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PDBsum entry 1crk

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1crk
Jmol
Contents
Protein chains
380 a.a. *
Ligands
PO4 ×8
* Residue conservation analysis
PDB id:
1crk
Name: Transferase
Title: Mitochondrial creatine kinase
Structure: Creatine kinase. Chain: a, b, c, d. Ec: 2.7.3.2
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organ: heart. Tissue: muscle. Cell: sarcomer. Organelle: mitochondria
Biol. unit: Octamer (from PDB file)
Resolution:
3.00Å     R-factor:   0.217     R-free:   0.264
Authors: K.Fritz-Wolf,T.Schnyder,T.Wallimann,W.Kabsch
Key ref: K.Fritz-Wolf et al. (1996). Structure of mitochondrial creatine kinase. Nature, 381, 341-345. PubMed id: 8692275
Date:
08-Mar-96     Release date:   07-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P11009  (KCRS_CHICK) -  Creatine kinase S-type, mitochondrial
Seq:
Struc:
419 a.a.
380 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.3.2  - Creatine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Creatine Biosynthesis
      Reaction: ATP + creatine = ADP + phosphocreatine
ATP
+ creatine
= ADP
+ phosphocreatine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     phosphorylation   1 term 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
Nature 381:341-345 (1996)
PubMed id: 8692275  
 
 
Structure of mitochondrial creatine kinase.
K.Fritz-Wolf, T.Schnyder, T.Wallimann, W.Kabsch.
 
  ABSTRACT  
 
Creatine kinase (CK, EC 2.7.3.2), an enzyme important for energy metabolism in cells of high and fluctuating energy requirements, catalyses the reversible transfer of a phosphoryl goup from phosphocreatine to ADP. We have solved the structure of the octameric mitochondrial isoform, Mib-CK, which is located in the intermembrane compartment and along the cristae membranes. Mib-CK consumes ATP produced in the mitochondria for the production of phosphocreatine, which is then exported into the cytosol for fast regeneration of ATP by the cytosolic CK isoforms. The octamer has 422 point-group symmetry, and appears as a cube of side length 93 angstrom with a channel 20 angstrom wide extending along the four-fold axis. Positively charged amino acids at the four-fold faces of the octamer possibly interact with negatively charged mitochondrial membranes. Each monomer consists of a small alpha-helical domain and a large domain containing an eight-stranded antiparallel beta-sheet flanked by seven alpha-helices. The conserved residues of the CK family form a compact cluster that covers the active site between the domains.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21448658 T.Wallimann, M.Tokarska-Schlattner, and U.Schlattner (2011).
The creatine kinase system and pleiotropic effects of creatine.
  Amino Acids, 40, 1271-1296.  
20098674 F.Karbassi, V.Quiros, V.Pancholi, and M.J.Kornblatt (2010).
Dissociation of the octameric enolase from S. pyogenes--one interface stabilizes another.
  PLoS One, 5, e8810.  
  20066127 A.Hermoso, J.Espadaler, E.Enrique Querol, F.X.Aviles, M.J.Sternberg, B.Oliva, and N.Fernandez-Fuentes (2009).
Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB).
  Bioinform Biol Insights, 1, 77-90.  
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.  
19289067 O.Maniti, M.F.Lecompte, O.Marcillat, B.Desbat, R.Buchet, C.Vial, and T.Granjon (2009).
Mitochondrial creatine kinase binding to phospholipid monolayers induces cardiolipin segregation.
  Biophys J, 96, 2428-2438.  
  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.  
18092936 I.Dalle-Donne, A.Milzani, N.Gagliano, R.Colombo, D.Giustarini, and R.Rossi (2008).
Molecular mechanisms and potential clinical significance of S-glutathionylation.
  Antioxid Redox Signal, 10, 445-473.  
18980670 L.M.Iyer, A.M.Burroughs, and L.Aravind (2008).
Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination.
  Biol Direct, 3, 45.  
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.  
17028143 R.F.Epand, U.Schlattner, T.Wallimann, M.L.Lacombe, and R.M.Epand (2007).
Novel lipid transfer property of two mitochondrial proteins that bridge the inner and outer membranes.
  Biophys J, 92, 126-137.  
16870939 J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2006).
Identification of function-associated loop motifs and application to protein function prediction.
  Bioinformatics, 22, 2237-2243.  
16545071 N.V.Fedurkina, L.V.Belousova, L.G.Mitskevich, H.M.Zhou, Z.Chang, and B.I.Kurganov (2006).
Change in kinetic regime of protein aggregation with temperature increase. Thermal aggregation of rabbit muscle creatine kinase.
  Biochemistry (Mosc), 71, 325-331.  
16283667 N.Vernoux, T.Granjon, O.Marcillat, F.Besson, and C.Vial (2006).
Interfacial behavior of cytoplasmic and mitochondrial creatine kinase oligomeric states.
  Biopolymers, 81, 270-281.  
16981706 P.F.Wang, A.J.Flynn, M.M.Naor, J.H.Jensen, G.Cui, K.M.Merz, G.L.Kenyon, and M.J.McLeish (2006).
Exploring the role of the active site cysteine in human muscle creatine kinase.
  Biochemistry, 45, 11464-11472.  
15735334 A.Janner (2005).
Strongly correlated structure of axial-symmetric proteins. I. Orthorhombic, tetragonal, trigonal and hexagonal symmetries.
  Acta Crystallogr D Biol Crystallogr, 61, 247-255.  
16006628 H.W.He, J.Zhang, H.M.Zhou, and Y.B.Yan (2005).
Conformational change in the C-terminal domain is responsible for the initiation of creatine kinase thermal aggregation.
  Biophys J, 89, 2650-2658.  
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.  
16008553 K.Uda, N.Saishoji, S.Ichinari, W.R.Ellington, and T.Suzuki (2005).
Origin and properties of cytoplasmic and mitochondrial isoforms of taurocyamine kinase.
  FEBS J, 272, 3521-3530.  
15881668 S.SinhaRoy, S.Banerjee, M.Ray, and S.Ray (2005).
Possible involvement of glutamic and/or aspartic acid residue(s) and requirement of mitochondrial integrity for the protective effect of creatine against inhibition of cardiac mitochondrial respiration by methylglyoxal.
  Mol Cell Biochem, 271, 167-176.  
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.  
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.  
15229886 N.Fernandez-Fuentes, A.Hermoso, J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2004).
Classification of common functional loops of kinase super-families.
  Proteins, 56, 539-555.  
15044463 U.Schlattner, F.Gehring, N.Vernoux, M.Tokarska-Schlattner, D.Neumann, O.Marcillat, C.Vial, and T.Wallimann (2004).
C-terminal lysines determine phospholipid interaction of sarcomeric mitochondrial creatine kinase.
  J Biol Chem, 279, 24334-24342.  
12592023 C.L.Borders, K.M.MacGregor, P.L.Edmiston, E.R.Gbeddy, M.J.Thomenius, G.B.Mulligan, and M.J.Snider (2003).
Asparagine 285 plays a key role in transition state stabilization in rabbit muscle creatine kinase.
  Protein Sci, 12, 532-537.  
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.  
12493833 M.S.Yousef, S.A.Clark, P.K.Pruett, T.Somasundaram, W.R.Ellington, and M.S.Chapman (2003).
Induced fit in guanidino kinases--comparison of substrate-free and transition state analog structures of arginine kinase.
  Protein Sci, 12, 103-111.
PDB code: 1m80
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
12401781 S.Wendt, U.Schlattner, and T.Wallimann (2003).
Differential effects of peroxynitrite on human mitochondrial creatine kinase isoenzymes. Inactivation, octamer destabilization, and identification of involved residues.
  J Biol Chem, 278, 1125-1130.  
12454458 M.S.Yousef, F.Fabiola, J.L.Gattis, T.Somasundaram, and M.S.Chapman (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.
PDB code: 1m15
12127572 T.Suzuki, N.Sugimura, T.Taniguchi, Y.Unemi, T.Murata, M.Hayashida, K.Yokouchi, K.Uda, and T.Furukohri (2002).
Two-domain arginine kinases from the clams Solen strictus and Corbicula japonica: exceptional amino acid replacement of the functionally important D(62) by G.
  Int J Biochem Cell Biol, 34, 1221-1229.  
11173463 D.Tisi, B.Bax, and A.Loew (2001).
The three-dimensional structure of cytosolic bovine retinal creatine kinase.
  Acta Crystallogr D Biol Crystallogr, 57, 187-193.
PDB code: 1g0w
11258919 J.S.Cantwell, W.R.Novak, P.F.Wang, M.J.McLeish, G.L.Kenyon, and P.C.Babbitt (2001).
Mutagenesis of two acidic active site residues in human muscle creatine kinase: implications for the catalytic mechanism.
  Biochemistry, 40, 3056-3061.  
11295435 P.L.Edmiston, K.L.Schavolt, E.A.Kersteen, N.R.Moore, and C.L.Borders (2001).
Creatine kinase: a role for arginine-95 in creatine binding and active site organization.
  Biochim Biophys Acta, 1546, 291-298.  
11258911 T.Granjon, M.J.Vacheron, C.Vial, and R.Buchet (2001).
Structural changes of mitochondrial creatine kinase upon binding of ADP, ATP, or Pi, observed by reaction-induced infrared difference spectra.
  Biochemistry, 40, 2988-2994.  
11352737 T.Granjon, M.J.Vacheron, C.Vial, and R.Buchet (2001).
Mitochondrial creatine kinase binding to phospholipids decreases fluidity of membranes and promotes new lipid-induced beta structures as monitored by red edge excitation shift, laurdan fluorescence, and FTIR.
  Biochemistry, 40, 6016-6026.  
  11602586 U.Schlattner, M.Dolder, T.Wallimann, and M.Tokarska-Schlattner (2001).
Mitochondrial creatine kinase and mitochondrial outer membrane porin show a direct interaction that is modulated by calcium.
  J Biol Chem, 276, 48027-48030.  
10692338 G.Zhou, W.R.Ellington, and M.S.Chapman (2000).
Induced fit in arginine kinase.
  Biophys J, 78, 1541-1550.  
10924118 H.Hagemann, O.Marcillat, R.Buchet, and C.Vial (2000).
Magnesium-adenosine diphosphate binding sites in wild-type creatine kinase and in mutants: role of aromatic residues probed by Raman and infrared spectroscopies.
  Biochemistry, 39, 9251-9256.  
11037185 K.Arahata (2000).
Muscular dystrophy.
  Neuropathology, 20, S34-S41.  
10702255 L.Kay, K.Nicolay, B.Wieringa, V.Saks, and T.Wallimann (2000).
Direct evidence for the control of mitochondrial respiration by mitochondrial creatine kinase in oxidative muscle cells in situ.
  J Biol Chem, 275, 6937-6944.  
10737943 M.Eder, K.Fritz-Wolf, W.Kabsch, T.Wallimann, and U.Schlattner (2000).
Crystal structure of human ubiquitous mitochondrial creatine kinase.
  Proteins, 39, 216-225.
PDB code: 1qk1
11154064 U.Schlattner, M.Eder, M.Dolder, Z.A.Khuchua, A.W.Strauss, and T.Wallimann (2000).
Divergent enzyme kinetics and structural properties of the two human mitochondrial creatine kinase isoenzymes.
  Biol Chem, 381, 1063-1070.  
10759600 V.A.Saks, O.Kongas, M.Vendelin, and L.Kay (2000).
Role of the creatine/phosphocreatine system in the regulation of mitochondrial respiration.
  Acta Physiol Scand, 168, 635-641.  
10447674 A.O.Pineda, and W.R.Ellington (1999).
Structural and functional implications of the amino acid sequences of dimeric, cytoplasmic and octameric mitochondrial creatine kinases from a protostome invertebrate.
  Eur J Biochem, 264, 67-73.  
  10396141 D.O.Fürst, W.M.Obermann, and P.F.van der Ven (1999).
Structure and assembly of the sarcomeric M band.
  Rev Physiol Biochem Pharmacol, 138, 163-202.  
10089314 G.Zhou, T.Somasundaram, E.Blanc, Z.Chen, and M.S.Chapman (1999).
Critical initial real-space refinement in the structure determination of arginine kinase.
  Acta Crystallogr D Biol Crystallogr, 55, 835-845.  
10089465 L.Tang, H.M.Zhou, and Z.J.Lin (1999).
Crystallization and preliminary X-ray analysis of human muscle creatine kinase.
  Acta Crystallogr D Biol Crystallogr, 55, 669-670.  
  10595529 M.Eder, U.Schlattner, A.Becker, T.Wallimann, W.Kabsch, and K.Fritz-Wolf (1999).
Crystal structure of brain-type creatine kinase at 1.41 A resolution.
  Protein Sci, 8, 2258-2269.
PDB code: 1qh4
10387096 S.S.David, and B.E.Haley (1999).
ATP nucleotidylation of creatine kinase.
  Biochemistry, 38, 8492-8500.  
11701502 T.F.Budinger, D.A.Benaron, and A.P.Koretsky (1999).
Imaging transgenic animals.
  Annu Rev Biomed Eng, 1, 611-648.  
9562560 A.Matte, L.W.Tari, and L.T.Delbaere (1998).
How do kinases transfer phosphoryl groups?
  Structure, 6, 413-419.  
9860874 C.Leydier, E.Clottes, F.Couthon, O.Marcillat, C.Ebel, and C.Vial (1998).
Evidence for kinetic intermediate states during the refolding of GdnHCl-denatured MM-creatine kinase. Characterization of a trapped monomeric species.
  Biochemistry, 37, 17579-17589.  
9672041 C.Perraut, E.Clottes, C.Leydier, C.Vial, and O.Marcillat (1998).
Role of quaternary structure in muscle creatine kinase stability: tryptophan 210 is important for dimer cohesion.
  Proteins, 32, 43-51.  
9693008 G.E.Morris, S.G.Sedgwick, J.M.Ellis, A.Pereboev, J.S.Chamberlain, and Nguyen thi Man (1998).
An epitope structure for the C-terminal domain of dystrophin and utrophin.
  Biochemistry, 37, 11117-11127.  
9671698 G.Zhou, T.Somasundaram, E.Blanc, G.Parthasarathy, W.R.Ellington, and M.S.Chapman (1998).
Transition state structure of arginine kinase: implications for catalysis of bimolecular reactions.
  Proc Natl Acad Sci U S A, 95, 8449-8454.
PDB code: 1bg0
9837966 H.W.Sun, C.F.Hui, and J.L.Wu (1998).
Cloning, characterization, and expression in Escherichia coli of three creatine kinase muscle isoenzyme cDNAs from carp (Cyprinus carpio) striated muscle.
  J Biol Chem, 273, 33774-33780.  
9748514 K.L.Min, J.P.Steghens, R.Henry, A.Doutheau, and C.Collombel (1998).
Identification of the creatine binding domain of creatine kinase by photoaffinity labeling.
  Biochim Biophys Acta, 1387, 80-88.  
9675202 M.Forstner, M.Kriechbaum, P.Laggner, and T.Wallimann (1998).
Structural changes of creatine kinase upon substrate binding.
  Biophys J, 75, 1016-1023.  
9520370 T.D.Wood, Z.Guan, C.L.Borders, L.H.Chen, G.L.Kenyon, and F.W.McLafferty (1998).
Creatine kinase: essential arginine residues at the nucleotide binding site identified by chemical modification and high-resolution tandem mass spectrometry.
  Proc Natl Acad Sci U S A, 95, 3362-3365.  
9843436 T.Shimizu, and H.Morii (1998).
Spectroscopic studies of the ncd motor domain.ADP complex: CD spectrum of ADP induced by binding to the motor domain of ncd.
  Biochemistry, 37, 16680-16685.  
  9914824 T.Wallimann, M.Dolder, U.Schlattner, M.Eder, T.Hornemann, E.O'Gorman, A.Rück, and D.Brdiczka (1998).
Some new aspects of creatine kinase (CK): compartmentation, structure, function and regulation for cellular and mitochondrial bioenergetics and physiology.
  Biofactors, 8, 229-234.  
9541010 W.R.Ellington, K.Roux, and A.O.Pineda (1998).
Origin of octameric creatine kinases.
  FEBS Lett, 425, 75-78.  
  9865958 Y.X.Fan, J.M.Zhou, H.Kihara, and C.L.Tsou (1998).
Unfolding and refolding of dimeric creatine kinase equilibrium and kinetic studies.
  Protein Sci, 7, 2631-2641.  
9774729 Y.Yang, and H.M.Zhou (1998).
Reactivation kinetics of 5,5'-dithiobis-(2-nitrobenzoic acid)-modified creatine kinase reactivated by dithiothreitol.
  Biochim Biophys Acta, 1388, 190-198.  
9722522 Z.A.Khuchua, W.Qin, J.Boero, J.Cheng, R.M.Payne, V.A.Saks, and A.W.Strauss (1998).
Octamer formation and coupling of cardiac sarcomeric mitochondrial creatine kinase are mediated by charged N-terminal residues.
  J Biol Chem, 273, 22990-22996.  
9218780 A.Humm, E.Fritsche, S.Steinbacher, and R.Huber (1997).
Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis.
  EMBO J, 16, 3373-3385.
PDB codes: 1jdw 2jdw 3jdw 4jdw
9461301 C.Raimbault, C.Perraut, O.Marcillat, R.Buchet, and C.Vial (1997).
Nucleotide binding sites in wild-type creatine kinase and in W227Y mutant probed by photochemical release of nucleotides and infrared difference spectroscopy.
  Eur J Biochem, 250, 773-782.  
9288948 C.Raimbault, E.Clottes, C.Leydier, C.Vial, and R.Buchet (1997).
ADP-binding and ATP-binding sites in native and proteinase-K-digested creatine kinase, probed by reaction-induced difference infrared spectroscopy.
  Eur J Biochem, 247, 1197-1208.  
9118999 C.Raimbault, F.Besson, and R.Buchet (1997).
Conformational changes of arginine kinase induced by photochemical release of nucleotides from caged nucleotides--an infrared difference-spectroscopy investigation.
  Eur J Biochem, 244, 343-351.  
  9041648 G.Zhou, G.Parthasarathy, T.Somasundaram, A.Ables, L.Roy, S.J.Strong, W.R.Ellington, and M.S.Chapman (1997).
Expression, purification from inclusion bodies, and crystal characterization of a transition state analog complex of arginine kinase: a model for studying phosphagen kinases.
  Protein Sci, 6, 444-449.  
9370460 M.Arrio-Dupont, G.Foucault, M.Vacher, A.Douhou, and S.Cribier (1997).
Mobility of creatine phosphokinase and beta-enolase in cultured muscle cells.
  Biophys J, 73, 2667-2673.  
  9041634 M.Forstner, A.Müller, M.Stolz, and T.Wallimann (1997).
The active site histidines of creatine kinase. A critical role of His 61 situated on a flexible loop.
  Protein Sci, 6, 331-339.  
9434900 W.Kabsch, and K.Fritz-Wolf (1997).
Mitochondrial creatine kinase--a square protein.
  Curr Opin Struct Biol, 7, 811-818.  
8885829 B.Sankaran, A.J.Chavan, and B.E.Haley (1996).
Identification of adenine binding domain peptides of the NADP+ active site within porcine heart NADP(+)-dependent isocitrate dehydrogenase.
  Biochemistry, 35, 13501-13510.  
8797846 C.Raimbault, R.Buchet, and C.Vial (1996).
Changes of creatine kinase secondary structure induced by the release of nucleotides from caged compounds. An infrared difference-spectroscopy study.
  Eur J Biochem, 240, 134-142.  
8952506 O.Stachowiak, M.Dolder, and T.Wallimann (1996).
Membrane-binding and lipid vesicle cross-linking kinetics of the mitochondrial creatine kinase octamer.
  Biochemistry, 35, 15522-15528.  
8673595 R.M.Stroud (1996).
Balancing ATP in the cell.
  Nat Struct Biol, 3, 567-569.  
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.