4BHL

Crystal structure of Litopenaeus vannamei arginine kinase in binary complex with arginine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

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Literature

Crystal Structure of Shrimp Arginine Kinase in Binary Complex with Arginine-A Molecular View of the Phosphagen Precursor Binding to the Enzyme.

Lopez-Zavala, A.A., Garcia-Orozco, K.D., Carrasco-Miranda, J.S., Sugich-Miranda, R., Velazquez-Contreras, E.F., Criscitiello, M.F., Brieba, L.G., Rudino-Pinera, E., Sotelo-Mundo, R.R.

(2013) J Bioenerg Biomembr 45: 511

  • DOI: 10.1007/s10863-013-9521-0
  • Primary Citation of Related Structures:  
    4BG4, 4BHL

  • PubMed Abstract: 

    • Arginine kinase (AK) is a key enzyme for energetic balance in invertebrates. Although AK is a well-studied system that provides fast energy to invertebrates using the phosphagen phospho-arginine, the structural details on the AK-arginine binary complex interaction remain unclear ...

    Arginine kinase (AK) is a key enzyme for energetic balance in invertebrates. Although AK is a well-studied system that provides fast energy to invertebrates using the phosphagen phospho-arginine, the structural details on the AK-arginine binary complex interaction remain unclear. Herein, we determined two crystal structures of the Pacific whiteleg shrimp (Litopenaeus vannamei) arginine kinase, one in binary complex with arginine (LvAK-Arg) and a ternary transition state analog complex (TSAC). We found that the arginine guanidinium group makes ionic contacts with Glu225, Cys271 and a network of ordered water molecules. On the zwitterionic side of the amino acid, the backbone amide nitrogens of Gly64 and Val65 coordinate the arginine carboxylate. Glu314, one of proposed acid-base catalytic residues, did not interact with arginine in the binary complex. This residue is located in the flexible loop 310-320 that covers the active site and only stabilizes in the LvAK-TSAC. This is the first binary complex crystal structure of a guanidine kinase in complex with the guanidine substrate and could give insights into the nature of the early steps of phosphagen biosynthesis.

    Organizational Affiliation: 

    Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD). Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora, 83304, Mexico.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ARGININE KINASEA356Penaeus vannameiMutation(s): 0 
EC: 2.7.3.3
UniProt
Find proteins for Q004B5 (Penaeus vannamei)
Explore Q004B5 
Go to UniProtKB:  Q004B5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ004B5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG
Download Ideal Coordinates CCD File 
B [auth A]ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O		 Ligand Interaction
BME
Query on BME
Download Ideal Coordinates CCD File 
C [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.368α = 90
b = 70.338β = 90
c = 82.054γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-11-27
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other