6QMM

Crystal structure of Synecochoccus Spermidine Synthase in complex with putrescine, spermidine and MTA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of dimericSynechococcusspermidine synthase with bound polyamine substrate and product.

Guedez, G.Pothipongsa, A.Siren, S.Liljeblad, A.Jantaro, S.Incharoensakdi, A.Salminen, T.A.

(2019) Biochem J 476: 1009-1020

  • DOI: https://doi.org/10.1042/BCJ20180811
  • Primary Citation of Related Structures:  
    6QMM

  • PubMed Abstract: 

    Spermidine is a ubiquitous polyamine synthesized by spermidine synthase (SPDS) from the substrates, putrescine and decarboxylated S-adenosylmethionine (dcAdoMet). SPDS is generally active as homodimer, but higher oligomerization states have been reported in SPDS from thermophiles, which are less specific to putrescine as the aminoacceptor substrate. Several crystal structures of SPDS have been solved with and without bound substrates and/or products as well as inhibitors. Here, we determined the crystal structure of SPDS from the cyanobacterium Synechococcus ( Sy SPDS) that is a homodimer, which we also observed in solution. Unlike crystal structures reported for bacterial and eukaryotic SPDS with bound ligands, Sy SPDS structure has not only bound putrescine substrate taken from the expression host, but also spermidine product most probably as a result of an enzymatic reaction. Hence, to the best of our knowledge, this is the first structure reported with both amino ligands in the same structure. Interestingly, the gate-keeping loop is disordered in the putrescine-bound monomer while it is stabilized in the spermidine-bound monomer of the Sy SPDS dimer. This confirms the gate-keeping loop as the key structural element that prepares the active site upon binding of dcAdoMet for the catalytic reaction of the amine donor and putrescine.


  • Organizational Affiliation

    Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Tykistökatu 6A, 20520 Turku, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyamine aminopropyltransferase281Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: speESynpcc7942_0628
EC: 2.5.1.16
UniProt
Find proteins for Q31QK9 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q31QK9 
Go to UniProtKB:  Q31QK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31QK9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polyamine aminopropyltransferase280Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: speESynpcc7942_0628
EC: 2.5.1.16
UniProt
Find proteins for Q31QK9 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q31QK9 
Go to UniProtKB:  Q31QK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31QK9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PXN
Query on PXN

Download Ideal Coordinates CCD File 
F [auth B](2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol
C17 H36 O8
GXEZGLLPFFKHGE-FPCVCCKLSA-N
MTA (Subject of Investigation/LOI)
Query on MTA

Download Ideal Coordinates CCD File 
E [auth B]5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
SPD (Subject of Investigation/LOI)
Query on SPD

Download Ideal Coordinates CCD File 
D [auth B]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
PUT (Subject of Investigation/LOI)
Query on PUT

Download Ideal Coordinates CCD File 
C [auth A]1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.64α = 90
b = 63.82β = 92.72
c = 73.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sigrid Juselius FoundationFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description