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PDBsum entry 1bjf
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protein metals Protein-protein interface(s) links
Calcium-binding PDB id
1bjf

 

 

 

 

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Contents
Protein chains
181 a.a. *
Metals
_CA ×6
Waters ×44
* Residue conservation analysis
PDB id:
1bjf
Name: Calcium-binding
Title: Crystal structure of recombinant bovine neurocalcin delta at 2.4 angstroms
Structure: Neurocalcin delta. Chain: a, b. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Strain: dh5-alpha. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.218     R-free:   0.308
Authors: S.Vijay-Kumar,V.D.Kumar
Key ref:
S.Vijay-Kumar and V.D.Kumar (1999). Crystal structure of recombinant bovine neurocalcin. Nat Struct Biol, 6, 80-88. PubMed id: 9886296 DOI: 10.1038/4956
Date:
25-Jun-98     Release date:   22-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P61602  (NCALD_BOVIN) -  Neurocalcin-delta from Bos taurus
Seq:
Struc: 		193 a.a.
181 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1038/4956 Nat Struct Biol 6:80-88 (1999)
PubMed id: 9886296  
 
 
Crystal structure of recombinant bovine neurocalcin.
S.Vijay-Kumar, V.D.Kumar.
 
  ABSTRACT  
 
The crystal structure of calcium-bound unmyristoylated bovine neurocalcin from Escherichia coli has been determined at 2.4 A resolution. The three-dimensional structure reveals a highly compact structure consisting of: (i) two pairs of calcium-binding EF-hands (EF1-EF2 and EF3-EF4); (ii) a calcium ion bound at EF2, EF3 and EF4 sites; and (iii) an EF1-hand that is disabled from calcium-binding due to a Cys-Pro sequence in the Ca2+-binding loop. The crystal structure of neurocalcin resembles photoreceptor recoverin in overall topology, however its EF2- and EF4-hands differ. Recently, neurocalcin in the calcium-bound state has been shown to stimulate mammalian rod outer segment membrane guanylate cyclase. A possible site for cyclase activity based on the three-dimensional structure is discussed.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Representation of the four EF-hands of neurocalcin (EF1, EF2, EF3, EF4). Calcium atoms are shown in magenta, oxygens in red, sulfur in yellow and water in red. Residues involved in the calcium coordination are shown. a, Disabled EF1-hand showing the location of Lys 36 and Cys 38, which prevent the EF1-hand from binding calcium, b, Ca^2+-bound EF2-hand, c, Ca^2+-bound EF3-hand and d, Ca^2+-bound EF4-hand. 		Figure 5.
Figure 5. Stereo view of 2|F[o] - F[c]| electron density map contoured at 1.5 for residues 72-78 of the EF2-hand. The corresponding residues in bovine recoverin (73-79) are not evident due to disorder^30.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 80-88) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21465563 X.Xu, R.Ishima, and J.B.Ames (2011).
Conformational dynamics of recoverin's Ca(2+) -myristoyl switch probed by (15) N NMR relaxation dispersion and chemical shift analysis.
  Proteins, 79, 1910-1922.  
19851889 S.Lim, and J.B.Ames (2009).
(1)H, (15)N, and (13)C chemical shift assignments of neuronal calcium sensor-1 homolog from fission yeast.
  Biomol NMR Assign, 3, 269-271.  
18559337 J.N.Wingard, J.Ladner, M.Vanarotti, A.J.Fisher, H.Robinson, K.T.Buchanan, D.M.Engman, and J.B.Ames (2008).
Structural Insights into Membrane Targeting by the Flagellar Calcium-binding Protein (FCaBP), a Myristoylated and Palmitoylated Calcium Sensor in Trypanosoma cruzi.
  J Biol Chem, 283, 23388-23396.
PDB code: 3cs1
18346093 R.Stephen, S.Filipek, K.Palczewski, and M.C.Sousa (2008).
Ca2+ -dependent regulation of phototransduction.
  Photochem Photobiol, 84, 903-910.  
18500817 V.Venkataraman, T.Duda, S.Ravichandran, and R.K.Sharma (2008).
Neurocalcin delta modulation of ROS-GC1, a new model of Ca(2+) signaling.
  Biochemistry, 47, 6590-6601.  
17962406 L.Yu, C.Sun, R.Mendoza, J.Wang, E.D.Matayoshi, E.Hebert, A.Pereda-Lopez, P.J.Hajduk, and E.T.Olejniczak (2007).
Solution structure and calcium-binding properties of EF-hands 3 and 4 of calsenilin.
  Protein Sci, 16, 2502-2509.
PDB code: 2e6w
17671797 M.Kamiyama, M.Kobayashi, S.Araki, A.Iida, T.Tsunoda, K.Kawai, M.Imanishi, M.Nomura, T.Babazono, Y.Iwamoto, A.Kashiwagi, K.Kaku, R.Kawamori, D.P.Ng, T.Hansen, P.Gaede, O.Pedersen, Y.Nakamura, and S.Maeda (2007).
Polymorphisms in the 3' UTR in the neurocalcin delta gene affect mRNA stability, and confer susceptibility to diabetic nephropathy.
  Hum Genet, 122, 397-407.  
17311005 R.D.Burgoyne (2007).
Neuronal calcium sensor proteins: generating diversity in neuronal Ca2+ signalling.
  Nat Rev Neurosci, 8, 182-193.  
17997965 R.Stephen, G.Bereta, M.Golczak, K.Palczewski, and M.C.Sousa (2007).
Stabilizing function for myristoyl group revealed by the crystal structure of a neuronal calcium sensor, guanylate cyclase-activating protein 1.
  Structure, 15, 1392-1402.
PDB code: 2r2i
17720810 T.Strahl, I.G.Huttner, J.D.Lusin, M.Osawa, D.King, J.Thorner, and J.B.Ames (2007).
Structural insights into activation of phosphatidylinositol 4-kinase (Pik1) by yeast frequenin (Frq1).
  J Biol Chem, 282, 30949-30959.
PDB code: 2ju0
16951992 C.P.Chen, L.Lee, and L.S.Chang (2006).
Effects of metal-binding properties of human Kv channel-interacting proteins on their molecular structure and binding with Kv4.2 channel.
  Protein J, 25, 345-351.  
16703469 F.F.Jheng, L.Wang, L.Lee, and L.S.Chang (2006).
Functional contribution of Ca2+ and Mg2+ to the intermolecular interaction of visinin-like proteins.
  Protein J, 25, 250-256.  
17020884 J.B.Ames, K.Levay, J.N.Wingard, J.D.Lusin, and V.Z.Slepak (2006).
Structural basis for calcium-induced inhibition of rhodopsin kinase by recoverin.
  J Biol Chem, 281, 37237-37245.
PDB code: 2i94
16432210 M.Ikura, and J.B.Ames (2006).
Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: two ways to promote multifunctionality.
  Proc Natl Acad Sci U S A, 103, 1159-1164.  
17015448 O.H.Weiergräber, I.I.Senin, E.Y.Zernii, V.A.Churumova, N.A.Kovaleva, A.A.Nazipova, S.E.Permyakov, E.A.Permyakov, P.P.Philippov, J.Granzin, and K.W.Koch (2006).
Tuning of a neuronal calcium sensor.
  J Biol Chem, 281, 37594-37602.
PDB code: 2het
16710297 Y.B.Ammar, S.Takeda, T.Hisamitsu, H.Mori, and S.Wakabayashi (2006).
Crystal structure of CHP2 complexed with NHE1-cytosolic region and an implication for pH regulation.
  EMBO J, 25, 2315-2325.
PDB code: 2bec
15574431 H.R.Gentry, A.U.Singer, L.Betts, C.Yang, J.D.Ferrara, J.Sondek, and L.V.Parise (2005).
Structural and biochemical characterization of CIB1 delineates a new family of EF-hand-containing proteins.
  J Biol Chem, 280, 8407-8415.
PDB code: 1xo5
16147998 J.N.Wingard, J.Chan, I.Bosanac, F.Haeseleer, K.Palczewski, M.Ikura, and J.B.Ames (2005).
Structural analysis of Mg2+ and Ca2+ binding to CaBP1, a neuron-specific regulator of calcium channels.
  J Biol Chem, 280, 37461-37470.  
15746104 M.Osawa, A.Dace, K.I.Tong, A.Valiveti, M.Ikura, and J.B.Ames (2005).
Mg2+ and Ca2+ differentially regulate DNA binding and dimerization of DREAM.
  J Biol Chem, 280, 18008-18014.  
15987692 Y.Naoe, K.Arita, H.Hashimoto, H.Kanazawa, M.Sato, and T.Shimizu (2005).
Structural characterization of calcineurin B homologous protein 1.
  J Biol Chem, 280, 32372-32378.
PDB code: 2ct9
14726528 D.W.O'Callaghan, and R.D.Burgoyne (2004).
Identification of residues that determine the absence of a Ca(2+)/myristoyl switch in neuronal calcium sensor-1.
  J Biol Chem, 279, 14347-14354.  
15448139 I.V.Peshenko, E.V.Olshevskaya, and A.M.Dizhoor (2004).
Ca(2+)-dependent conformational changes in guanylyl cyclase-activating protein 2 (GCAP-2) revealed by site-specific phosphorylation and partial proteolysis.
  J Biol Chem, 279, 50342-50349.  
14739275 K.Oikawa, S.Kimura, N.Aoki, Y.Atsuta, Y.Takiyama, T.Nagato, M.Yanai, H.Kobayashi, K.Sato, T.Sasajima, and M.Tateno (2004).
Neuronal calcium sensor protein visinin-like protein-3 interacts with microsomal cytochrome b5 in a Ca2+-dependent manner.
  J Biol Chem, 279, 15142-15152.  
14722091 N.Hamasaki-Katagiri, T.Molchanova, K.Takeda, and J.B.Ames (2004).
Fission yeast homolog of neuronal calcium sensor-1 (Ncs1p) regulates sporulation and confers calcium tolerance.
  J Biol Chem, 279, 12744-12754.  
14980207 R.H.Scannevin, K.Wang, F.Jow, J.Megules, D.C.Kopsco, W.Edris, K.C.Carroll, Q.Lü, W.Xu, Z.Xu, A.H.Katz, S.Olland, L.Lin, M.Taylor, M.Stahl, K.Malakian, W.Somers, L.Mosyak, M.R.Bowlby, P.Chanda, and K.J.Rhodes (2004).
Two N-terminal domains of Kv4 K(+) channels regulate binding to and modulation by KChIP1.
  Neuron, 41, 587-598.
PDB codes: 1s1e 1s1g
14980206 W.Zhou, Y.Qian, K.Kunjilwar, P.J.Pfaffinger, and S.Choe (2004).
Structural insights into the functional interaction of KChIP1 with Shal-type K(+) channels.
  Neuron, 41, 573-586.
PDB code: 1s6c
  14739996 I.Sokal, A.Alekseev, and K.Palczewski (2003).
Photoreceptor guanylate cyclase variants: cGMP production under control.
  Acta Biochim Pol, 50, 1075-1095.  
12871972 M.Nagae, A.Nozawa, N.Koizumi, H.Sano, H.Hashimoto, M.Sato, and T.Shimizu (2003).
The crystal structure of the novel calcium-binding protein AtCBL2 from Arabidopsis thaliana.
  J Biol Chem, 278, 42240-42246.
PDB code: 1uhn
12686556 O.H.Weiergräber, I.I.Senin, P.P.Philippov, J.Granzin, and K.W.Koch (2003).
Impact of N-terminal myristoylation on the Ca2+-dependent conformational transition in recoverin.
  J Biol Chem, 278, 22972-22979.
PDB codes: 1omr 1omv
12918021 S.L.Veney, C.Peabody, G.W.Smith, and J.Wade (2003).
Sexually dimorphic neurocalcin expression in the developing zebra finch telencephalon.
  J Neurobiol, 56, 372-386.  
14512421 T.Strahl, B.Grafelmann, J.Dannenberg, J.Thorner, and O.Pongs (2003).
Conservation of regulatory function in calcium-binding proteins: human frequenin (neuronal calcium sensor-1) associates productively with yeast phosphatidylinositol 4-kinase isoform, Pik1.
  J Biol Chem, 278, 49589-49599.  
12928444 X.Ren, S.H.Shand, and K.Takimoto (2003).
Effective association of Kv channel-interacting proteins with Kv4 channel is mediated with their unique core peptide.
  J Biol Chem, 278, 43564-43570.  
11980481 J.B.Ames, N.Hamasaki, and T.Molchanova (2002).
Structure and calcium-binding studies of a recoverin mutant (E85Q) in an allosteric intermediate state.
  Biochemistry, 41, 5776-5787.
PDB code: 1la3
11524415 I.Sokal, N.Li, C.S.Klug, S.Filipek, W.L.Hubbell, W.Baehr, and K.Palczewski (2001).
Calcium-sensitive regions of GCAP1 as observed by chemical modifications, fluorescence, and EPR spectroscopies.
  J Biol Chem, 276, 43361-43373.  
11579136 K.H.Braunewell, M.Brackmann, M.Schaupp, C.Spilker, R.Anand, and E.D.Gundelfinger (2001).
Intracellular neuronal calcium sensor (NCS) protein VILIP-1 modulates cGMP signalling pathways in transfected neural cells and cerebellar granule neurones.
  J Neurochem, 78, 1277-1286.  
11114499 A.Lewit-Bentley, and S.Réty (2000).
EF-hand calcium-binding proteins.
  Curr Opin Struct Biol, 10, 637-643.  
10625670 F.Haeseleer, I.Sokal, C.L.Verlinde, H.Erdjument-Bromage, P.Tempst, A.N.Pronin, J.L.Benovic, R.N.Fariss, and K.Palczewski (2000).
Five members of a novel Ca(2+)-binding protein (CABP) subfamily with similarity to calmodulin.
  J Biol Chem, 275, 1247-1260.  
11015193 J.B.Ames, K.B.Hendricks, T.Strahl, I.G.Huttner, N.Hamasaki, and J.Thorner (2000).
Structure and calcium-binding properties of Frq1, a novel calcium sensor in the yeast Saccharomyces cerevisiae.
  Biochemistry, 39, 12149-12161.
PDB code: 1fpw
10861367 R.Galeano, A.Germanà, F.Abbate, D.Calvo, F.J.Naves, H.Hidaka, G.Germanà, and J.A.Vega (2000).
Neurocalcin-immunoreactive neurons in the mammalian dorsal root ganglia, including humans.
  Anat Rec, 259, 347-352.  
10652319 S.Tachibanaki, K.Nanda, K.Sasaki, K.Ozaki, and S.Kawamura (2000).
Amino acid residues of S-modulin responsible for interaction with rhodopsin kinase.
  J Biol Chem, 275, 3313-3319.  
10464292 E.V.Olshevskaya, A.N.Ermilov, and A.M.Dizhoor (1999).
Dimerization of guanylyl cyclase-activating protein and a mechanism of photoreceptor guanylyl cyclase activation.
  J Biol Chem, 274, 25583-25587.  
10391927 I.Sokal, A.E.Otto-Bruc, I.Surgucheva, C.L.Verlinde, C.K.Wang, W.Baehr, and K.Palczewski (1999).
Conformational changes in guanylyl cyclase-activating protein 1 (GCAP1) and its tryptophan mutants as a function of calcium concentration.
  J Biol Chem, 274, 19829-19837.  
10383444 J.B.Ames, A.M.Dizhoor, M.Ikura, K.Palczewski, and L.Stryer (1999).
Three-dimensional structure of guanylyl cyclase activating protein-2, a calcium-sensitive modulator of photoreceptor guanylyl cyclases.
  J Biol Chem, 274, 19329-19337.
PDB code: 1jba
10591109 K.L.Yap, J.B.Ames, M.B.Swindells, and M.Ikura (1999).
Diversity of conformational states and changes within the EF-hand protein superfamily.
  Proteins, 37, 499-507.  
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.

 

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