Niche (protein structural motif)

In the area of protein structural motifs, niches are three or four amino acid residue features in which main-chain CO groups are bridged by positively charged or δ+ groups.[1][2][3] The δ+ groups include groups with two hydrogen bond donor atoms such as NH2 groups and water molecules. In typical proteins, 7% of amino acid residues belong to niches bound to a δ+ group, while another 7% have the conformation but no single cationic bridging group is detected. Two websites are available for examining niches in proteins, Motivated Proteins: ;[4] or PDBeMotif: .[5]

Niche3 bound to a water molecule via two O-H...O hydrogen bonds. The red sphere is the oxygen of the water. The mainchain atoms of the niche3 tripeptide are shown as sticks. Oxygen, red; nitrogen, blue; carbon, grey. Hydrogen atoms not shown.

Niches are of two kinds, distinguished as niche3 (3 residues, i to i+2) and niche4 (4 residues, i to i+3). In a niche3 motif the δ+-binding carbonyl group is from residues i and i+2 while in a niche4 motif it is from residues i and i+3.

A niche3 has the α conformation for residue i+1 and the β conformation for residue i+2; a niche4 has the α conformation for residues i+1 and i+2 and the β conformation for residue i+3.

A niche occurs commonly at the C-terminus of α-helices especially of 310 helices.

Metal ions that occur bound to niches in proteins are Na+, K+, Ca++ and Mg++. Proteins with regulatory cations often employ niches for metal binding (thrombin, Na+; annexin, Ca++; pyruvate dehydrogenase, K+).

A major cation transporter in cells is calcium ATPase.[6] In the Ca++-bound crystal structures the two calcium ions side-by-side within the transmembrane domain are thought to be at the halfway stage of being transported. As well as being bound by various side chain carbonyl groups, one of these calcium ions is bound by a niche3/niche4 (both in the one motif) at residues 304–307 at the C-terminus of an α-helix.

Another small tripeptide motif that binds cations or δ+ groups via main-chain CO groups is called the catgrip.

References

  1. ↑ Torrance, GM; Leader DP (2009). "A Novel Main Chain Motif in Proteins Bridged by Cationic Groups: The Niche". Journal of Molecular Biology 385 (4): 1076–1086. doi:10.1016/j.jmb.2008.11.007.
  2. ↑ Regad, L; Martin J (2011). "Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs". BMC Bioinformatics 12 (1): 247. doi:10.1186/1471-2105-12-247.
  3. ↑ Cianci, M; Tomaszewski (2010). "Crystallographic Analysis of Counterion Effects on Subtilisin Enzymatic Action in Acetonitrile". Journal of the American Chemical Society 132 (7): 2293–2300. doi:10.1021/ja908703c.
  4. ↑ Leader, DP; Milner-White (2009). "Motivated Proteins: A web application for studying small three-dimensional protein motifs". BMC Bioinformatics 10 (1): 60. doi:10.1186/1471-2105-10-60. PMC 2651126. PMID 19210785.
  5. ↑ Golovin, A; Henrick (2008). "MSDmotif: exploring protein sites and motifs". BMC Bioinformatics 9 (1): 312. doi:10.1186/1471-2105-9-312. PMC 2491636. PMID 18637174.
  6. ↑ Toyoshima, C; Mizutani (2004). "Crystal structure of the calcium pump with a bound ATP analogue". Nature 430 (6999): 529–535. doi:10.1038/nature02680.


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