4BWV

Structure of Adenosine 5-prime-phosphosulfate Reductase apr-b from Physcomitrella Patens

• PDB DOI: https://doi.org/10.2210/pdb4BWV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Physcomitrium patens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-04 Released: 2013-11-27 
• Deposition Author(s): Stevenson, C.E.M., Hughes, R.K., McManus, M.T., Lawson, D.M., Kopriva, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.194 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Starting Model: experimental

Literature

The X-Ray Crystal Structure of Apr-B, an Atypical Adenosine 5-Prime-Phosphosulfate Reductase from Physcomitrella Patens

Stevenson, C.E.M., Hughes, R.K., Mcmanus, M.T., Lawson, D.M., Kopriva, S.

(2013) FEBS Lett 587: 3626

• PubMed: 24100135 
• DOI: https://doi.org/10.1016/j.febslet.2013.09.034
• Primary Citation of Related Structures:  
  4BWV


• PubMed Abstract: 
  

  Sulfonucleotide reductases catalyse the first reductive step of sulfate assimilation. Their substrate specificities generally correlate with the requirement for a [Fe4S4] cluster, where adenosine 5'-phosphosulfate (APS) reductases possess a cluster and 3'-phosphoadenosine 5'-phosphosulfate reductases do not. The exception is the APR-B isoform of APS reductase from the moss Physcomitrella patens, which lacks a cluster. The crystal structure of APR-B, the first for a plant sulfonucleotide reductase, is consistent with a preference for APS. Structural conservation with bacterial APS reductase rules out a structural role for the cluster, but supports the contention that it enhances the activity of conventional APS reductases.

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Organizational Affiliation: 

Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 64.42 kDa 
• Atom Count: 4,168 
• Modelled Residue Count: 454 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOADENOSINE-PHOSPHOSULPHATE REDUCTASE	A, B	283	Physcomitrium patens	Mutation(s): 0  EC: 1.8.4.10
UniProt
Find proteins for Q8L5D0 (Physcomitrium patens) Explore Q8L5D0  Go to UniProtKB:  Q8L5D0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.194 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.99	α = 90
b = 82.42	β = 90
c = 127.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Stevenson, C.E.M., Hughes, R.K., McManus, M.T., Lawson, D.M., Kopriva, S.

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2019-05-29
  Changes: Data collection, Experimental preparation
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description