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PDBsum entry 1m15

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protein ligands metals links
Transferase PDB id
1m15
Jmol
Contents
Protein chain
356 a.a. *
Ligands
NO3 ×2
ARG
ADP
Metals
_MG
Waters ×557
* Residue conservation analysis
PDB id:
1m15
Name: Transferase
Title: Transition state structure of arginine kinase
Structure: Arginine kinase. Chain: a. Synonym: ak. Engineered: yes. Mutation: yes
Source: Limulus polyphemus. Atlantic horseshoe crab. Organism_taxid: 6850. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.20Å     R-factor:   0.122     R-free:   0.140
Authors: M.S.Yousef,F.Fabiola,J.L.Gattis,T.Somasundaram,M.S.Chapman
Key ref:
M.S.Yousef et al. (2002). Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution: mechanistic insights. Acta Crystallogr D Biol Crystallogr, 58, 2009-2017. PubMed id: 12454458 DOI: 10.1107/S0907444902014683
Date:
17-Jun-02     Release date:   04-Dec-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P51541  (KARG_LIMPO) -  Arginine kinase
Seq:
Struc:
357 a.a.
356 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.7.3.3  - Arginine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-arginine = ADP + N(omega)-phospho-L-arginine
ATP
+
L-arginine
Bound ligand (Het Group name = ARG)
corresponds exactly
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ N(omega)-phospho-L-arginine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     phosphorylation   1 term 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444902014683 Acta Crystallogr D Biol Crystallogr 58:2009-2017 (2002)
PubMed id: 12454458  
 
 
Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution: mechanistic insights.
M.S.Yousef, F.Fabiola, J.L.Gattis, T.Somasundaram, M.S.Chapman.
 
  ABSTRACT  
 
The three-dimensional crystal structure of an arginine kinase transition-state analogue complex has been refined at 1.2 A resolution, with an overall R factor of 12.3%. The current model provides a unique opportunity to analyze the structure of a bimolecular (phosphagen kinase) enzyme in its transition state. This atomic resolution structure confirms in-line transfer of the phosphoryl group and the catalytic importance of the precise alignment of the substrates. The structure is consistent with a concerted proton transfer that has been proposed for an unrelated kinase. Refinement of anisotropic temperature factors and translation-libration-screw (TLS) analyses led to the identification of four rigid groups and their prevalent modes of motion in the transition state. The relative magnitudes of the mobility of rigid groups are consistent with their proposed roles in catalysis.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 (a) Precise alignment of the substrates in the active site as revealed by the 2F[o] - F[c] electron-density map contoured at 3 . (b) The in-line transfer of the phosphoryl group and the hydrogen-bond geometry between O[ 1] of ADP and O[1] of nitrate. Angles in parentheses correspond to the optimal reaction trajectory (Zhou et al., 1998[Zhou, G., Somasundaram, T., Blanc, E., Parthsarathy, G., Ellington, W. R. & Chapman, M. S. (1998). Proc. Natl Acad. Sci. USA, 95, 8449-8454.]).
Figure 4.
Figure 4 Coordination of Mg2+ in the active site. Distances are shown in .
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 2009-2017) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21507330 N.Liu, J.S.Wang, W.D.Wang, and J.C.Pan (2011).
The role of Cys271 in conformational changes of arginine kinase.
  Int J Biol Macromol, 49, 98.  
  18765922 A.M.Awama, P.Paracuellos, S.Laurent, C.Dissous, O.Marcillat, and P.Gouet (2008).
Crystallization and X-ray analysis of the Schistosoma mansoni guanidino kinase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 854-857.  
19016839 A.R.Mattoo, A.Arora, S.Maiti, and Y.Singh (2008).
Identification, characterization and activation mechanism of a tyrosine kinase of Bacillus anthracis.
  FEBS J, 275, 6237-6247.  
17940016 A.Korostelev, S.Trakhanov, H.Asahara, M.Laurberg, L.Lancaster, and H.F.Noller (2007).
Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.
  Proc Natl Acad Sci U S A, 104, 16840-16843.
PDB codes: 1vsp 2qnh
17292830 M.S.Chapman (2007).
Normalizing normal mode analysis.
  Structure, 15, 135-136.  
17623863 P.Fernandez, A.Haouz, C.A.Pereira, C.Aguilar, and P.M.Alzari (2007).
The crystal structure of Trypanosoma cruzi arginine kinase.
  Proteins, 69, 209-212.
PDB code: 2j1q
17322533 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Domain motions of glucosamine-6P synthase: comparison of the anisotropic displacements in the crystals and the catalytic hinge-bending rotation.
  Protein Sci, 16, 485-493.  
16163393 J.Kirstein, D.Zühlke, U.Gerth, K.Turgay, and M.Hecker (2005).
A tyrosine kinase and its activator control the activity of the CtsR heat shock repressor in B. subtilis.
  EMBO J, 24, 3435-3445.  
14978299 A.Azzi, S.A.Clark, W.R.Ellington, and M.S.Chapman (2004).
The role of phosphagen specificity loops in arginine kinase.
  Protein Sci, 13, 575-585.
PDB code: 1rl9
15211520 C.Lehmann, V.Doseeva, S.Pullalarevu, W.Krajewski, A.Howard, and O.Herzberg (2004).
YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays.
  Proteins, 56, 376-383.
PDB code: 1r8g
15181469 J.C.Pan, Z.H.Yu, E.F.Hui, and H.M.Zhou (2004).
Conformational change and inactivation of arginine kinase from shrimp Feneropenaeus chinensis in oxidized dithiothreitol solutions.
  Biochem Cell Biol, 82, 361-367.  
15215531 J.C.Pan, Z.Yu, X.Y.Su, Y.Q.Sun, X.M.Rao, and H.M.Zhou (2004).
Unassisted refolding of urea-denatured arginine kinase from shrimp Feneropenaeus chinensis: evidence for two equilibrium intermediates in the refolding pathway.
  Protein Sci, 13, 1892-1901.  
12732621 P.S.Pruett, A.Azzi, S.A.Clark, M.S.Yousef, J.L.Gattis, T.Somasundaram, W.R.Ellington, and M.S.Chapman (2003).
The putative catalytic bases have, at most, an accessory role in the mechanism of arginine kinase.
  J Biol Chem, 278, 26952-26957.
PDB codes: 1p50 1p52
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.