SASDAX8: Ribokinase ThiM (ThiM)

Basic information

• Entry: Database: SASBDB / ID: SASDAX8

Sample

Ribokinase ThiM

• Ribokinase ThiM (protein), ThiM, Staphylococcus aureus

• Biological species: Staphylococcus aureus (bacteria)
• Citation: Journal: Sci Rep / Year: 2016; Title: Structure of ThiM from Vitamin B1 biosynthetic pathway of Staphylococcus aureus - Insights into a novel pro-drug approach addressing MRSA infections.; Authors: Julia Drebes / Madeleine Künz / Björn Windshügel / Alexey G Kikhney / Ingrid B Müller / Raphael J Eberle / Dominik Oberthür / Huaixing Cang / Dmitri I Svergun / Markus Perbandt / Christian Betzel / Carsten Wrenger / ; Abstract: Infections caused by the methicillin-resistant Staphylococcus aureus (MRSA) are today known to be a substantial threat for global health. Emerging multi-drug resistant bacteria have created a substantial need to identify and discover new drug targets and to develop novel strategies to treat bacterial infections. A promising and so far untapped antibiotic target is the biosynthesis of vitamin B1 (thiamin). Thiamin in its activated form, thiamin pyrophosphate, is an essential co-factor for all organisms. Therefore, thiamin analogous compounds, when introduced into the vitamin B1 biosynthetic pathway and further converted into non-functional co-factors by the bacterium can function as pro-drugs which thus block various co-factor dependent pathways. We characterized one of the key enzymes within the S. aureus vitamin B1 biosynthetic pathway, 5-(hydroxyethyl)-4-methylthiazole kinase (SaThiM; EC 2.7.1.50), a potential target for pro-drug compounds and analyzed the native structure of SaThiM and complexes with the natural substrate 5-(hydroxyethyl)-4-methylthiazole (THZ) and two selected substrate analogues.

Contact author

• Al Kikhney (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #338: ; Type: atomic / Software: CORAL (05) / Symmetry: P3 / Chi-square value: 0.569; Search similar-shape structures of this assembly by Omokage search (details)
• Model #339: ; Type: dummy / Software: dammif (r4556) / Radius of dummy atoms: 2.00 A / Symmetry: P3 / Chi-square value: 0.484; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Ribokinase ThiM / Specimen concentration: 1.33-9.85
• Buffer: Name: Potassium phosphate / Concentration: 50.00 mM / pH: 7.5 / Composition: 10 mM MgCl2

Entity #205

Name: ThiM / Type: protein / Description: Ribokinase ThiM / Formula weight: 29.8 / Num. of mol.: 3 / Source: Staphylococcus aureus
Sequence:

MNYLNNIRIE NPLTICYTND VVKNFTANGL LSIGASPAMS EAPEEAEEFY KVAQALLINI GTLTAQNEQD IIAIAQTANE AGLPIVFDPV AVGASTYRKQ FCKLLLKSAK VSVIKGNASE ILALIDDTAT MKGTDSDANL DAVTIAKKAY AIYKTAIVIT GKEDVIVQGD KAIVLANGSP LLARVTGAGC LLGGIIAGFL FRETEPDIEA LIEAVSVFNI AAEVAAENEN CGGPGTFSPL LLDTLYHLNE TTYQQRIRIQ EVEenlyfqs ghhhhhh

Experimental information

• Beam: Instrument name: DORIS III X33 / City: Hamburg / 国: Germany / Shape: 0.6 / Type of source: X-ray synchrotron / Wavelength: 0.15 Å / Dist. spec. to detc.: 2.7 mm
• Detector: Name: Pilatus 1M-W / Pixsize x: 0.172 mm

Scan

Title: Ribokinase ThiM / Measurement date: Nov 19, 2010 / Cell temperature: 12 °C / Exposure time: 15 sec. / Number of frames: 8 / Unit: 1/nm /

	Min	Max
Q	0.1821	6.0155

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 982 /

	Min	Max
Q	0.288623	2.97175
P(R) point	1	982
R	0	9

Result

Type of curve: merged /

	Experimental	Porod
MW	77 kDa	90.66 kDa
Volume	-	145.06 nm3

	Guinier	P(R)	Guinier error
Forward scattering, I0	47.26	-	-
Radius of gyration, Rg	2.972 nm	2.866 nm	0.198

	Min	Max
D	-	9
Guinier point	32	95