5NM8

Structure of PipY, the COG0325 family member of Synechococcus elongatus PCC7942, with PLP bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Studies on cyanobacterial protein PipY shed light on structure, potential functions, and vitamin B6 -dependent epilepsy.

Tremino, L.Forcada-Nadal, A.Contreras, A.Rubio, V.

(2017) FEBS Lett. 591: 3431-3442

  • DOI: 10.1002/1873-3468.12841
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Synechococcus elongatus COG0325 gene pipY functionally interacts with the nitrogen regulatory gene pipX. As a first step toward a molecular understanding of such interactions, we characterized PipY. This 221-residue protein is monomeric and hosts ...

    The Synechococcus elongatus COG0325 gene pipY functionally interacts with the nitrogen regulatory gene pipX. As a first step toward a molecular understanding of such interactions, we characterized PipY. This 221-residue protein is monomeric and hosts pyridoxal phosphate (PLP), binding it with limited affinity and losing it upon incubation with D-cycloserine. PipY crystal structures with and without PLP reveal a single-domain monomer folded as the TIM barrel of type-III fold PLP enzymes, with PLP highly exposed, fitting a role for PipY in PLP homeostasis. The mobile PLP phosphate-anchoring C-terminal helix might act as a trigger for PLP exchange. Exploiting the universality of COG0325 functions, we used PipY in site-directed mutagenesis studies to shed light on disease causation by epilepsy-associated mutations in the human COG0325 gene PROSC.


    Organizational Affiliation

    Instituto de Biomedicina de Valencia (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER-ISCIII), Valencia, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PipY
A, B
228Synechococcus elongatus (strain PCC 7942)Mutation(s): 0 
Find proteins for Q31LH9 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  Q31LH9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.627α = 90.00
b = 98.937β = 90.00
c = 103.737γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
BUCCANEERmodel building
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish GovernmentSpainBFU2014-58229-P
Spanish GovernmentSpainBES-2012-058304
Valencian GovernmentSpainPrometeoII/2014/029

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Structure summary
  • Version 1.2: 2017-09-27
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Database references