NiCoT family: Difference between revisions

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Proteins currently known to belong to the Ni²⁺-Co²⁺ Transporter (NiCoT) family (TC# 2.A.52) can be found in organisms ranging from Gram-negative and Gram-positive bacteria to archaea and some eukaryotes. Members of this family catalyze uptake of Ni²⁺ and/or Co²⁺ in a proton motive force-dependent process.^[1]

Structure

These proteins range in size from about 300 to 400 amino acyl residues and possess 6, 7, or 8 transmembrane segments (TMSs), thought to result from an intragenic 4 TMS duplication, followed by a deletion of one or two TMSs in the cases of the 7 or 6 TMS proteins. Topological analyses with the HoxN Ni²⁺ transporter of Ralstonia eutropha (Alcaligenes eutrophus) suggest that it possesses 8 TMSs with its N- and C-termini in the cytoplasm. The Co²⁺ (Ni²⁺) transporter of Rhodococcus rhodochrous, NhlF, exhibits eight putative TMSs, and eight apparent TMSs are revealed by hydropathy analyses of multiple alignments of family protein sequences. An HX⁴DH motif in helix 2 of the HoxN protein has been implicated in Ni²⁺ binding, and both helix 1 and helix 2, which interact spatially, form the selectivity filter.^[2] In the Helicobacter pylori NixA homologue, several conserved motifs have been shown to be important for Ni²⁺ binding and transport.^[1]^[3]

At least one crystal structure is known, determined by Yu et al.,^[4] available at PDB: 4M58.

Reaction

The overall reaction catalyzed by the proteins of the NiCoT family is:^[1]

[Ni²⁺ and/or Co²⁺] (out) → [Ni²⁺ and/or Co²⁺] (in).

Proteins

Several characterized proteins belong to the Ni²⁺-Co²⁺ Transporter (NiCoT) Family (TC# 2.A.43). A complete list of these proteins along with their transporter classification identification numbers (TCID), domain, kingdom/phylum, and some examples can be found in the Transporter Classification Database.

References

^ ^a ^b ^c Saier, Milton. "Transporter Classification Database: 2.A.52 The Ni2+-Co2+ Transporter (NiCoT) Family". tcdb.org. Retrieved 4 January 2016.
^ Degen, O; Eitinger, T (July 2002). "Substrate specificity of nickel/cobalt permeases: insights from mutants altered in transmembrane domains I and II". J. Bacteriol. 184 (13): 3569–77. doi:10.1128/jb.184.13.3569-3577.2002. PMC 135128. PMID 12057951.
^ Wolfram, L; Bauerfeind, P (March 2002). "Conserved low-affinity nickel-binding amino acids are essential for the function of the nickel permease NixA of Helicobacter pylori". J. Bacteriol. 184 (5): 1438–43. doi:10.1128/JB.184.5.1438-1443.2002. PMC 134868. PMID 11844775.
^ Yu, Y; Zhou, M; Kirsch, F; Xu, C; Zhang, L; Wang, Y; Jiang, Z; Wang, N; Li, J; Eitinger, T; Yang, M (December 24, 2013). "Planar substrate-binding site dictates the specificity of ECF-type nickel/cobalt transporters". Cell Research. 24 (3): 267–277. doi:10.1038/cr.2013.172. PMC 3945884. PMID 24366337.

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+{{Short description|Family of transport proteins}}
-Proteins currently known to belong to the '''Ni<sup>2+</sup>-Co<sup>2+</sup> Transporter (NiCoT) Family''' ([http://www.tcdb.org/search/result.php?tc=2.A.52 TC# 2.A.52]) can be found in organisms ranging from [[Gram-negative bacteria|Gram-negative]] and [[Gram-positive bacteria]] to [[archaea]] and some [[eukaryotes]]. Members of this family catalyze uptake of [[nickel|Ni<sup>2+</sup>]] and/or [[Cobalt|Co<sup>2+</sup>]] in a [[proton motive force]]-dependent process. <ref name=TCDB>{{cite web|last1=Saier|first1=Milton|title=Transporter Classification Database: 2.A.43 The Lysosomal Cystine Transporter (LCT) Family|url=http://www.tcdb.org/search/result.php?tc=2.a.43|website=tcdb.org|accessdate=4 January 2016}}</ref>
+Proteins currently known to belong to the '''Ni<sup>2+</sup>-Co<sup>2+</sup> Transporter (NiCoT) family''' ([http://www.tcdb.org/search/result.php?tc=2.A.52 TC# 2.A.52]) can be found in organisms ranging from [[Gram-negative bacteria|Gram-negative]] and [[Gram-positive bacteria]] to [[archaea]] and some [[eukaryotes]]. Members of this family catalyze uptake of [[nickel|Ni<sup>2+</sup>]] and/or [[Cobalt|Co<sup>2+</sup>]] in a [[proton motive force]]-dependent process.<ref name="TCDB">{{cite web|last1=Saier|first1=Milton|title=Transporter Classification Database: 2.A.52 The Ni2+-Co2+ Transporter (NiCoT) Family|url=http://www.tcdb.org/search/result.php?tc=2.a.52|website=tcdb.org|accessdate=4 January 2016}}</ref>
 ==Structure==
-These proteins range in size from about 300 to 400 amino acyl residues and possess 7 or 8 transmembrane segments (TMSs) thought to result from [[Intragenic region|intragenic]] 4 TMS duplication, followed by a deletion in the case of the 7 TMS variety. Topological analyses with the HoxN Ni<sup>2+</sup> transporter of Ralstonia eutropha (Alcaligenes eutrophus) suggest that it possesses 8 TMSs with its N- and C-termini in the cytoplasm. The Co<sup>2+</sup> (Ni<sup>2+</sup>) transporter of Rhodococcus rhodochrous, NhlF, exhibits eight putative TMSs, and eight apparent TMSs are revealed by a [[hydropathy]] analysis of the [[Multiple sequence alignment|multiple alignment]] of the NiCoT family protein sequences. An HX4DH sequence in helix 2 of the HoxN protein has been implicated in Ni<sup>2+</sup> binding, and both helix 1 and helix 2 which interact spatially, form the selectivity filter<ref name="Degan Eitinger">{{cite journal|last1=Degen|first1=O|last2=Eitinger|first2=T|title=Substrate specificity of nickel/cobalt permeases: insights from mutants altered in transmembrane domains I and II.|journal=J Bacteriol.|date=July 2002|volume=184|issue=13|pages=3569-77|pmid=12057951}}</ref>. In the H. pylori NixA homologue, several conserved motifs have been shown to be important for Ni<sup>2+</sup> binding and transport. <ref name="W and B">{{cite journal|last1=Wolfram|first1=L|last2=Bauerfeind|first2=P|title=Conserved low-affinity nickel-binding amino acids are essential for the function of the nickel permease NixA of Helicobacter pylori.|journal=J Bacteriol.|date=March 2002|volume=184|issue=5|pages=1438-43|pmid=11844775}}</ref><ref name=TCDB/>
+These proteins range in size from about 300 to 400 amino acyl residues and possess 6, 7, or 8 transmembrane segments (TMSs), thought to result from an [[Intragenic region|intragenic]] 4 TMS duplication, followed by a deletion of one or two TMSs in the cases of the 7 or 6 TMS proteins. Topological analyses with the HoxN Ni<sup>2+</sup> transporter of ''Ralstonia eutropha'' (''Alcaligenes eutrophus'') suggest that it possesses 8 TMSs with its N- and C-termini in the cytoplasm. The Co<sup>2+</sup> (Ni<sup>2+</sup>) transporter of ''[[Rhodococcus rhodochrous]]'', NhlF, exhibits eight putative TMSs, and eight apparent TMSs are revealed by [[hydropathy]] analyses of multiple alignments of family protein sequences. An HX<sup>4</sup>DH motif in helix 2 of the HoxN protein has been implicated in Ni<sup>2+</sup> binding, and both helix 1 and helix 2, which interact spatially, form the selectivity filter.<ref name="Degan Eitinger">{{cite journal|last1=Degen|first1=O|last2=Eitinger|first2=T|title=Substrate specificity of nickel/cobalt permeases: insights from mutants altered in transmembrane domains I and II.|journal=J. Bacteriol.|date=July 2002|volume=184|issue=13|pages=3569–77|pmc=135128|pmid=12057951|doi=10.1128/jb.184.13.3569-3577.2002}}</ref> In the ''[[Helicobacter pylori]]'' NixA homologue, several conserved motifs have been shown to be important for Ni<sup>2+</sup> binding and transport.<ref name="TCDB" /><ref name="W and B">{{cite journal|last1=Wolfram|first1=L|last2=Bauerfeind|first2=P|title=Conserved low-affinity nickel-binding amino acids are essential for the function of the nickel permease NixA of ''Helicobacter pylori'' |journal=J. Bacteriol.|date=March 2002|volume=184|issue=5|pages=1438–43|doi=10.1128/JB.184.5.1438-1443.2002 |pmid=11844775|pmc=134868}}</ref>
-At least one crystal structure is known, found by Yu et. al. <ref>{{cite journal|last1=Yu|first1=Y|last2=Zhou|first2=M|last3=Kirsch|first3=F|last4=Xu|first4=C|last5=Zhang|first5=L|last6=Wang|first6=Y|last7=Jiang|first7=Z|last8=Wang|first8=N|last9=Li|first9=J|last10=Eitinger|first10=T|last11=Yang|first11=M|title=Planar substrate-binding site dictates the specificity of ECF-type nickel/cobalt transporters|journal=Cell research|date=December 24, 2013|volume=24|issue=3|pages=267–277|doi=10.1038/cr.2013.172}}</ref>, available at {{PDB|4M58}}.
+At least one crystal structure is known, determined by Yu et al.,<ref>{{cite journal|last1=Yu|first1=Y|last2=Zhou|first2=M|last3=Kirsch|first3=F|last4=Xu|first4=C|last5=Zhang|first5=L|last6=Wang|first6=Y|last7=Jiang|first7=Z|last8=Wang|first8=N|last9=Li|first9=J|last10=Eitinger|first10=T|last11=Yang|first11=M|title=Planar substrate-binding site dictates the specificity of ECF-type nickel/cobalt transporters|journal=Cell Research|date=December 24, 2013|volume=24|issue=3|pages=267–277|doi=10.1038/cr.2013.172|pmid=24366337|pmc=3945884}}</ref> available at {{PDB|4M58}}.
 ==Reaction==
-The overall reaction catalyzed by the proteins of the NiCoT family is: <ref name=TCDB/>
+The overall reaction catalyzed by the proteins of the NiCoT family is:<ref name="TCDB" />
 ::[Ni<sup>2+</sup> and/or Co<sup>2+</sup>] (out) → [Ni<sup>2+</sup> and/or Co<sup>2+</sup>] (in).
 ==Proteins==
-Several known proteins belong to the Ni<sup>2+</sup>-Co<sup>2+</sup> Transporter (NiCoT) Family. A complete list of these proteins along with their transporter classification identification number (TCID), domain, kingdom/phylum, and some examples can be found in the [http://www.tcdb.org/search/result.php?tc=2.A.52.4 Transporter Classification Database].
+Several characterized proteins belong to the Ni<sup>2+</sup>-Co<sup>2+</sup> Transporter (NiCoT) Family (TC# 2.A.43). A complete list of these proteins along with their transporter classification identification numbers (TCID), domain, kingdom/phylum, and some examples can be found in the [http://www.tcdb.org/search/result.php?tc=2.A.52.4 Transporter Classification Database].
 ==References==
-{{reflist}}
+{{reflist|40em}}
-==Further Reading==
+==Further reading==
-{{refbegin}}
+{{refbegin|30em}}
-* {{cite journal|last1=Deng|first1=X|last2=He|first2=J|last3=He|first3=N|title=Comparative study on Ni(2+)-affinity transport of nickel/cobalt permeases (NiCoTs) and the potential of recombinant Escherichia coli for Ni(2+) bioaccumulation.|journal=Bioresour Technol.|date=February 2013|volume=130|pages=69-74|doi=10.1016/j.biortech.2012.11.133|pmid=23306112|url=http://www.ncbi.nlm.nih.gov/pubmed/23306112}}
+* {{cite journal|last1=Deng|first1=X|last2=He|first2=J|last3=He|first3=N|title=Comparative study on Ni(2+)-affinity transport of nickel/cobalt permeases (NiCoTs) and the potential of recombinant Escherichia coli for Ni(2+) bioaccumulation.|journal=Bioresour. Technol.|date=February 2013|volume=130|pages=69–74|doi=10.1016/j.biortech.2012.11.133|pmid=23306112}}
-* {{cite journal|last1=Rodionov|first1=D|last2=Hebbeln|first2=P|last3=Gelfand|first3=M|last4=Eitinger|first4=T|title=Comparative and Functional Genomic Analysis of Prokaryotic Nickel and Cobalt Uptake Transporters: Evidence for a Novel Group of ATP-Binding Cassette Transporters|journal=Journal of Bacteriology|date=January 2006|volume=188|issue=1|pages=317–327|doi=10.1128/JB.188.1.317-327.2006|pmid=PMC1317602}}
+* {{cite journal|last1=Rodionov|first1=D|last2=Hebbeln|first2=P|last3=Gelfand|first3=M|last4=Eitinger|first4=T|title=Comparative and Functional Genomic Analysis of Prokaryotic Nickel and Cobalt Uptake Transporters: Evidence for a Novel Group of ATP-Binding Cassette Transporters|journal=J. Bacteriol.|date=January 2006|volume=188|issue=1|pages=317–327|doi=10.1128/JB.188.1.317-327.2006|pmc=1317602|pmid=16352848}}
 {{refend}}
+{{Portal bar|Biology|border=no}}
 [[Category:Membrane proteins]]
 [[Category:Enzymes of known structure]]
+[[Category:Solute carrier family]]
+[[Category:Transmembrane proteins]]
+[[Category:Transmembrane transporters]]
+[[Category:Transport proteins]]
+{{membrane-protein-stub}}