 H10 O5
DCQFFOLNJVGHLW-RDQKPOQOSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
K [auth A], L [auth A], T [auth B], U [auth B], W [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A], N [auth B], V [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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M [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.07α = 90
b = 133.07β = 90
c = 223.94γ = 90
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 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations