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PDBsum entry 1m80

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protein Protein-protein interface(s) links
Transferase PDB id
1m80
Jmol
Contents
Protein chains
344 a.a. *
Waters ×624
* Residue conservation analysis
Superseded by: 3m10
PDB id:
1m80
Name: Transferase
Title: Substrate free form of arginine kinase
Structure: Arginine kinase. Chain: a, b. Synonym: ak. Engineered: yes. Mutation: yes
Source: Limulus polyphemus. Atlantic horseshoe crab. Organism_taxid: 6850. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.35Å     R-factor:   0.223     R-free:   0.237
Authors: M.S.Yousef,S.A.Clark,P.K.Pruett,T.Somasundaram, W.R.Ellington,M.S.Chapman
Key ref:
M.S.Yousef et al. (2003). Induced fit in guanidino kinases--comparison of substrate-free and transition state analog structures of arginine kinase. Protein Sci, 12, 103-111. PubMed id: 12493833 DOI: 10.1110/ps.0226303
Date:
23-Jul-02     Release date:   31-Dec-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P51541  (KARG_LIMPO) -  Arginine kinase
Seq:
Struc:
357 a.a.
344 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
= ADP
+ N(omega)-phospho-L-arginine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1110/ps.0226303 Protein Sci 12:103-111 (2003)
PubMed id: 12493833  
 
 
Induced fit in guanidino kinases--comparison of substrate-free and transition state analog structures of arginine kinase.
M.S.Yousef, S.A.Clark, P.K.Pruett, T.Somasundaram, W.R.Ellington, M.S.Chapman.
 
  ABSTRACT  
 
Arginine kinase (AK) is a member of the guanidino kinase family that plays an important role in buffering ATP concentration in cells with high and fluctuating energy demands. The AK specifically catalyzes the reversible phosphoryl transfer between ATP and arginine. We have determined the crystal structure of AK from the horseshoe crab (Limulus polyphemus) in its open (substrate-free) form. The final model has been refined at 2.35 A with a final R of 22.3% (R(free) = 23.7%). The structure of the open form is compared to the previously determined structure of the transition state analog complex in the closed form. Classically, the protein would be considered two domain, but dynamic domain (DynDom) analysis shows that most of the differences between the two structures can be considered as the motion between four rigid groups of nonsequential residues. ATP binds near a cluster of positively charged residues of a fixed dynamic domain. The other three dynamic domains close the active site with separate hinge rotations relative to the fixed domain. Several residues of key importance for the induced motion are conserved within the phosphagen kinase family, including creatine kinase. Substantial conformational changes are induced in different parts of the enzyme as intimate interactions are formed with both substrates. Thus, although induced fit occurs in a number of phosphoryl transfer enzymes, the conformational changes in phosphagen kinases appear to be more complicated than in prior examples.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Example electron density: a 2F[o] - F[c] omit map, contoured at 1.5 , around residues Phe[218], Leu[219], and Val[220].
Figure 3.
Figure 3. Space-filling models comparing open and closed forms of arginine kinase. (A) The substrate-free conformation is shown with the substrates in stick model as they would be bound in the closed form. (B) The closed form shields the substrates from solvent access.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2003, 12, 103-111) copyright 2003.  
  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.  
20516627 M.S.Chapman, and T.Somasundaram (2010).
De-icing: recovery of diffraction intensities in the presence of ice rings.
  Acta Crystallogr D Biol Crystallogr, 66, 741-744.  
19836335 O.Davulcu, P.F.Flynn, M.S.Chapman, and J.J.Skalicky (2009).
Intrinsic domain and loop dynamics commensurate with catalytic turnover in an induced-fit enzyme.
  Structure, 17, 1356-1367.  
  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.  
18064398 M.Conejo, M.Bertin, S.A.Pomponi, and W.R.Ellington (2008).
The early evolution of the phosphagen kinases-insights from choanoflagellate and poriferan arginine kinases.
  J Mol Evol, 66, 11-20.  
17897673 A.Korostelev, and H.F.Noller (2007).
Analysis of structural dynamics in the ribosome by TLS crystallographic refinement.
  J Mol Biol, 373, 1058-1070.  
17327675 J.F.Ohren, M.L.Kundracik, C.L.Borders, P.Edmiston, and R.E.Viola (2007).
Structural asymmetry and intersubunit communication in muscle creatine kinase.
  Acta Crystallogr D Biol Crystallogr, 63, 381-389.  
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
16034675 O.Davulcu, S.A.Clark, M.S.Chapman, and J.J.Skalicky (2005).
Main chain 1H, 13C, and 15N resonance assignments of the 42-kDa enzyme arginine kinase.
  J Biomol NMR, 32, 178.  
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
14739330 H.Mazon, O.Marcillat, E.Forest, and C.Vial (2004).
Hydrogen/deuterium exchange studies of native rabbit MM-CK dynamics.
  Protein Sci, 13, 476-486.  
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.  
15627388 Q.Guo, B.Chen, and X.Wang (2004).
Evidence for proximal cysteine and lysine residues at or near the active site of arginine kinase of Stichopus japonicus.
  Biochemistry (Mosc), 69, 1336-1343.  
14622006 H.Mazon, O.Marcillat, E.Forest, and C.Vial (2003).
Changes in MM-CK conformational mobility upon formation of the ADP-Mg(2+)-NO(3)(-)-creatine transition state analogue complex as detected by hydrogen/deuterium exchange.
  Biochemistry, 42, 13596-13604.  
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 code is shown on the right.