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PDBsum entry 1a25

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protein ligands metals Protein-protein interface(s) links
Calcium-binding protein PDB id
1a25
Jmol
Contents
Protein chains
132 a.a. *
Ligands
PSE
Metals
_CA ×6
Waters ×49
* Residue conservation analysis
PDB id:
1a25
Name: Calcium-binding protein
Title: C2 domain from protein kinasE C (beta)
Structure: Protein kinasE C (beta). Chain: a, b. Fragment: calcium/phospholipid binding domain. Synonym: calb. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.70Å     R-factor:   0.222     R-free:   0.254
Authors: R.B.Sutton,S.R.Sprang
Key ref:
R.B.Sutton and S.R.Sprang (1998). Structure of the protein kinase Cbeta phospholipid-binding C2 domain complexed with Ca2+. Structure, 6, 1395-1405. PubMed id: 9817842 DOI: 10.1016/S0969-2126(98)00139-7
Date:
16-Jan-98     Release date:   06-May-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P68403  (KPCB_RAT) -  Protein kinase C beta type
Seq:
Struc:
 
Seq:
Struc:
671 a.a.
132 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.11.13  - Protein kinase C.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
= ADP
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(98)00139-7 Structure 6:1395-1405 (1998)
PubMed id: 9817842  
 
 
Structure of the protein kinase Cbeta phospholipid-binding C2 domain complexed with Ca2+.
R.B.Sutton, S.R.Sprang.
 
  ABSTRACT  
 
BACKGROUND: Conventional isoforms (alpha, beta and gamma) of protein kinase C (PKC) are synergistically activated by phosphatidylserine and Ca2+; both bind to C2 domains located within the PKC amino-terminal regulatory regions. C2 domains contain a bipartite or tripartite Ca2+-binding site formed by opposing loops at one end of the protein. Neither the structural basis for cooperativity between phosphatidylserine and Ca2+, nor the binding site for phosphatidylserine are known. RESULTS: The structure of the C2 domain from PKCbeta complexed with Ca2+ and o-phospho-L-serine has been determined to 2.7 A resolution using X-ray crystallography. The eight-stranded, Greek key beta-sandwich fold of PKCbeta-C2 is similar to that of the synaptotagmin I type I C2 domain. Three Ca2+ ions, one at a novel site, were located, each sharing common aspartate ligands. One of these ligands is donated by a dyad-related C2 molecule. A phosphoserine molecule binds to a lysine-rich cluster in C2. CONCLUSIONS: Shared ligation among the three Ca2+ ions suggests that they bind cooperatively to PKCbeta-C2. Cooperativity may be compromised by the accumulation of positive charge in the binding site as successive ions are bound. Model building shows that the C1 domain could provide carboxylate and carbonyl ligands for two of the three Ca2+ sites. Ca2+-mediated interactions between the two domains could contribute to enzyme activation as well as to the creation of a positively charged phosphatidylserine-binding site.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Schematic diagram of the structure of PKCβ-C2. (a) A ribbon model of the two C2 molecules of the asymmetric unit. β Strands are in slate blue, α helices in gold and calcium ions in red. Sidechain atoms of the five conserved acidic residues involved in calcium ligation (aspartate residues 187, 193, 246, 248 and 254) together with the intermolecular Ca^2+ ligand, Glu281, are shown as ball-and-stick figures. Ca^2+-binding loops (CBR) are numbered. (b) A single C2 domain is shown with Ca^2+ sites designated in Roman numerals and CBR loops numbered. β Strands are numbered with strands of sheet A in royal blue and sheet B in azure.
Figure 3.
Figure 3. Conserved β bulges in PKCβ-C2. Water molecules are shown as large red spheres and hydrogen bonds as green dashed lines.
 
  The above figures are reprinted by permission from Cell Press: Structure (1998, 6, 1395-1405) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21215369 T.A.Leonard, B.Różycki, L.F.Saidi, G.Hummer, and J.H.Hurley (2011).
Crystal structure and allosteric activation of protein kinase C βII.
  Cell, 144, 55-66.
PDB code: 3pfq
  20824061 M.Xue, T.K.Craig, O.H.Shin, L.Li, C.A.Brautigam, D.R.Tomchick, T.C.Südhof, C.Rosenmund, and J.Rizo (2010).
Structural and mutational analysis of functional differentiation between synaptotagmins-1 and -7.
  PLoS One, 5, 0.
PDB code: 3n5a
20192774 P.A.Leventis, and S.Grinstein (2010).
The distribution and function of phosphatidylserine in cellular membranes.
  Annu Rev Biophys, 39, 407-427.  
20826345 R.Guan, H.Dai, D.Han, S.C.Harrison, and T.Kirchhausen (2010).
Structure of the PTEN-like region of auxilin, a detector of clathrin-coated vesicle budding.
  Structure, 18, 1191-1198.
PDB code: 3n0a
19056296 E.N.Churchill, N.Qvit, and D.Mochly-Rosen (2009).
Rationally designed peptide regulators of protein kinase C.
  Trends Endocrinol Metab, 20, 25-33.  
19139265 R.H.Roberts-Galbraith, J.S.Chen, J.Wang, and K.L.Gould (2009).
The SH3 domains of two PCH family members cooperate in assembly of the Schizosaccharomyces pombe contractile ring.
  J Cell Biol, 184, 113-127.  
18266053 M.S.Parker, Y.Y.Wong, and S.L.Parker (2008).
An ion-responsive motif in the second transmembrane segment of rhodopsin-like receptors.
  Amino Acids, 35, 1.  
  18923184 S.F.Steinberg (2008).
Structural basis of protein kinase C isoform function.
  Physiol Rev, 88, 1341-1378.  
17500509 H.Al-Ali, T.J.Ragan, X.Gao, and T.K.Harris (2007).
Reconstitution of modular PDK1 functions on trans-splicing of the regulatory PH and catalytic kinase domains.
  Bioconjug Chem, 18, 1294-1302.  
17367165 J.A.Corbin, J.H.Evans, K.E.Landgraf, and J.J.Falke (2007).
Mechanism of specific membrane targeting by C2 domains: localized pools of target lipids enhance Ca2+ affinity.
  Biochemistry, 46, 4322-4336.  
17553426 K.Tanaka, L.Khiroug, F.Santamaria, T.Doi, H.Ogasawara, G.C.Ellis-Davies, M.Kawato, and G.J.Augustine (2007).
Ca2+ requirements for cerebellar long-term synaptic depression: role for a postsynaptic leaky integrator.
  Neuron, 54, 787-800.  
17166855 P.Montaville, C.Schlicker, A.Leonov, M.Zweckstetter, G.M.Sheldrick, and S.Becker (2007).
The C2A-C2B linker defines the high affinity Ca(2+) binding mode of rabphilin-3A.
  J Biol Chem, 282, 5015-5025.
PDB codes: 2cm5 2cm6
17142835 R.Brandman, M.H.Disatnik, E.Churchill, and D.Mochly-Rosen (2007).
Peptides derived from the C2 domain of protein kinase C epsilon (epsilon PKC) modulate epsilon PKC activity and identify potential protein-protein interaction surfaces.
  J Biol Chem, 282, 4113-4123.  
17472963 R.V.Stahelin, P.Subramanian, M.Vora, W.Cho, and C.E.Chalfant (2007).
Ceramide-1-phosphate binds group IVA cytosolic phospholipase a2 via a novel site in the C2 domain.
  J Biol Chem, 282, 20467-20474.  
17085504 S.Varma, and E.Jakobsson (2007).
The cPLA2 C2alpha domain in solution: structure and dynamics of its Ca2+-activated and cation-free states.
  Biophys J, 92, 966-976.  
17580120 V.Kheifets, and D.Mochly-Rosen (2007).
Insight into intra- and inter-molecular interactions of PKC: design of specific modulators of kinase function.
  Pharmacol Res, 55, 467-476.  
16515538 A.J.Groffen, R.Friedrich, E.C.Brian, U.Ashery, and M.Verhage (2006).
DOC2A and DOC2B are sensors for neuronal activity with unique calcium-dependent and kinetic properties.
  J Neurochem, 97, 818-833.  
16616874 J.H.Hurley (2006).
Membrane binding domains.
  Biochim Biophys Acta, 1761, 805-811.  
16338929 L.Liu, X.Song, D.He, C.Komma, A.Kita, J.V.Virbasius, G.Huang, H.D.Bellamy, K.Miki, M.P.Czech, and G.W.Zhou (2006).
Crystal structure of the C2 domain of class II phosphatidylinositide 3-kinase C2alpha.
  J Biol Chem, 281, 4254-4260.
PDB code: 2b3r
16790935 M.Biadene, P.Montaville, G.M.Sheldrick, and S.Becker (2006).
Structure of the C2A domain of rabphilin-3A.
  Acta Crystallogr D Biol Crystallogr, 62, 793-799.
PDB code: 2chd
15576364 I.Voskoboinik, M.C.Thia, J.Fletcher, A.Ciccone, K.Browne, M.J.Smyth, and J.A.Trapani (2005).
Calcium-dependent plasma membrane binding and cell lysis by perforin are mediated through its C2 domain: A critical role for aspartate residues 429, 435, 483, and 485 but not 491.
  J Biol Chem, 280, 8426-8434.  
15919667 M.Flores-Díaz, A.Alape-Girón, G.Clark, B.Catimel, Y.Hirabayashi, E.Nice, J.M.Gutiérrez, R.Titball, and M.Thelestam (2005).
A cellular deficiency of gangliosides causes hypersensitivity to Clostridium perfringens phospholipase C.
  J Biol Chem, 280, 26680-26689.  
16186260 M.L.Craske, M.Fivaz, N.N.Batada, and T.Meyer (2005).
Spines and neurite branches function as geometric attractors that enhance protein kinase C action.
  J Cell Biol, 170, 1147-1158.  
16168654 N.W.Andrews, and S.Chakrabarti (2005).
There's more to life than neurotransmission: the regulation of exocytosis by synaptotagmin VII.
  Trends Cell Biol, 15, 626-631.  
15994899 S.Málková, F.Long, R.V.Stahelin, S.V.Pingali, D.Murray, W.Cho, and M.L.Schlossman (2005).
X-ray reflectivity studies of cPLA2{alpha}-C2 domains adsorbed onto Langmuir monolayers of SOPC.
  Biophys J, 89, 1861-1873.  
15869386 W.Cho, and R.V.Stahelin (2005).
Membrane-protein interactions in cell signaling and membrane trafficking.
  Annu Rev Biophys Biomol Struct, 34, 119-151.  
14718922 J.Garcia, S.H.Gerber, S.Sugita, T.C.Südhof, and J.Rizo (2004).
A conformational switch in the Piccolo C2A domain regulated by alternative splicing.
  Nat Struct Mol Biol, 11, 45-53.
PDB code: 1rh8
12531893 R.V.Stahelin, J.D.Rafter, S.Das, and W.Cho (2003).
The molecular basis of differential subcellular localization of C2 domains of protein kinase C-alpha and group IVa cytosolic phospholipase A2.
  J Biol Chem, 278, 12452-12460.  
14529276 S.Corbalán-Garcia, S.Sánchez-Carrillo, J.García-García, and J.C.Gómez-Fernández (2003).
Characterization of the membrane binding mode of the C2 domain of PKC epsilon.
  Biochemistry, 42, 11661-11668.  
12391024 J.C.Lenz, H.P.Reusch, N.Albrecht, G.Schultz, and M.Schaefer (2002).
Ca2+-controlled competitive diacylglycerol binding of protein kinase C isoenzymes in living cells.
  J Cell Biol, 159, 291-302.  
11782454 L.Banci, G.Cavallaro, V.Kheifets, and D.Mochly-Rosen (2002).
Molecular dynamics characterization of the C2 domain of protein kinase Cbeta.
  J Biol Chem, 277, 12988-12997.  
11988478 T.P.Sakmar, S.T.Menon, E.P.Marin, and E.S.Awad (2002).
Rhodopsin: insights from recent structural studies.
  Annu Rev Biophys Biomol Struct, 31, 443-484.  
11258923 E.A.Nalefski, M.A.Wisner, J.Z.Chen, S.R.Sprang, M.Fukuda, K.Mikoshiba, and J.J.Falke (2001).
C2 domains from different Ca2+ signaling pathways display functional and mechanistic diversity.
  Biochemistry, 40, 3089-3100.  
11179977 J.García-García, J.C.Gómez-Fernández, and S.Corbalán-García (2001).
Structural characterization of the C2 domain of novel protein kinase Cepsilon.
  Eur J Biochem, 268, 1107-1117.  
11285225 S.H.Gerber, J.Garcia, J.Rizo, and T.C.Südhof (2001).
An unusual C(2)-domain in the active-zone protein piccolo: implications for Ca(2+) regulation of neurotransmitter release.
  EMBO J, 20, 1605-1619.  
10956022 A.Arbuzova, L.Wang, J.Wang, G.Hangyás-Mihályné, D.Murray, B.Honig, and S.McLaughlin (2000).
Membrane binding of peptides containing both basic and aromatic residues. Experimental studies with peptides corresponding to the scaffolding region of caveolin and the effector region of MARCKS.
  Biochemistry, 39, 10330-10339.  
10985781 J.E.Johnson, J.Giorgione, and A.C.Newton (2000).
The C1 and C2 domains of protein kinase C are independent membrane targeting modules, with specificity for phosphatidylserine conferred by the C1 domain.
  Biochemistry, 39, 11360-11369.  
10940243 J.H.Hurley, and S.Misra (2000).
Signaling and subcellular targeting by membrane-binding domains.
  Annu Rev Biophys Biomol Struct, 29, 49-79.  
11018476 P.Conesa-Zamora, J.C.Gómez-Fernández, and S.Corbalán-García (2000).
The C2 domain of protein kinase calpha is directly involved in the diacylglycerol-dependent binding of the C1 domain to the membrane.
  Biochim Biophys Acta, 1487, 246-254.  
10555148 J.O.Lee, H.Yang, M.M.Georgescu, A.Di Cristofano, T.Maehama, Y.Shi, J.E.Dixon, P.Pandolfi, and N.P.Pavletich (1999).
Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association.
  Cell, 99, 323-334.
PDB code: 1d5r
10092653 L.Bittova, M.Sumandea, and W.Cho (1999).
A structure-function study of the C2 domain of cytosolic phospholipase A2. Identification of essential calcium ligands and hydrophobic membrane binding residues.
  J Biol Chem, 274, 9665-9672.  
10391930 M.Medkova, and W.Cho (1999).
Interplay of C1 and C2 domains of protein kinase C-alpha in its membrane binding and activation.
  J Biol Chem, 274, 19852-19861.  
10562545 N.Verdaguer, S.Corbalan-Garcia, W.F.Ochoa, I.Fita, and J.C.Gómez-Fernández (1999).
Ca(2+) bridges the C2 membrane-binding domain of protein kinase Calpha directly to phosphatidylserine.
  EMBO J, 18, 6329-6338.
PDB code: 1dsy
10329700 O.Perisic, H.F.Paterson, G.Mosedale, S.Lara-González, and R.L.Williams (1999).
Mapping the phospholipid-binding surface and translocation determinants of the C2 domain from cytosolic phospholipase A2.
  J Biol Chem, 274, 14979-14987.  
10545502 R.B.Sutton, J.A.Ernst, and A.T.Brunger (1999).
Crystal structure of the cytosolic C2A-C2B domains of synaptotagmin III. Implications for Ca(+2)-independent snare complex interaction.
  J Cell Biol, 147, 589-598.
PDB code: 1dqv
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.