6FH1

Protein arginine kinase McsB in the apo state

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1038/s41589-019-0265-y
  • Primary Citation of 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 ...

    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.

    Organizational Affiliation: 

    Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria. tim.clausen@imp.ac.at.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein-arginine kinase
A, B
366Geobacillus stearothermophilusMutation(s): 0 
Gene Names: mcsB
EC: 2.7.14.1
UniProt
Find proteins for P0DMM5 (Geobacillus stearothermophilus)
Explore P0DMM5 
Go to UniProtKB:  P0DMM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DMM5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD
Download Ideal Coordinates CCD File 
T [auth A],
W [auth B],
X [auth B],
Y [auth B]		IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
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		 Ligand Interaction
FMT
Query on FMT
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.72α = 90
b = 83.41β = 98.9
c = 97.78γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
Omodel building
ARP/wARPmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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