Niche (protein structural motif): Difference between revisions
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In the area of [[protein]] [[structural motif]]s, '''niches''' are three or four [[amino acid]] residue features in which main-chain CO groups are bridged by positively charged or δ+ groups.<ref>{{cite journal|last=Torrance|first=GM|author2=Leader DP |title=A Novel Main Chain Motif in Proteins Bridged by Cationic Groups: The Niche|journal=Journal of Molecular Biology|year=2009|volume=385|issue=4|pages=1076–1086}}</ref><ref>{{cite journal|last=Regad|first=L|author2=Martin J |title=Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs|journal=BMC Bioinformatics|year=2011|volume=12|pages=247}}</ref><ref>{{cite journal|last=Cianci|first=M|author2=Tomaszewski |title=Crystallographic Analysis of Counterion Effects on Subtilisin Enzymatic Action in Acetonitrile|journal=Journal of the American Chemical Society|year=2010|volume=132|issue=7|pages=2293–2300}}</ref> The δ+ groups include groups with two [[hydrogen bond]] donor atoms such as NH<sub>2</sub> 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 [[cation]]ic bridging group is detected. Two websites are available for examining niches in proteins, Motivated Proteins: [http://motif.gla.ac.uk/motif/index.html];<ref>{{cite journal|last=Leader|first=DP|author2=Milner-White |title=Motivated Proteins: A web application for studying small three-dimensional protein motifs|journal=BMC Bioinformatics|year=2009|volume=10|pages=60}}</ref> or PDBeMotif: [http://www.ebi.ac.uk/pdbe-site/pdbemotif/].<ref>{{cite journal|last=Golovin|first=A|author2=Henrick |title=MSDmotif: exploring protein sites and motifs|journal=BMC Bioinformatics|year=2008|volume=9|pages=312}}</ref> |
In the area of [[protein]] [[structural motif]]s, '''niches''' are three or four [[amino acid]] residue features in which main-chain CO groups are bridged by positively charged or δ+ groups.<ref>{{cite journal|last=Torrance|first=GM|author2=Leader DP |title=A Novel Main Chain Motif in Proteins Bridged by Cationic Groups: The Niche|journal=Journal of Molecular Biology|year=2009|volume=385|issue=4|pages=1076–1086|doi=10.1016/j.jmb.2008.11.007}}</ref><ref>{{cite journal|last=Regad|first=L|author2=Martin J |title=Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs|journal=BMC Bioinformatics|year=2011|volume=12|pages=247|doi=10.1186/1471-2105-12-247}}</ref><ref>{{cite journal|last=Cianci|first=M|author2=Tomaszewski |title=Crystallographic Analysis of Counterion Effects on Subtilisin Enzymatic Action in Acetonitrile|journal=Journal of the American Chemical Society|year=2010|volume=132|issue=7|pages=2293–2300|doi=10.1021/ja908703c}}</ref> The δ+ groups include groups with two [[hydrogen bond]] donor atoms such as NH<sub>2</sub> 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 [[cation]]ic bridging group is detected. Two websites are available for examining niches in proteins, Motivated Proteins: [http://motif.gla.ac.uk/motif/index.html];<ref>{{cite journal|last=Leader|first=DP|author2=Milner-White |title=Motivated Proteins: A web application for studying small three-dimensional protein motifs|journal=BMC Bioinformatics|year=2009|volume=10|pages=60|doi=10.1186/1471-2105-10-60}}</ref> or PDBeMotif: [http://www.ebi.ac.uk/pdbe-site/pdbemotif/].<ref>{{cite journal|last=Golovin|first=A|author2=Henrick |title=MSDmotif: exploring protein sites and motifs|journal=BMC Bioinformatics|year=2008|volume=9|pages=312|doi=10.1186/1471-2105-9-312}}</ref> |
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[[File:A_niche3_bound_to_a_water_molecule.pdf|thumb|right|Niche3 bound to a water molecule. The red sphere is the oxygen of the water. The mainchain atoms of the niche3 tripeptide is shown as sticks. Oxygen, red; nitrogen, blue; carbon, grey.]] |
[[File:A_niche3_bound_to_a_water_molecule.pdf|thumb|right|Niche3 bound to a water molecule. The red sphere is the oxygen of the water. The mainchain atoms of the niche3 tripeptide is shown as sticks. Oxygen, red; nitrogen, blue; carbon, grey.]] |
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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+). |
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+). |
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A major cation transporter in cells is [[calcium ATPase]].<ref>{{cite journal|last=Toyoshima|first=C|author2=Mizutani |title=Crystal structure of the calcium pump with a bound ATP analogue|journal=Nature|year=2004|volume=430|pages=529–535}}</ref> 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 group]]s, 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. |
A major cation transporter in cells is [[calcium ATPase]].<ref>{{cite journal|last=Toyoshima|first=C|author2=Mizutani |title=Crystal structure of the calcium pump with a bound ATP analogue|journal=Nature|year=2004|volume=430|pages=529–535|doi=10.1038/nature02680}}</ref> 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 group]]s, 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. |
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Another small tripeptide motif that binds cations or δ+ groups is called the [[catgrip]]. |
Another small tripeptide motif that binds cations or δ+ groups is called the [[catgrip]]. |
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Revision as of 10:54, 15 August 2014
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: [1];[4] or PDBeMotif: [2].[5]
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 is called the catgrip.
References
- ^ 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.
- ^ Regad, L; Martin J (2011). "Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs". BMC Bioinformatics. 12: 247. doi:10.1186/1471-2105-12-247.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ 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.
- ^ Leader, DP; Milner-White (2009). "Motivated Proteins: A web application for studying small three-dimensional protein motifs". BMC Bioinformatics. 10: 60. doi:10.1186/1471-2105-10-60.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Golovin, A; Henrick (2008). "MSDmotif: exploring protein sites and motifs". BMC Bioinformatics. 9: 312. doi:10.1186/1471-2105-9-312.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Toyoshima, C; Mizutani (2004). "Crystal structure of the calcium pump with a bound ATP analogue". Nature. 430: 529–535. doi:10.1038/nature02680.
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