5CC8 | pdb_00005cc8

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.194 (Depositor), 0.196 (DCC)
R-Value Work:
0.159 (Depositor), 0.161 (DCC)
R-Value Observed:
0.161 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-019-40558-x
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 70.11 kDa
Atom Count: 5,103
Modeled Residue Count: 592
Deposited Residue Count: 626
Unique protein chains: 1

Macromolecules

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| 3D Structure

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	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain O [auth A] MOL2 format, chain C [auth A] MOL2 format, chain O [auth A] mmCIF format, chain C [auth A] mmCIF format, chain O [auth A]	C [auth A], O [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain O [auth A] Interactions & Density Focus chain C [auth A] Focus chain O [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	I [auth A], J [auth A], M [auth A], N [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth A] Focus chain N [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth A]	E [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain K [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B]	D [auth A] F [auth A] G [auth A] H [auth A] L [auth A] D [auth A], F [auth A], G [auth A], H [auth A], L [auth A], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth A] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth A] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.194 (Depositor), 0.196 (DCC)
R-Value Work: 0.159 (Depositor), 0.161 (DCC)
R-Value Observed: 0.161 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-09-02

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

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
Version 1.4: 2026-03-04
Changes: Refinement description, Structure summary