Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

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

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 2.7.3.3). 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 (PpAK), from its complementary DNA to the crystal structure. The PpAK 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 (Km) was 1.7 mM with a kcat of 75 s–1. Two crystal structures are presented, the apoPvAK and PpAK 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. Lastly, these results contribute to knowledge of mechanistic details of the function of arginine kinase.

Authors:
 [1];  [2];  [3];  [3];  [1];  [4];  [3];  [1]
+ Show Author Affiliations
  1. Univ. Nacional de La Plata, Buenos Aires (Argentina)
  2. Univ. de Sonora, Sonora (Mexico)
  3. Centro de Investigacion en Alimentacion y Desarrollo, Sonora (Mexico)
  4. Brookhaven National Lab. (BNL), Upton, NY (United States)
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1435730
Report Number(s):
BNL-203458-2018-JAAM
Journal ID: ISSN 2167-8359
Grant/Contract Number:  
SC0012704
Resource Type:
Accepted Manuscript
Journal Name:
PeerJ
Additional Journal Information:
Journal Volume: 5; Journal ID: ISSN 2167-8359
Publisher:
PeerJ Inc.
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; Arginine kinase; Spider; cDNA cloning; Crystal structure; Phosphagen; Polybetes pytagoricus; Arthropoda; Arachnida; Open conformation; Allergen

Citation Formats

Laino, Aldana, Lopez-Zavala, Alonso A., Garcia-Orozco, Karina D., Carrasco-Miranda, Jesus S., Santana, Marianela, Stojanoff, Vivian, Sotelo-Mundo, Rogerio R., and Garcia, Carlos Fernando. Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus. United States: N. p., 2017. Web. doi:10.7717/peerj.3787.
Copy to clipboard
Laino, Aldana, Lopez-Zavala, Alonso A., Garcia-Orozco, Karina D., Carrasco-Miranda, Jesus S., Santana, Marianela, Stojanoff, Vivian, Sotelo-Mundo, Rogerio R., & Garcia, Carlos Fernando. Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus. United States. https://doi.org/10.7717/peerj.3787
Copy to clipboard
Laino, Aldana, Lopez-Zavala, Alonso A., Garcia-Orozco, Karina D., Carrasco-Miranda, Jesus S., Santana, Marianela, Stojanoff, Vivian, Sotelo-Mundo, Rogerio R., and Garcia, Carlos Fernando. Mon . "Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus". United States. https://doi.org/10.7717/peerj.3787. https://www.osti.gov/servlets/purl/1435730.
Copy to clipboard
@article{osti_1435730,
title = {Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus},
author = {Laino, Aldana and Lopez-Zavala, Alonso A. and Garcia-Orozco, Karina D. and Carrasco-Miranda, Jesus S. and Santana, Marianela and Stojanoff, Vivian and Sotelo-Mundo, Rogerio R. and Garcia, Carlos Fernando},
abstractNote = {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 (PpAK), from its complementary DNA to the crystal structure. The PpAK 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 (Km) was 1.7 mM with a kcat of 75 s–1. Two crystal structures are presented, the apoPvAK and PpAK 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. Lastly, these results contribute to knowledge of mechanistic details of the function of arginine kinase.},
doi = {10.7717/peerj.3787},
journal = {PeerJ},
number = ,
volume = 5,
place = {United States},
year = {2017},
month = {9}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.7717/peerj.3787
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 2 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Isolation and sequence analysis of the gene for arginine kinase from the chelicerate arthropod, Limulus polyphemus: insights into catalytically important residues
journal, January 1995

  • Strong, Scott J.; Ellington, W. Ross
  • Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 1246, Issue 2
  • DOI: 10.1016/0167-4838(94)00218-6

CATH: an expanded resource to predict protein function through structure and sequence
journal, November 2016

  • Dawson, Natalie L.; Lewis, Tony E.; Das, Sayoni
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw1098

Presenting your structures: the CCP 4 mg molecular-graphics software
journal, March 2011

  • McNicholas, S.; Potterton, E.; Wilson, K. S.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911007281

Purification and characterization of arginine kinase from sea-urchin eggs
journal, May 1988

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

Dali server: conservation mapping in 3D
journal, May 2010

  • Holm, Liisa; Rosenstr�m, P�ivi
  • Nucleic Acids Research, Vol. 38, Issue suppl_2
  • DOI: 10.1093/nar/gkq366

The role of phosphagen specificity loops in arginine kinase
journal, February 2004

Characteristics of arthropod arginine kinases
journal, June 1968

The Creatine-Creatine Phosphate Energy Shuttle
journal, June 1985

Periplaneta americana Arginine Kinase as a Major Cockroach Allergen among Thai Patients with Major Cockroach Allergies
journal, June 2006

  • Sookrung, Nitat; Chaicumpa, Wanpen; Tungtrongchitr, Anchalee
  • Environmental Health Perspectives, Vol. 114, Issue 6
  • DOI: 10.1289/ehp.8650

Cloning, expression, characterization and phylogenetic analysis of arginine kinase from greasyback shrimp (Metapenaeus ensis)
journal, July 2009

  • Wang, Jin-Song; Zheng, Zhong-Liang; Lei, Jing
  • Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, Vol. 153, Issue 3
  • DOI: 10.1016/j.cbpb.2009.03.010

Cloning, expression, purification, and characterization of arginine kinase from Locusta migratoria manilensis
journal, December 2007

  • Wu, Qing-Yun; Li, Feng; Zhu, Wen-Jing
  • Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, Vol. 148, Issue 4
  • DOI: 10.1016/j.cbpb.2007.07.002

A novel arginine kinase from the shrimp Neocaridina denticulata: The fourth arginine kinase gene lineage
journal, May 2009

Enzyme activity patterns in muscles of the lycosid spider,Cupiennius salei
journal, January 1975

  • Linzen, B.; Gallowitz, P.
  • Journal of Comparative Physiology ? B, Vol. 96, Issue 2
  • DOI: 10.1007/BF00706589

Arginine kinase of the sheep blowfly Lucilia cuprina: Gene identification and characterization of the native and recombinant enzyme
journal, February 2012

Crystallization and X-ray diffraction studies of arginine kinase from the white Pacific shrimp Litopenaeus vannamei
journal, June 2012

  • Lopez-Zavala, Alonso A.; Sotelo-Mundo, Rogerio R.; Garcia-Orozco, Karina D.
  • Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 68, Issue 7
  • DOI: 10.1107/S1744309112020180

Arginine kinase shows nucleoside diphosphate kinase-like activity toward deoxythymidine diphosphate
journal, April 2016

  • Lopez-Zavala, Alonso A.; Sotelo-Mundo, Rogerio R.; Hernandez-Flores, Jose M.
  • Journal of Bioenergetics and Biomembranes, Vol. 48, Issue 3
  • DOI: 10.1007/s10863-016-9660-1

Arginine kinase from the beetle Cissites cephalotes (Olivier). Molecular cloning, phylogenetic analysis and enzymatic properties
journal, April 2007

  • Tanaka, Kumiko; Ichinari, Shuichi; Iwanami, Kentaro
  • Insect Biochemistry and Molecular Biology, Vol. 37, Issue 4
  • DOI: 10.1016/j.ibmb.2006.12.006

Arginine Kinase from Nautilus pompilius , a Living Fossil : SITE-DIRECTED MUTAGENESIS STUDIES ON THE ROLE OF AMINO ACID RESIDUES IN THE GUANIDINO SPECIFICITY REGION
journal, May 2000

  • Suzuki, Tomohiko; Fukuta, Hideki; Nagato, Hiromi
  • Journal of Biological Chemistry, Vol. 275, Issue 31
  • DOI: 10.1074/jbc.M002926200

Structure of nucleoside diphosphate kinase from pacific shrimp ( Litopenaeus vannamei ) in binary complexes with purine and pyrimidine nucleoside diphosphates
journal, August 2014

  • López-Zavala, Alonso A.; Quintero-Reyes, Idania E.; Carrasco-Miranda, Jesús S.
  • Acta Crystallographica Section F Structural Biology Communications, Vol. 70, Issue 9
  • DOI: 10.1107/S2053230X1401557X

XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

Crystal structure of shrimp arginine kinase in binary complex with arginine—a molecular view of the phosphagen precursor binding to the enzyme
journal, July 2013

  • López-Zavala, Alonso A.; García-Orozco, Karina D.; Carrasco-Miranda, Jesús S.
  • Journal of Bioenergetics and Biomembranes, Vol. 45, Issue 6
  • DOI: 10.1007/s10863-013-9521-0

The crystal structure of Trypanosoma cruzi arginine kinase
journal, July 2007

  • Fernandez, Pablo; Haouz, Ahmed; Pereira, Claudio A.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 69, Issue 1
  • DOI: 10.1002/prot.21557

Metabolic rates of spiders
journal, March 1970

Likelihood-enhanced fast translation functions
journal, March 2005

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Storoni, Laurent C.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 61, Issue 4
  • DOI: 10.1107/S0907444905001617

The mechanism and modes of inhibition of arginine kinase from the cockroach (Periplaneta americana)
journal, January 2004

  • Brown, Ashli E.; Grossman, Steven H.
  • Archives of Insect Biochemistry and Physiology, Vol. 57, Issue 4
  • DOI: 10.1002/arch.20026

InterPro in 2017—beyond protein family and domain annotations
journal, November 2016

  • Finn, Robert D.; Attwood, Teresa K.; Babbitt, Patricia C.
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw1107

Adenosine 5′-Triphosphate-Arginine Phosphotransferase from Lobster Muscle: Purification and Properties
journal, March 1965

  • Virden, R.; Watts, Dc; Baldwin, E.
  • Biochemical Journal, Vol. 94, Issue 3
  • DOI: 10.1042/bj0940536

Induced Fit in Arginine Kinase
journal, March 2000

Polder maps: improving OMIT maps by excluding bulk solvent
journal, February 2017

  • Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.
  • Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 2, p. 148-157
  • DOI: 10.1107/S2059798316018210

Evolution of Phosphagen Kinase
journal, March 1994

  • Suzuki, Tomohiko; Furukohri, Takahiro
  • Journal of Molecular Biology, Vol. 237, Issue 3
  • DOI: 10.1006/jmbi.1994.1237

Role of amino-acid residue 95 in substrate specificity of phosphagen kinases
journal, August 2004

Arginine Kinase from the Cellar Spider <i>(Holocnemus pluchei): </i>A New Asthma-Causing Allergen
journal, December 2010

  • Bobolea, Irina; Barranco, Pilar; Pastor-Vargas, Carlos
  • International Archives of Allergy and Immunology, Vol. 155, Issue 2
  • DOI: 10.1159/000319822

MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Identification of novel allergen in edible insect, Gryllus bimaculatus and its cross-reactivity with Macrobrachium spp. allergens
journal, October 2015

Kinetic properties of the arginine kinase isoenzyme of Limulus polyphemus
journal, March 1972

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Arginine kinase from the housefly, Musca domestica: Purification and properties
journal, September 1972

Participation of book lungs in evaporative water loss in Paraphysa parvula, a migalomorph spider from Chilean Andes
journal, July 2010

Molecular Characterization of Arginine Kinase, an Allergen from the Shrimp <i>Litopenaeus vannamei</i>
journal, January 2007

  • García-Orozco, Karina D.; Aispuro-Hernández, Emmanuel; Yepiz-Plascencia, Gloria
  • International Archives of Allergy and Immunology, Vol. 144, Issue 1
  • DOI: 10.1159/000102610

Identification and characterization of two arginine kinases from the parasitic insect Ctenocephalides felis
journal, September 2009

  • Werr, Margaret; Cramer, Jörg; Ilg, Thomas
  • Insect Biochemistry and Molecular Biology, Vol. 39, Issue 9
  • DOI: 10.1016/j.ibmb.2009.07.001

Solvent content of protein crystals
journal, April 1968

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains
journal, March 2015

  • Wang, Zhiming; Qiao, Zhu; Ye, Sheng
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 4
  • DOI: 10.1107/S1399004715001169

The constraints on maximal activity in spiders: I. Evidence against the fluid insufficiency hypothesis
journal, January 1988

  • Prestwich, Kenneth N.
  • Journal of Comparative Physiology B, Vol. 158, Issue 4
  • DOI: 10.1007/BF00691141

Transition state structure of arginine kinase: Implications for catalysis of bimolecular reactions
journal, July 1998

  • Zhou, G.; Somasundaram, T.; Blanc, E.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 15
  • DOI: 10.1073/pnas.95.15.8449

Purification, characterization, and unfolding studies of arginine kinase from Antarctic krill
journal, June 2014

The effect of rutin on arginine kinase: Inhibition kinetics and thermodynamics merging with docking simulation
journal, March 2009

  • Wu, Xue-Qiang; Zhu, Wen-Jing; Lü, Zhi-Rong
  • International Journal of Biological Macromolecules, Vol. 44, Issue 2
  • DOI: 10.1016/j.ijbiomac.2008.11.007

Characterization and distribution of arginine kinase in the tissues of the scorpion, Palamneus phipsoni
journal, October 1985

  • Arjunwadkar, A. V.; Reddy, S. Raghupathi Rami
  • Canadian Journal of Zoology, Vol. 63, Issue 10
  • DOI: 10.1139/z85-335

Respiration in spiders (Araneae)
journal, January 2016

Arginine kinase in the demosponge Suberites domuncula: regulation of its expression and catalytic activity by silicic acid
journal, February 2005

  • Perovic-Ottstadt, S.
  • Journal of Experimental Biology, Vol. 208, Issue 4
  • DOI: 10.1242/jeb.01428

Creatine kinase: a role for arginine-95 in creatine binding and active site organization
journal, April 2001

  • Edmiston, Paul L.; Schavolt, Kristy L.; Kersteen, Elizabeth A.
  • Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 1546, Issue 2
  • DOI: 10.1016/S0167-4838(01)00159-5
    Sort by:
    [ × clear filter / sort ]

    Similar Records in DOE PAGES and OSTI.GOV collections: