7XIF

Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic crenarchaeon, Pyrobaculum calidifontis in complex with 5'-methylthioadenosine (MTA) alone or together with spermidine or thermospermine

• PDB DOI: https://doi.org/10.2210/pdb7XIF/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrobaculum calidifontis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-04-13 Released: 2022-06-15 
• Deposition Author(s): Mizohata, E., Yasuda, Y.
• Funding Organization(s): Japan Science and Technology, Ministry of Education, Culture, Sports, Science and Technology (Japan), New Energy and Industrial Technology Development Organization (NEDO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.190 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Substrate Specificity of an Aminopropyltransferase and the Biosynthesis Pathway of Polyamines in the Hyperthermophilic Crenarchaeon Pyrobaculum calidifontis.

Fukuda, W., Osaki, M., Yasuda, Y., Hidese, R., Higuchi, T., Umezawa, N., Fujiwara, S., Mizohata, E.

(2022) Catalysts 12

• DOI: https://doi.org/10.3390/catal12050567

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 423.22 kDa 
• Atom Count: 28,933 
• Modelled Residue Count: 3,434 
• Deposited Residue Count: 3,708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyamine aminopropyltransferase	A, B, C, D, E, F, G, H, I, J, K, L	309	Pyrobaculum calidifontis	Mutation(s): 0  Gene Names: speE, Pcal_0772 EC: 2.5.1.16
UniProt
Find proteins for A3MU81 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1)) Explore A3MU81  Go to UniProtKB:  A3MU81

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTA (Subject of Investigation/LOI)	AA [auth H], CA [auth I], DA [auth J], EA [auth K], FA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
TER (Subject of Investigation/LOI)	V [auth E], X [auth F], Z [auth G]	N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE C10 H26 N4 DODDBCGMRAFLEB-UHFFFAOYSA-N
SPD (Subject of Investigation/LOI)	BA [auth H], N [auth A], P [auth B], R [auth C], T [auth D]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.190 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.159	α = 90
b = 166.159	β = 90
c = 149.586	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Coot	model building
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): Mizohata, E., Yasuda, Y.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJPR17GB
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H05780
New Energy and Industrial Technology Development Organization (NEDO)	Japan	JPNP18016

Revision History  

• Version 1.0: 2022-06-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description