1v8p
From Proteopedia
(New page: 200px<br /><applet load="1v8p" size="450" color="white" frame="true" align="right" spinBox="true" caption="1v8p, resolution 2.52Å" /> '''Crystal structure of...) |
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| - | [[Image:1v8p.gif|left|200px]]<br /><applet load="1v8p" size=" | + | [[Image:1v8p.gif|left|200px]]<br /><applet load="1v8p" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1v8p, resolution 2.52Å" /> | caption="1v8p, resolution 2.52Å" /> | ||
'''Crystal structure of PAE2754 from Pyrobaculum aerophilum'''<br /> | '''Crystal structure of PAE2754 from Pyrobaculum aerophilum'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Genome sequencing projects have focused attention on the problem of | + | Genome sequencing projects have focused attention on the problem of discovering the functions of protein domains that are widely distributed throughout living species but which are, as yet, largely uncharacterized. One such example is the PIN domain, found in eukaryotes, bacteria, and Archaea, and with suggested roles in signaling, RNase editing, and/or nucleotide binding. The first reported crystal structure of a PIN domain (open reading frame PAE2754, derived from the crenarchaeon, Pyrobaculum aerophilum) has been determined to 2.5 A resolution and is presented here. Mapping conserved residues from a multiple sequence alignment onto the structure identifies a putative active site. The discovery of distant structural homology with several exonucleases, including T4 phage RNase H and flap endonuclease (FEN1), further suggests a likely function for PIN domains as Mg2+-dependent exonucleases, a hypothesis that we have confirmed in vitro. The tetrameric structure of PAE2754, with the active sites inside a tunnel, suggests a mechanism for selective cleavage of single-stranded overhangs or flap structures. These results indicate likely DNA or RNA editing roles for prokaryotic PIN domains, which are strikingly numerous in thermophiles, and in organisms such as Mycobacterium tuberculosis. They also support previous hypotheses that eukaryotic PIN domains participate in RNAi and nonsense-mediated RNA degradation. |
==About this Structure== | ==About this Structure== | ||
| - | 1V8P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum] with CL as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1V8P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum] with <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8P OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Pyrobaculum aerophilum]] | [[Category: Pyrobaculum aerophilum]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Arcus, V | + | [[Category: Arcus, V L.]] |
[[Category: Backbro, K.]] | [[Category: Backbro, K.]] | ||
| - | [[Category: Baker, E | + | [[Category: Baker, E N.]] |
| - | [[Category: Daniel, E | + | [[Category: Daniel, E L.]] |
[[Category: Roos, A.]] | [[Category: Roos, A.]] | ||
[[Category: CL]] | [[Category: CL]] | ||
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[[Category: tetramer]] | [[Category: tetramer]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:32:38 2008'' |
Revision as of 13:32, 21 February 2008
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Crystal structure of PAE2754 from Pyrobaculum aerophilum
Overview
Genome sequencing projects have focused attention on the problem of discovering the functions of protein domains that are widely distributed throughout living species but which are, as yet, largely uncharacterized. One such example is the PIN domain, found in eukaryotes, bacteria, and Archaea, and with suggested roles in signaling, RNase editing, and/or nucleotide binding. The first reported crystal structure of a PIN domain (open reading frame PAE2754, derived from the crenarchaeon, Pyrobaculum aerophilum) has been determined to 2.5 A resolution and is presented here. Mapping conserved residues from a multiple sequence alignment onto the structure identifies a putative active site. The discovery of distant structural homology with several exonucleases, including T4 phage RNase H and flap endonuclease (FEN1), further suggests a likely function for PIN domains as Mg2+-dependent exonucleases, a hypothesis that we have confirmed in vitro. The tetrameric structure of PAE2754, with the active sites inside a tunnel, suggests a mechanism for selective cleavage of single-stranded overhangs or flap structures. These results indicate likely DNA or RNA editing roles for prokaryotic PIN domains, which are strikingly numerous in thermophiles, and in organisms such as Mycobacterium tuberculosis. They also support previous hypotheses that eukaryotic PIN domains participate in RNAi and nonsense-mediated RNA degradation.
About this Structure
1V8P is a Single protein structure of sequence from Pyrobaculum aerophilum with as ligand. Full crystallographic information is available from OCA.
Reference
Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease., Arcus VL, Backbro K, Roos A, Daniel EL, Baker EN, J Biol Chem. 2004 Apr 16;279(16):16471-8. Epub 2004 Jan 20. PMID:14734548
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