Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.61 kDa 
• Atom Count: 3096 
• Modelled Residue Count: 359 
• Deposited Residue Count: 361 
• Unique protein chains: 1

6KY2

Crystal Structure of Arginine Kinase wild type from Daphnia magna

• PDB DOI: 10.2210/pdb6KY2/pdb

• Classification: TRANSFERASE
• Organism(s): Daphnia magna
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-09-16 Released: 2020-09-16 
• Deposition Author(s): Park, J.H., Rao, Z., Kim, S.Y., Kim, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.230 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Insight into Structural Aspects of Histidine 284 of Daphnia magna Arginine Kinase.

Rao, Z., Kim, S.Y., Li, X., Kim, D.S., Kim, Y.J., Park, J.H.

(2020) Mol Cells 43: 784-792

• PubMed: 32863281 
• DOI: 10.14348/molcells.2020.0136
• Primary Citation of Related Structures:  
  6KY2, 6KY3


• PubMed Abstract: 
  

Arginine kinase (AK), a bioenergy-related enzyme, is distributed widely in invertebrates. The role of highly conserved histidines in AKs is still unascertained. In this study, the highly conserved histidine 284 (H284) in AK of Daphnia magna ( Dm AK) was replaced with alanine to elucidate the role of H284. We examined the alteration of catalytic activity and structural changes of H284A in Dm AK. The catalytic activity of H284A was reduced dramatically compared to that in wild type (WT). Thus the crystal structure of H284A displayed several structural changes, including the alteration of D324, a hydrogen-bonding network around H284, and the disruption of π-stacking between the imidazole group of the H284 residue and the adenine ring of ATP. These findings suggest that such alterations might affect a conformational change of the specific loop consisting of G310-V322 at the antiparallel β-sheet region. Thus, we speculated that the H284 residue might play an important role in the conformational change of the specific loop when ATP binds to the substrate-binding site of Dm AK.

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Organizational Affiliation: 

Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Jeonbuk National University, Iksan 54596, Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginine kinase	A	361	Daphnia magna	Mutation(s): 0  EC: 2.7.3.3
UniProt
Find proteins for A0A0A7CK57 (Daphnia magna) Explore A0A0A7CK57  Go to UniProtKB:  A0A0A7CK57

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.230 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.997	α = 90
b = 57.893	β = 100.09
c = 74.447	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-09-16 
• Released Date: 2020-09-16 
Deposition Author(s): Park, J.H., Rao, Z., Kim, S.Y., Kim, D.S.

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references