6FH1 | pdb_00006fh1

Protein arginine kinase McsB in the apo state

• PDB DOI: https://doi.org/10.2210/pdb6FH1/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-01-12 Released: 2019-02-06 
• Deposition Author(s): Suskiewicz, M.J., Heuck, A., Vu, L.D., Clausen, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Structure of McsB, a protein kinase for regulated arginine phosphorylation.

Suskiewicz, M.J., Hajdusits, B., Beveridge, R., Heuck, A., Vu, L.D., Kurzbauer, R., Hauer, K., Thoeny, V., Rumpel, K., Mechtler, K., Meinhart, A., Clausen, T.

(2019) Nat Chem Biol 15: 510-518

• PubMed: 30962626 
• DOI: https://doi.org/10.1038/s41589-019-0265-y
• Primary Citation Related Structures: 
  6FH1, 6FH2, 6FH3, 6FH4


• PubMed Abstract: 
  

  Protein phosphorylation regulates key processes in all organisms. In Gram-positive bacteria, protein arginine phosphorylation plays a central role in protein quality control by regulating transcription factors and marking aberrant proteins for degradation. Here, we report structural, biochemical, and in vivo data of the responsible kinase, McsB, the founding member of an arginine-specific class of protein kinases. McsB differs in structure and mechanism from protein kinases that act on serine, threonine, and tyrosine residues and instead has a catalytic domain related to that of phosphagen kinases (PhKs), metabolic enzymes that phosphorylate small guanidino compounds. In McsB, the PhK-like phosphotransferase domain is structurally adapted to target protein substrates and is accompanied by a novel phosphoarginine (pArg)-binding domain that allosterically controls protein kinase activity. The identification of distinct pArg reader domains in this study points to a remarkably complex signaling system, thus challenging simplistic views of bacterial protein phosphorylation.

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Organizational Affiliation: 
• Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
VIB/UGent, Ghent, Belgium.
Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.
Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria. [e-mail].
Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria. [e-mail].

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)

Biological Assembly Evidence: mass spectrometry, light scattering

Macromolecule Content 

• Total Structure Weight: 83.93 kDa 
• Atom Count: 6,066 
• Modeled Residue Count: 695 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-arginine kinase	A, B	366	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: mcsB EC: 2.7.14.1
UniProt
Find proteins for P0DMM5 (Geobacillus stearothermophilus) Explore P0DMM5  Go to UniProtKB:  P0DMM5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	T [auth A], W [auth B], X [auth B], Y [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], U [auth B], V [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	C [auth A], D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.72	α = 90
b = 83.41	β = 98.9
c = 97.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
O	model building
ARP/wARP	model building
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Suskiewicz, M.J., Heuck, A., Vu, L.D., Clausen, T.

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-04-10
  Changes: Data collection, Database references
• Version 1.2: 2019-04-17
  Changes: Data collection, Database references
• Version 1.3: 2019-04-24
  Changes: Data collection, Database references
• Version 1.4: 2024-01-17
  Changes: Data collection, Database references, Refinement description