1SD0

Structure of arginine kinase C271A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The active site cysteine of arginine kinase: structural and functional analysis of partially active mutants

Gattis, J.L.Ruben, E.Fenley, M.O.Ellington, W.R.Chapman, M.S.

(2004) Biochemistry 43: 8680-8689

  • DOI: 10.1021/bi049793i
  • Primary Citation of Related Structures:  
    1SD0

  • PubMed Abstract: 
  • Arginine kinase buffers cellular ATP levels by catalyzing reversible phosphoryl transfer between ATP and arginine. A conserved cysteine has long been thought important in catalysis. Here, cysteine 271 of horseshoe crab arginine kinase has been mutate ...

    Arginine kinase buffers cellular ATP levels by catalyzing reversible phosphoryl transfer between ATP and arginine. A conserved cysteine has long been thought important in catalysis. Here, cysteine 271 of horseshoe crab arginine kinase has been mutated to serine, alanine, asparagine, or aspartate. Catalytic turnover rates were 0.02-1.0% of wild type, but the activity of uncharged mutations could be partially rescued with chloride. Steady-state binding constants were slightly increased, more so for phospho-L-arginine than ADP. Substrate binding synergy observed in many phosphagen kinases was reduced or eliminated in mutant enzymes. The crystallographic structure of the alanine mutant at 2.3 A resolution, determined as a transition state analogue complex with arginine, nitrate, and MgADP, was nearly identical to wild type. Enzyme-substrate interactions are maintained as in wild type, and substrates remain at least roughly aligned for in-line phosphoryl transfer. Homology models with serine, asparagine, or aspartate replacing the active site cysteine similarly show only minor structural changes. Most striking, however, is the presence in the C271A mutant crystallographic structure of a chloride ion within 3.5 A of the nonreactive N(eta) substrate nitrogen, approximating the position of the sulfur in the wild-type's cysteine. Together, the results contradict prevailing speculation that the cysteine mediates a substrate-induced conformational change, confirm that it is the thiolate form that is relevant to catalysis, and suggest that one of its roles is to help to enhance the catalytic rate through electrostatic stabilization of the transition state.


    Related Citations: 
    • 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 U S A 95: 8449
    • Refinement of the arginine kianse transition-state analogue complex at 1.2 A resolution: mechanistic insights
      Yousef, M.S., Fabiola, F., Gattis, J.L., Somasundaram, T., Chapman, M.S.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 2009
    • Induced fit in guanidino kinases- comparison of substrate-free and transition state analog structures of arginine kinase
      Yousef, M.S., Clark, S.A., Pruett, P.K., Somasundaram, T., Ellington, W.R., Chapman, M.S.
      (2003) Protein Sci 12: 103

    Organizational Affiliation

    Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4380, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arginine kinaseA357Limulus polyphemusMutation(s): 1 
Gene Names: ak
EC: 2.7.3.3
Find proteins for P51541 (Limulus polyphemus)
Explore P51541 
Go to UniProtKB:  P51541
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

Download Ideal Coordinates CCD File 
A
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
NO3
Query on NO3

Download Ideal Coordinates CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.905α = 90
b = 71.255β = 90
c = 79.98γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance