PDBsum entry 2k2i

Go to PDB code: 
protein Protein-protein interface(s) links
Cell cycle PDB id
Protein chains
79 a.a. *
20 a.a. *
* Residue conservation analysis
PDB id:
Name: Cell cycle
Title: Nmr solution structure of thE C-terminal domain (t94-y172) of the human centrin 2 in complex with a repeat sequence of human sfi1 (r641-t660)
Structure: Centrin-2. Chain: a. Fragment: unp residues 94-172. Synonym: caltractin isoform 1. Engineered: yes. Sfi1 peptide. Chain: b. Fragment: unp residues 610-629. Engineered: yes
Source: Homo sapiens. Gene: cetn2, calt, cen2. Expressed in: escherichia coli. Synthetic: yes. Other_details: the peptide is chemically synthesized. It is found naturally in humans.
NMR struc: 15 models
Authors: J.Martinez-Sanz,L.Assairi,Y.Blouquit,P.Duchambon,L.Mouawad, C.Craescu
Key ref:
J.Martinez-Sanz et al. (2010). Structure, dynamics and thermodynamics of the human centrin 2/hSfi1 complex. J Mol Biol, 395, 191-204. PubMed id: 19857500 DOI: 10.1016/j.jmb.2009.10.041
02-Apr-08     Release date:   17-Feb-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P41208  (CETN2_HUMAN) -  Centrin-2
172 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
A8K8P3  (SFI1_HUMAN) -  Protein SFI1 homolog
1242 a.a.
20 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleotide-excision repair   1 term 
  Biochemical function     nucleic acid binding     4 terms  


DOI no: 10.1016/j.jmb.2009.10.041 J Mol Biol 395:191-204 (2010)
PubMed id: 19857500  
Structure, dynamics and thermodynamics of the human centrin 2/hSfi1 complex.
J.Martinez-Sanz, F.Kateb, L.Assairi, Y.Blouquit, G.Bodenhausen, D.Abergel, L.Mouawad, C.T.Craescu.
Centrin, an EF-hand calcium-binding protein, has been shown to be involved in the duplication of centrosomes, and Sfi1 (Suppressor of fermentation-induced loss of stress resistance protein 1) is one of its centrosomal targets. There are three isoforms of human centrin, but here we only considered centrin 2 (HsCen2). This protein has the ability to bind to any of the approximately 25 repeats of human Sfi1 (hSfi1) with more or less affinity. In this study, we mainly focused on the 17th repeat (R17-hSfi1-20), which presents the highest level of similarity with a well-studied 17-residue peptide (P17-XPC) from human xeroderma pigmentosum complementation group C protein, another centrin target for DNA repair. The only known structure of HsCen2 was resolved in complex with P17-XPC. The 20-residue peptide R17-hSfi1-20 exhibits the motif L8L4W1, which is the reverse of the XPC motif, W1L4L8. Consequently, the dipole of the helix formed by this motif has a reverse orientation. We wished to ascertain the impact of this reversal on the structure, dynamics and affinity of centrin. To address this question, we determined the structure of C-HsCen2 [the C-terminal domain of HsCen2 (T94-Y172)] in complex with R17-hSfi1-20 and monitored its dynamics by NMR, after having verified that the N-terminal domain of HsCen2 does not interact with the peptide. The structure shows that the binding mode is similar to that of P17-XPC. However, we observed a 2 -A translation of the R17-hSfi1-20 helix along its axis, inducing less anchorage in the protein and the disruption of a hydrogen bond between a tryptophan residue in the peptide and a well-conserved nearby glutamate in C-HsCen2. NMR dynamic studies of the complex strongly suggested the existence of an unusual calcium secondary binding mode in calcium-binding loop III, made possible by the uncommon residue composition of this loop. The secondary metal site is only populated at high calcium concentration and depends on the type of bound ligand.
  Selected figure(s)  
Figure 4.
Fig. 4. Structural features of the C-HsCen2/R17-hSfi1-20 complex. (a) Stereoview of the superposition of the 15 best NMR structures obtained in this work. The centrin domain is shown in black, and the peptide is shown in red. The structure was determined for C-HsCen2 in complex with R17-hSfi1-20, but only relatively ordered structural fragments are shown. (b) The accessible surface representation of the best C-HsCen2 structure, colored according to residue type (hydrophobic, white; polar, green; basic, blue; acidic, red). Only the structured part of the peptide is shown in transparent yellow. It can be seen that the binding site consists of two deep hydrophobic cavities separated by F113. (c) Superposition of the backbones of C-HsCen2 in complex with R17-hSfi1-20 and that with P17-XPC (PDB code 2GGM). The color code of the C-terminal domain is the same as that in (b). In the C-HsCen2/P17-XPC structure, residue E148 and the peptide are shown in yellow. In the C-HsCen2/R17-hSfi1-20 structure, E148 and the peptide are in gray. In addition, in the latter case, the backbone of the peptide is drawn with the following color code: carbon atoms in cyan, nitrogens in blue and oxygens in red. The carbonyl groups of the hSfi1 peptide indicate the orientation of the helix dipole. The Trp side chain is shown in both structures. Panels (d) and (e) represent comparisons of the C-HsCen2/R17-hSfi1-20 and HsCen2/P17-XPC complexes, respectively. Residue F113 (black sticks) of C-HsCen2 interacts less strongly with L8 of hSfi1 [cyan spheres in (d)] than L8 of XPC [yellow spheres in (e)]. In both (d) and (e), the target peptide is shown as a ribbon and the color code of the accessible surface of the fragment of C-HsCen2 is the same as in (b).
Figure 7.
Fig. 7. Proposed alternative binding site of Ca2+ in loop III of HsCen2. The yellow sphere shows the canonical Ca2+ position, while the green sphere indicates the position of the Nδ2 atom of N125. Calcium ion could exchange between these two positions provided the side chain of N125 moves in concert. Side chains are color coded according to charge as in Fig. 4b. The side chain of K124 was omitted for clarity.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2010, 395, 191-204) copyright 2010.  
  Figures were selected by the author.