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PDBsum entry 1nwd

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protein metals Protein-protein interface(s) links
Binding protein/hydrolase PDB id
1nwd
Jmol
Contents
Protein chains
148 a.a. *
28 a.a. *
Metals
_CA ×4
* Residue conservation analysis
PDB id:
1nwd
Name: Binding protein/hydrolase
Title: Solution structure of ca2+/calmodulin bound to thE C- terminal domain of petunia glutamate decarboxylase
Structure: Calmodulin. Chain: a. Engineered: yes. Glutamate decarboxylase. Chain: b, c. Fragment: c-terminal calmodulin binding domain (residues 470-495). Synonym: gad. Engineered: yes
Source: Xenopus laevis. African clawed frog. Organism_taxid: 8355. Gene: (calm1 or cam1 or calm or cam) and (calm2 or cam2 or camb) and (calm3 or cam3 or camc). Expressed in: escherichia coli. Expression_system_taxid: 562. Petunia x hybrida. Organism_taxid: 4102.
NMR struc: 20 models
Authors: K.L.Yap,T.Yuan,T.K.Mal,H.J.Vogel,M.Ikura
Key ref:
K.L.Yap et al. (2003). Structural basis for simultaneous binding of two carboxy-terminal peptides of plant glutamate decarboxylase to calmodulin. J Mol Biol, 328, 193-204. PubMed id: 12684008 DOI: 10.1016/S0022-2836(03)00271-7
Date:
06-Feb-03     Release date:   08-Apr-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62155  (CALM_XENLA) -  Calmodulin
Seq:
Struc:
149 a.a.
148 a.a.
Protein chains
Pfam   ArchSchema ?
Q07346  (DCE_PETHY) -  Glutamate decarboxylase
Seq:
Struc:
500 a.a.
28 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains B, C: E.C.4.1.1.15  - Glutamate decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-glutamate = 4-aminobutanoate + CO2
L-glutamate
= 4-aminobutanoate
+ CO(2)
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     protein binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(03)00271-7 J Mol Biol 328:193-204 (2003)
PubMed id: 12684008  
 
 
Structural basis for simultaneous binding of two carboxy-terminal peptides of plant glutamate decarboxylase to calmodulin.
K.L.Yap, T.Yuan, T.K.Mal, H.J.Vogel, M.Ikura.
 
  ABSTRACT  
 
Activation of glutamate decarboxylase (GAD) by calcium-bound calmodulin (CaM) is required for normal plant growth through regulation of gamma-aminobutyrate and glutamate metabolism. The interaction of CaM with the C-terminal domain of GAD is believed to induce dimerization of the enzyme, an event implicated for Ca(2+)-dependent enzyme activation. Here, we present the solution structure of CaM in complex with a dimer of peptides derived from the C-terminus of Petunia hybrida GAD. The 23 kDa ternary complex is pseudo-symmetrical with each domain of CaM bound to one of the two antiparallel GAD peptides, which form an X-shape with an interhelical angle of 60 degrees. To accommodate the dimeric helical GAD target, the two domains of CaM adopt an orientation markedly different from that seen in other CaM-target complexes. Although the dimeric GAD domain is much larger than previously studied CaM-binding peptides, the two CaM domains appear closer together and make a number of interdomain contacts not observed in earlier complexes. The present structure of a single CaM molecule interacting with two target peptides provides new evidence for the conformational flexibility of CaM as well as a structural basis for the ability of CaM to activate two enzyme molecules simultaneously.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. The NMR structure of Ca^2+-bound CaM in complex with GADp. (a) Stereo-view of the superposition of 20 energy-minimized structures. The view is along the axis of GAD peptide A. CaM helices are in blue, strands in cyan and calcium ions in yellow. Peptide helices are in magenta. (b) Representative structure of the 20 structures illustrated in (a). (c) Same structure rotated to illustrate its pseudo-symmetric orientation. Calcium ions are indicated with roman numerals.
Figure 4.
Figure 4. The interaction between CaM and GADp. (a) Schematic showing observed peptide-peptide NOEs (brown lines) and peptide-CaM NOEs (interacting CaM residues are boxed). Key interacting residues M481, I482 and W485 of GADp are coloured magenta, green and blue, respectively. Potential pseudo-substrate residues E476 and E480 are shown in cyan. (b) Surface representation of CaM showing the same orientation of peptides as in (a). Hydrophobic residues of CaM are shown in yellow. The peptide backbone ribbons and side-chains are coloured as in (a). For clarity, only GADp residues 472-493 are shown as ribbons. Note that E476 and E480 are both facing away from the CaM surface, suggesting that either residue could serve as a pseudo substrate in the absence of CaM. (c) Closer view of GADp residues interacting with the hydrophobic pockets of CaM. The structure is in the same orientation as in Figure 3(a) and (b).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 328, 193-204) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20054830 H.Huang, H.Ishida, and H.J.Vogel (2010).
The solution structure of the Mg2+ form of soybean calmodulin isoform 4 reveals unique features of plant calmodulins in resting cells.
  Protein Sci, 19, 475-485.
PDB code: 2ksz
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.  
20163733 I.Barrantes, G.Glockner, S.Meyer, and W.Marwan (2010).
Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum.
  BMC Genomics, 11, 115.  
19076716 A.Amtmann, and M.R.Blatt (2009).
Regulation of macronutrient transport.
  New Phytol, 181, 35-52.  
19667066 H.Ishida, M.Rainaldi, and H.J.Vogel (2009).
Structural studies of soybean calmodulin isoform 4 bound to the calmodulin-binding domain of tobacco mitogen-activated protein kinase phosphatase-1 provide insights into a sequential target binding mode.
  J Biol Chem, 284, 28292-28305.
PDB code: 2kn2
19129626 H.W.Kim, Y.Kashima, K.Ishikawa, and N.Yamano (2009).
Purification and characterization of the first archaeal glutamate decarboxylase from Pyrococcus horikoshii.
  Biosci Biotechnol Biochem, 73, 224-227.  
19560485 W.J.Tang, and Q.Guo (2009).
The adenylyl cyclase activity of anthrax edema factor.
  Mol Aspects Med, 30, 423-430.  
18940602 E.Y.Kim, C.H.Rumpf, Y.Fujiwara, E.S.Cooley, F.Van Petegem, and D.L.Minor (2008).
Structures of CaV2 Ca2+/CaM-IQ domain complexes reveal binding modes that underlie calcium-dependent inactivation and facilitation.
  Structure, 16, 1455-1467.
PDB codes: 3dve 3dvj 3dvk 3dvm
18786401 S.L.Reichow, and T.Gonen (2008).
Noncanonical binding of calmodulin to aquaporin-0: implications for channel regulation.
  Structure, 16, 1389-1398.  
  19704657 A.P.Yamniuk, M.Rainaldi, and H.J.Vogel (2007).
Calmodulin has the Potential to Function as a Ca-Dependent Adaptor Protein.
  Plant Signal Behav, 2, 354-357.  
17437643 K.Chen, L.A.Kurgan, and J.Ruan (2007).
Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs.
  BMC Struct Biol, 7, 25.  
17202149 M.Rainaldi, A.P.Yamniuk, T.Murase, and H.J.Vogel (2007).
Calcium-dependent and -independent binding of soybean calmodulin isoforms to the calmodulin binding domain of tobacco MAPK phosphatase-1.
  J Biol Chem, 282, 6031-6042.  
17488107 V.Vacic, C.J.Oldfield, A.Mohan, P.Radivojac, M.S.Cortese, V.N.Uversky, and A.K.Dunker (2007).
Characterization of molecular recognition features, MoRFs, and their binding partners.
  J Proteome Res, 6, 2351-2366.  
16957991 J.Ruan, K.Chen, J.A.Tuszynski, and L.A.Kurgan (2006).
Quantitative analysis of the conservation of the tertiary structure of protein segments.
  Protein J, 25, 301-315.  
16721661 K.Chen, J.Ruan, and L.A.Kurgan (2006).
Prediction of three dimensional structure of calmodulin.
  Protein J, 25, 57-70.  
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.  
  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.  
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
15862103 N.Bouché, A.Yellin, W.A.Snedden, and H.Fromm (2005).
Plant-specific calmodulin-binding proteins.
  Annu Rev Plant Biol, 56, 435-466.  
16138079 Q.Guo, Y.Shen, Y.S.Lee, C.S.Gibbs, M.Mrksich, and W.J.Tang (2005).
Structural basis for the interaction of Bordetella pertussis adenylyl cyclase toxin with calmodulin.
  EMBO J, 24, 3190-3201.
PDB codes: 1yrt 1yru 1zot 2col
15298887 C.M.Shepherd, and H.J.Vogel (2004).
A molecular dynamics study of Ca(2+)-calmodulin: evidence of interdomain coupling and structural collapse on the nanosecond timescale.
  Biophys J, 87, 780-791.  
14765114 M.Matsubara, T.Nakatsu, H.Kato, and H.Taniguchi (2004).
Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal domain complexed with Ca2+/calmodulin.
  EMBO J, 23, 712-718.
PDB code: 1l7z
15003233 N.Bouché, and H.Fromm (2004).
GABA in plants: just a metabolite?
  Trends Plant Sci, 9, 110-115.  
14557048 T.Yang, B.W.Poovaiah, and B.W.Poovaiah (2003).
Calcium/calmodulin-mediated signal network in plants.
  Trends Plant Sci, 8, 505-512.  
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.