1BG0

TRANSITION STATE STRUCTURE OF ARGININE KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Transition state structure of arginine kinase: implications for catalysis of bimolecular reactions.

Zhou, G.Somasundaram, T.Blanc, E.Parthasarathy, G.Ellington, W.R.Chapman, M.S.

(1998) Proc.Natl.Acad.Sci.USA 95: 8449-8454


  • PubMed Abstract: 
  • Arginine kinase belongs to the family of enzymes, including creatine kinase, that catalyze the buffering of ATP in cells with fluctuating energy requirements and that has been a paradigm for classical enzymological studies. The 1.86-A resolution stru ...

    Arginine kinase belongs to the family of enzymes, including creatine kinase, that catalyze the buffering of ATP in cells with fluctuating energy requirements and that has been a paradigm for classical enzymological studies. The 1.86-A resolution structure of its transition-state analog complex, reported here, reveals its active site and offers direct evidence for the importance of precise substrate alignment in the catalysis of bimolecular reactions, in contrast to the unimolecular reactions studied previously. In the transition-state analog complex studied here, a nitrate mimics the planar gamma-phosphoryl during associative in-line transfer between ATP and arginine. The active site is unperturbed, and the reactants are not constrained covalently as in a bisubstrate complex, so it is possible to measure how precisely they are pre-aligned by the enzyme. Alignment is exquisite. Entropic effects may contribute to catalysis, but the lone-pair orbitals are also aligned close enough to their optimal trajectories for orbital steering to be a factor during nucleophilic attack. The structure suggests that polarization, strain toward the transition state, and acid-base catalysis also contribute, but, in contrast to unimolecular enzyme reactions, their role appears to be secondary to substrate alignment in this bimolecular reaction.


    Related Citations: 
    • Critical Initial Real Space Refinement in Structure Determination of Arginine Kinase
      Zhou, G.,Somasundaram, T.,Blanc, E.,Chen, Z.,Chapman, M.S.
      () TO BE PUBLISHED --: --
    • Expression, Purification from Inclusion Bodies, and Crystal Characterization of a Transition State Analog Complex of Arginine Kinase: A Model for Studying Phosphagen Kinases
      Zhou, G.,Parthasarathy, G.,Somasundaram, T.,Ables, A.,Roy, L.,Strong, S.J.,Ellington, W.R.,Chapman, M.S.
      (1997) Protein Sci. 6: 444


    Organizational Affiliation

    Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ARGININE KINASE
A
356Limulus polyphemusMutation(s): 3 
EC: 2.7.3.3
Find proteins for P51541 (Limulus polyphemus)
Go to UniProtKB:  P51541
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

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Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
DAR
Query on DAR

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Download CCD File 
A
D-ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-SCSAIBSYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.439α = 90.00
b = 70.885β = 90.00
c = 80.437γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-14
    Type: Database references, Other