6J27

Crystal structure of the branched-chain polyamine synthase from Thermus thermophilus (Tth-BpsA) in complex with N4-aminopropylspermidine and 5'-methylthioadenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


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Literature

The C-terminal flexible region of branched-chain polyamine synthase facilitates substrate specificity and catalysis.

Hidese, R.Toyoda, M.Yoshino, K.I.Fukuda, W.Wihardja, G.A.Kimura, S.Fujita, J.Niitsu, M.Oshima, T.Imanaka, T.Mizohata, E.Fujiwara, S.

(2019) FEBS J 286: 3926-3940

  • DOI: 10.1111/febs.14949
  • Primary Citation of Related Structures:  
    6J26, 6J27, 6J28

  • PubMed Abstract: 
  • Branched-chain polyamine synthase (BpsA) catalyzes sequential aminopropyl transfer from the donor, decarboxylated S-adenosylmethionine (dcSAM), to the acceptor, linear-chain polyamine, resulting in the production of a quaternary-branched polyamine via tertiary branched polyamine intermediates ...

    Branched-chain polyamine synthase (BpsA) catalyzes sequential aminopropyl transfer from the donor, decarboxylated S-adenosylmethionine (dcSAM), to the acceptor, linear-chain polyamine, resulting in the production of a quaternary-branched polyamine via tertiary branched polyamine intermediates. Here, we analyzed the catalytic properties and X-ray crystal structure of Tth-BpsA from Thermus thermophilus and compared them with those of Tk-BpsA from Thermococcus kodakarensis, which revealed differences in acceptor substrate specificity and C-terminal structure between these two enzymes. To investigate the role of the C-terminal flexible region in acceptor recognition, a region (QDEEATTY) in Tth-BpsA was replaced with that in Tk-BpsA (YDDEESSTT) to create chimeric Tth-BpsA C9, which showed a severe reduction in catalytic efficiency toward N 4 -aminopropylnorspermidine, but not toward N 4 -aminopropylspermidine, mimicking Tk-BpsA substrate specificity. Tth-BpsA C9 Tyr 346 and Thr 354 contributed to discrimination between tertiary branched-chain polyamine substrates, suggesting that the C-terminal region of BpsA recognizes acceptor substrates. Liquid chromatography-tandem mass spectrometry analysis on a Tk-BpsA reaction mixture with dcSAM revealed two aminopropyl groups bound to two of five aspartate/glutamate residues (Glu 339 , Asp 342 , Asp 343 , Glu 344 , and Glu 345 ) in the C-terminal flexible region. Mutating each of these five amino acid residues to asparagine/glutamine resulted in a slight decrease in activity. The quadruple mutant D342N/D343N/E344Q/E345Q exhibited a severe reduction in catalytic efficiency, suggesting that these aspartate/glutamate residues function to receive aminopropyl chains. In addition, the X-ray crystal structure of the Tk-BpsA ternary complex bound to N 4 -bis(aminopropyl)spermidine revealed that Asp 126 and Glu 259 interacted with the aminopropyl moiety in N 4 -aminopropylspermidine.


    Organizational Affiliation

    Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N(4)-bis(aminopropyl)spermidine synthaseA, B, C, D374Thermus thermophilus HB27Mutation(s): 0 
Gene Names: bpsATT_C0171
EC: 2.5.1.128
UniProt
Find proteins for Q72L89 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72L89 
Go to UniProtKB:  Q72L89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72L89
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTA
Query on MTA

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
R [auth C],
V [auth D]
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
 Ligand Interaction
N4P
Query on N4P

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
S [auth C],
W [auth D]
N,N-bis(3-aminopropyl)butane-1,4-diamine
C10 H26 N4
CAARYRKDWMNHCB-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
X [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
Y [auth D],
Z [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A],
Q [auth C]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.57α = 90
b = 158.606β = 118.95
c = 71.936γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Cootmodel building
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJPR17GB

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references