5U92

Crystal Structure of arginine kinase from the spider Polybetes pythagoricus in complex with arginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus.

Laino, A.Lopez-Zavala, A.A.Garcia-Orozco, K.D.Carrasco-Miranda, J.S.Santana, M.Stojanoff, V.Sotelo-Mundo, R.R.Garcia, C.F.

(2017) PeerJ 5: e3787-e3787

  • DOI: 10.7717/peerj.3787
  • Primary Citation of Related Structures:  
    5U8E, 5U92

  • PubMed Abstract: 
  • Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2 ...

    Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus ( Pp AK), from its complementary DNA to the crystal structure. The Pp AK cDNA from muscle was cloned, and it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant ( K m ) was 1.7 mM with a k cat of 75 s -1 . Two crystal structures are presented, the apo Pv AK and Pp AK bound to arginine, both in the open conformation with the active site lid (residues 310-320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Finally, these results contribute to knowledge of mechanistic details of the function of arginine kinase.


    Organizational Affiliation

    Instituto de Investigaciones Bioquímicas de La Plata "Dr. Prof. Rodolfo R. Brenner", Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
arginine kinaseA384Polybetes pythagoricusMutation(s): 0 
EC: 2.7.3.3
UniProt
Find proteins for A0A286R7K5 (Polybetes pythagoricus)
Explore A0A286R7K5 
Go to UniProtKB:  A0A286R7K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A286R7K5
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
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.09α = 90
b = 61.45β = 95.75
c = 60.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)MexicoINFR-2014-01-225455
Consejo Nacional de Ciencia y Tecnologia (CONACYT)MexicoC0005-2012-189333
Consejo Nacional de Investigaciones Cientificas y TecnicasArgentinaCOOP-CTES-D680
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)ArgentinaPICT 2014-2580
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM111244
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
Department of Energy (DOE, United States)United States451DESC0012704
Department of Energy (DOE, United States)United StatesDEAC0276SF00515

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence