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PDBsum entry 1iq5
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protein metals Protein-protein interface(s) links
Metal binding protein/protein binding PDB id
1iq5

 

 

 

 

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Contents
Protein chains
144 a.a. *
24 a.a. *
Metals
_CA ×4
Waters ×67
* Residue conservation analysis
PDB id:
1iq5
Name: Metal binding protein/protein binding
Title: Calmodulin/nematode ca2+/calmodulin dependent kinase kinase fragment
Structure: Calmodulin. Chain: a. Engineered: yes. Ca2+/calmodulin dependent kinase kinase. Chain: b. Fragment: calmodulin binding domain (residues 331-357). Engineered: yes
Source: Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this sequence occurs naturally in caenorhabditis elegans
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.217     R-free:   0.248
Authors: H.Kurokawa,M.Osawa,H.Kurihara,N.Katayama,H.Tokumitsu,M.B.Swindells, M.Kainosho,M.Ikura
Key ref:
H.Kurokawa et al. (2001). Target-induced conformational adaptation of calmodulin revealed by the crystal structure of a complex with nematode Ca(2+)/calmodulin-dependent kinase kinase peptide. J Mol Biol, 312, 59-68. PubMed id: 11545585 DOI: 10.1006/jmbi.2001.4822
Date:
14-Jun-01     Release date:   26-Sep-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0DP33  (CALM1_XENLA) -  Calmodulin-1 from Xenopus laevis
Seq:
Struc: 		149 a.a.
144 a.a.
Protein chain
Pfam   ArchSchema ?
Q3Y416  (KKCC_CAEEL) -  Calcium/calmodulin-dependent protein kinase kinase from Caenorhabditis elegans
Seq:
Struc: 		 
Seq:
Struc: 		541 a.a.
24 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain B: E.C.2.7.11.17  - calcium/calmodulin-dependent protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H+
2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H+
L-seryl-[protein]
 + ATP
 = O-phospho-L-seryl-[protein]
 + ADP
 + H(+)
L-threonyl-[protein]
 + ATP
 = O-phospho-L-threonyl-[protein]
 + ADP
 + H(+)
      Cofactor: Ca(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2001.4822 J Mol Biol 312:59-68 (2001)
PubMed id: 11545585  
 
 
Target-induced conformational adaptation of calmodulin revealed by the crystal structure of a complex with nematode Ca(2+)/calmodulin-dependent kinase kinase peptide.
H.Kurokawa, M.Osawa, H.Kurihara, N.Katayama, H.Tokumitsu, M.B.Swindells, M.Kainosho, M.Ikura.
 
  ABSTRACT  
 
Calmodulin (CaM) is a ubiquitous calcium (Ca(2+)) sensor which binds and regulates protein serine/threonine kinases along with many other proteins in a Ca(2+)-dependent manner. For this multi-functionality, conformational plasticity is essential; however, the nature and magnitude of CaM's plasticity still remains largely undetermined. Here, we present the 1.8 A resolution crystal structure of Ca(2+)/CaM, complexed with the 27-residue synthetic peptide corresponding to the CaM-binding domain of the nematode Caenorhabditis elegans Ca(2+)/CaM-dependent kinase kinase (CaMKK). The peptide bound in this crystal structure is a homologue of the previously NMR-derived complex with rat CaMKK, but benefits from improved structural resolution. Careful comparison of the present structure to previous crystal structures of CaM complexed with unrelated peptides derived from myosin light chain kinase and CaM kinase II, allow a quantitative analysis of the differences in the relative orientation of the N and C-terminal domains of CaM, defined as a screw axis rotation angle ranging from 156 degrees to 196 degrees. The principal differences in CaM interaction with various peptides are associated with the N-terminal domain of CaM. Unlike the C-terminal domain, which remains unchanged internally, the N-terminal domain of CaM displays significant differences in the EF-hand helix orientation between this and other CaM structures. Three hydrogen bonds between CaM and the peptide (E87-R336, E87-T339 and K75-T339) along with two salt bridges (E11-R349 and E114-K334) are the most probable determinants for the binding direction of the CaMKK peptide to CaM.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Binding interface of CaM domains with the target peptide. The N-terminal domains ((a), (c) and (e)) and C-terminal domains ((b), (d) and (f)) of CaM are shown as a surface model. (a) and (b) CaM-cCaMKKp comlex; (c) and (d) CaM-smMLCKp complex; (e) and (f) CaM-CaMKIIp complex. The surfaces were colored by the distance from the peptide. Red is closer to the peptide while blue is far from the peptide. The bound peptides are shown as a yellow tube. (Side-chains of anchoring residues Leu337 and Phe352 ((a) and (b)), Leu813 and Trp800 ((c) and (d)) Leu308 and Leu299 ((e) and (f)), are shown as stick models. The Figure was produced using the program MOLMOL.[39] 		Figure 5.
Figure 5. (a) Ribbon and ball-and-stick drawing of residues showing electrostatic interactions between CaM (orange) and CaMKK peptide (green) around channel outlet 2. Hydrogen bonds are shown as dotted lines. The molecular surface of CaM is shown as a transparency. The channel made by two CaM domains runs perpendicular to the paper. (b) Similar diagram as (a), but rotated by 180°. (c) Schematic showing the main interactions between CaM and cCaMKKp. Figures were drawn using MOLSCRIPT,[37] Raster3d, [38] for (a) and (b), and LIGPLOT [40] for (c).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 312, 59-68) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20653564 H.Tokumitsu, N.Hatano, M.Tsuchiya, S.Yurimoto, T.Fujimoto, N.Ohara, R.Kobayashi, and H.Sakagami (2010).
Identification and characterization of PRG-1 as a neuronal calmodulin-binding protein.
  Biochem J, 431, 81-91.  
19996092 N.Juranic, E.Atanasova, A.G.Filoteo, S.Macura, F.G.Prendergast, J.T.Penniston, and E.E.Strehler (2010).
Calmodulin wraps around its binding domain in the plasma membrane Ca2+ pump anchored by a novel 18-1 motif.
  J Biol Chem, 285, 4015-4024.
PDB code: 2kne
20668654 P.Rellos, A.C.Pike, F.H.Niesen, E.Salah, W.H.Lee, F.von Delft, and S.Knapp (2010).
Structure of the CaMKIIdelta/calmodulin complex reveals the molecular mechanism of CaMKII kinase activation.
  PLoS Biol, 8, e1000426.
PDB codes: 2ux0 2v7o 2vn9 2vz6 2w2c 2wel
19998355 Y.Zhang, H.Tan, G.Chen, and Z.Jia (2010).
Investigating the disorder-order transition of calmodulin binding domain upon binding calmodulin using molecular dynamics simulation.
  J Mol Recognit, 23, 360-368.  
18384083 Q.Ye, H.Wang, J.Zheng, Q.Wei, and Z.Jia (2008).
The complex structure of calmodulin bound to a calcineurin peptide.
  Proteins, 73, 19-27.
PDB code: 2r28
16568447 A.Ganoth, E.Nachliel, R.Friedman, and M.Gutman (2006).
Molecular dynamics study of a calmodulin-like protein with an IQ peptide: spontaneous refolding of the protein around the peptide.
  Proteins, 64, 133-146.  
16844751 A.Ganoth, R.Friedman, E.Nachliel, and M.Gutman (2006).
A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides.
  Biophys J, 91, 2436-2450.  
16464867 A.Raichaudhuri, R.Bhattacharyya, S.Chaudhuri, P.Chakrabarti, and M.Dasgupta (2006).
Domain analysis of a groundnut calcium-dependent protein kinase: nuclear localization sequence in the junction domain is coupled with nonconsensus calcium binding domains.
  J Biol Chem, 281, 10399-10409.
PDB code: 2g3u
16721661 K.Chen, J.Ruan, and L.A.Kurgan (2006).
Prediction of three dimensional structure of calmodulin.
  Protein J, 25, 57-70.  
16846216 M.S.Marlow, and A.J.Wand (2006).
Conformational dynamics of calmodulin in complex with the calmodulin-dependent kinase kinase alpha calmodulin-binding domain.
  Biochemistry, 45, 8732-8741.  
17000753 T.Friedrich, B.Pils, T.Dandekar, J.Schultz, and T.Müller (2006).
Modelling interaction sites in protein domains with interaction profile hidden Markov models.
  Bioinformatics, 22, 2851-2857.  
15752366 A.G.Cook, L.N.Johnson, and J.M.McDonnell (2005).
Structural characterization of Ca2+/CaM in complex with the phosphorylase kinase PhK5 peptide.
  FEBS J, 272, 1511-1522.  
  16511158 C.L.Chyan, P.C.Huang, T.H.Lin, J.W.Huang, S.S.Lin, H.B.Huang, and Y.C.Chen (2005).
Purification, crystallization and preliminary crystallographic studies of a calmodulin-OLFp hybrid molecule.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 785-787.  
16299511 F.Van Petegem, F.C.Chatelain, and D.L.Minor (2005).
Insights into voltage-gated calcium channel regulation from the structure of the CaV1.2 IQ domain-Ca2+/calmodulin complex.
  Nat Struct Mol Biol, 12, 1108-1115.
PDB code: 2be6
15803393 G.M.Contessa, M.Orsale, S.Melino, V.Torre, M.Paci, A.Desideri, and D.O.Cicero (2005).
Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family.
  J Biomol NMR, 31, 185-199.
PDB code: 1sy9
15596444 I.Horváth, V.Harmat, A.Perczel, V.Pálfi, L.Nyitray, A.Nagy, E.Hlavanda, G.Náray-Szabó, and J.Ovádi (2005).
The structure of the complex of calmodulin with KAR-2: a novel mode of binding explains the unique pharmacology of the drug.
  J Biol Chem, 280, 8266-8274.
PDB code: 1xa5
15583004 L.Xiong, Q.K.Kleerekoper, R.He, J.A.Putkey, and S.L.Hamilton (2005).
Sites on calmodulin that interact with the C-terminal tail of Cav1.2 channel.
  J Biol Chem, 280, 7070-7079.  
15722444 V.Alexandrov, U.Lehnert, N.Echols, D.Milburn, D.Engelman, and M.Gerstein (2005).
Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.
  Protein Sci, 14, 633-643.  
14670974 A.P.Yamniuk, and H.J.Vogel (2004).
Structurally homologous binding of plant calmodulin isoforms to the calmodulin-binding domain of vacuolar calcium-ATPase.
  J Biol Chem, 279, 7698-7707.  
15213382 C.H.Yun, J.Bai, D.Y.Sun, D.F.Cui, W.R.Chang, and D.C.Liang (2004).
Structure of potato calmodulin PCM6: the first report of the three-dimensional structure of a plant calmodulin.
  Acta Crystallogr D Biol Crystallogr, 60, 1214-1219.
PDB code: 1rfj
14982921 H.Kurokawa, D.S.Lee, M.Watanabe, I.Sagami, B.Mikami, C.S.Raman, and T.Shimizu (2004).
A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor.
  J Biol Chem, 279, 20186-20193.
PDB codes: 1v9y 1v9z
12673015 H.Konishi, and S.Komatsu (2003).
A proteomics approach to investigating promotive effects of brassinolide on lamina inclination and root growth in rice seedlings.
  Biol Pharm Bull, 26, 401-408.  
14597710 J.M.Shifman, and S.L.Mayo (2003).
Exploring the origins of binding specificity through the computational redesign of calmodulin.
  Proc Natl Acad Sci U S A, 100, 13274-13279.  
12480931 K.A.McClintock, and G.S.Shaw (2003).
A novel S100 target conformation is revealed by the solution structure of the Ca2+-S100B-TRTK-12 complex.
  J Biol Chem, 278, 6251-6257.
PDB code: 1mq1
12574113 M.Aoyagi, A.S.Arvai, J.A.Tainer, and E.D.Getzoff (2003).
Structural basis for endothelial nitric oxide synthase binding to calmodulin.
  EMBO J, 22, 766-775.
PDB code: 1niw
12715898 M.Hentschke, C.Schulze, U.Süsens, and U.Borgmeyer (2003).
Characterization of calmodulin binding to the orphan nuclear receptor Errgamma.
  Biol Chem, 384, 473-482.  
11867640 H.Tokumitsu, H.Inuzuka, Y.Ishikawa, M.Ikeda, I.Saji, and R.Kobayashi (2002).
STO-609, a specific inhibitor of the Ca(2+)/calmodulin-dependent protein kinase kinase.
  J Biol Chem, 277, 15813-15818.  
11955428 K.P.Hoeflich, and M.Ikura (2002).
Calmodulin in action: diversity in target recognition and activation mechanisms.
  Cell, 108, 739-742.  
12111723 M.Ikura, M.Osawa, and J.B.Ames (2002).
The role of calcium-binding proteins in the control of transcription: structure to function.
  Bioessays, 24, 625-636.  
12441389 S.R.Martin, and P.M.Bayley (2002).
Regulatory implications of a novel mode of interaction of calmodulin with a double IQ-motif target sequence from murine dilute myosin V.
  Protein Sci, 11, 2909-2923.  
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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