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PDBsum entry 1jfk

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protein metals links
Metal binding protein PDB id
1jfk
Jmol
Contents
Protein chain
134 a.a. *
Metals
_CA ×4
* Residue conservation analysis
PDB id:
1jfk
Name: Metal binding protein
Title: Minimum energy representative structure of a calcium bound ef-hand protein from entamoeba histolytica
Structure: Calcium-binding protein. Chain: a. Synonym: ehcabp. Engineered: yes
Source: Entamoeba histolytica. Organism_taxid: 5759. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 1 models
Authors: H.S.Atreya,S.C.Sahu,A.Bhattacharya,K.V.R.Chary,G.Govil
Key ref:
H.S.Atreya et al. (2001). NMR derived solution structure of an EF-hand calcium-binding protein from Entamoeba Histolytica. Biochemistry, 40, 14392-14403. PubMed id: 11724551 DOI: 10.1021/bi0114978
Date:
21-Jun-01     Release date:   19-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P38505  (CALBP_ENTHI) -  Calcium-binding protein
Seq:
Struc:
134 a.a.
134 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     2 terms  

 

 
DOI no: 10.1021/bi0114978 Biochemistry 40:14392-14403 (2001)
PubMed id: 11724551  
 
 
NMR derived solution structure of an EF-hand calcium-binding protein from Entamoeba Histolytica.
H.S.Atreya, S.C.Sahu, A.Bhattacharya, K.V.Chary, G.Govil.
 
  ABSTRACT  
 
We present the three-dimensional (3D) solution structure of a calcium-binding protein from Entamoeba histolytica (EhCaBP), an etiologic agent of amoebiasis affecting millions worldwide. EhCaBP is a 14.7 kDa (134 residues) monomeric protein thought to play a role in the pathogenesis of amoebiasis. The 3D structure of Ca(2+)-bound EhCaBP has been derived using multidimensional nuclear magnetic resonance (NMR) spectroscopic techniques. The study reveals the presence of two globular domains connected by a flexible linker region spanning 8 amino acid residues. Each domain consists of a pair of helix-loop-helix motifs similar to the canonical EF-hand motif of calcium-binding proteins. EhCaBP binds to four Ca(2+) with high affinity (two in each domain), and it is structurally related to calmodulin (CaM) and troponin C (TnC) despite its low sequence homology ( approximately 29%) with these proteins. NMR-derived structures of EhCaBP converge within each domain with low RMSDs and angular order-parameters for backbone torsion angles close to 1.0. However, the presence of a highly flexible central linker region results in an ill-defined orientation of the two domains relative to one other. These findings are supported by backbone (15)N relaxation rate measurements and deuterium exchange studies, which reveal low structural order parameters for residues in the central linker region. Earlier, biochemical studies showed that EhCaBP is involved in a novel signal transduction mechanism, distinct from CaM. A possible reason for such a functional diversity is revealed by a detailed comparison of the 3D structure of EhCaBP with that of CaM and TnC. The studies indicate a more open C-terminal domain for EhCaBP with larger water exposed total hydrophobic surface area as compared to CaM and TnC. Further dissimilarities between the structures include the presence of two Gly residues (G63 and G67) in the central linker region of EhCaBP, which seem to impart it a greater flexibility compared to CaM and TnC and also play crucial role in its biological function. Thus, unlike in CaM and TnC, wherein the length and/or composition of the central linker have been found to be crucial for their function, in EhCaBP, both flexibility as well as amino acid composition is required for the function of the protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21235730 K.Chandra, S.M.Mustafi, S.Muthukumar, and K.V.Chary (2011).
Site-Specific Free Energy Changes in Proteins upon Ligand Binding by Nuclear Magnetic Resonance: Ca(2+) -Displacement by Ln(3+) in a Ca(2+) -Binding Protein from Entamoeba histolytica.
  Chem Biol Drug Des, 77, 272-280.  
20803498 A.K.Rout, R.P.Barnwal, G.Agarwal, and K.V.Chary (2010).
Root-mean-square-deviation-based rapid backbone resonance assignments in proteins.
  Magn Reson Chem, 48, 793-797.  
19067458 M.Venanzi, G.Bocchinfuso, E.Gatto, A.Palleschi, L.Stella, F.Formaggio, and C.Toniolo (2009).
Metal binding properties of fluorescent analogues of trichogin GA IV: a conformational study by time-resolved spectroscopy and molecular mechanics investigations.
  Chembiochem, 10, 91-97.  
19137330 S.M.Mustafi, R.B.Mutalik, R.Jain, K.Chandra, A.Bhattacharya, and K.V.Chary (2009).
Structural characterization of a novel Ca2+-binding protein from Entamoeba histolytica: structural basis for the observed functional differences with its isoform.
  J Biol Inorg Chem, 14, 471-483.  
17912755 P.M.Mohan, S.Mukherjee, and K.V.Chary (2008).
Differential native state ruggedness of the two Ca2+-binding domains in a Ca2+ sensor protein.
  Proteins, 70, 1147-1153.  
18341598 R.Jain, J.Santi-Rocca, N.Padhan, S.Bhattacharya, N.Guillen, and A.Bhattacharya (2008).
Calcium-binding protein 1 of Entamoeba histolytica transiently associates with phagocytic cups in a calcium-independent manner.
  Cell Microbiol, 10, 1373-1389.  
18810645 R.P.Barnwal, H.S.Atreya, and K.V.Chary (2008).
Chemical shift based editing of CH3 groups in fractionally 13C-labelled proteins using GFT (3, 2)D CT-HCCH-COSY: stereospecific assignments of CH3 groups of Val and Leu residues.
  J Biomol NMR, 42, 149-154.  
17914658 R.P.Barnwal, A.K.Rout, K.V.Chary, and H.S.Atreya (2007).
Rapid measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides.
  J Biomol NMR, 39, 259-263.  
17554780 S.Kumar, N.Padhan, N.Alam, and S.Gourinath (2007).
Crystal structure of calcium binding protein-1 from Entamoeba histolytica: a novel arrangement of EF hand motifs.
  Proteins, 68, 990-998.
PDB code: 2nxq
16981203 S.M.Mustafi, S.Mukherjee, K.V.Chary, and G.Cavallaro (2006).
Structural basis for the observed differential magnetic anisotropic tensorial values in calcium binding proteins.
  Proteins, 65, 656-669.
PDB codes: 2ev7 2i18
15929013 R.Bansal-Mutalik, S.M.Mustafi, A.Bhattacharya, and K.V.Chary (2005).
Sequence specific 1HN, 13C and 15N resonance assignments of a novel calcium-binding protein from Entamoeba histolytica.
  J Biomol NMR, 31, 379-380.  
  16511057 S.Gourinath, N.Padhan, N.Alam, and A.Bhattacharya (2005).
Crystallization and preliminary crystallographic analysis of calcium-binding protein-2 from Entamoeba histolytica and its complexes with strontium and the IQ1 motif of myosin V.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 417-420.  
16094534 S.Jyothi, S.M.Mustafi, K.V.Chary, and R.R.Joshi (2005).
Structure prediction of a multi-domain EF-hand Ca2+ binding protein by PROPAINOR.
  J Mol Model, 11, 481-488.  
14711825 P.Chakrabarty, D.K.Sethi, N.Padhan, K.J.Kaur, D.M.Salunke, S.Bhattacharya, and A.Bhattacharya (2004).
Identification and characterization of EhCaBP2. A second member of the calcium-binding protein family of the protozoan parasite Entamoeba histolytica.
  J Biol Chem, 279, 12898-12908.  
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.