5CC8

Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb5CC8/pdb

• Classification: TRANSFERASE
• Organism(s): Acinetobacter baumannii 6013150
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-01 Released: 2015-09-02 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.194 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Literature

Crystal structures of thiamine monophosphate kinase from Acinetobacter baumannii in complex with substrates and products.

Sullivan, A.H., Dranow, D.M., Horanyi, P.S., Lorimer, D.D., Edwards, T.E., Abendroth, J.

(2019) Sci Rep 9: 4392-4392

• PubMed: 30867460 
• DOI: https://doi.org/10.1038/s41598-019-40558-x
• Primary Citation of Related Structures:  
  5CC8, 5CM7, 5DD7, 6MFM


• PubMed Abstract: 
  

  Thiamine monophosphate kinase (ThiL) catalyzes the last step of thiamine pyrophosphate (TPP) synthesis, the ATP-dependent phosphorylation of thiamine monophosphate (TMP) to thiamine pyrophosphate. We solved the structure of ThiL from the human pathogen A. baumanii in complex with a pair of substrates TMP and a non-hydrolyzable adenosine triphosphate analog, and in complex with a pair of products TPP and adenosine diphosphate. High resolution of the data and anomalous diffraction allows for a detailed description of the binding mode of substrates and products, and their metal environment. The structures further support a previously proposed in-line attack reaction mechanism and show a distinct variability of metal content of the active site.

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Organizational Affiliation: 

UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA.

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: 70.11 kDa 
• Atom Count: 5,103 
• Modelled Residue Count: 592 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine-monophosphate kinase	A, B	313	Acinetobacter baumannii 6013150	Mutation(s): 0  Gene Names: thiL, HMPREF0021_00055 EC: 2.7.4.16

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A], O [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
K	I [auth A], J [auth A], M [auth A], N [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	E [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], F [auth A], G [auth A], H [auth A], L [auth A], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.194 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M35CC8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.14	α = 90
b = 93.76	β = 90
c = 72.49	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2019-04-03
  Changes: Data collection, Database references
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations