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2yph

From Proteopedia

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Current revision

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation H230S, crystallized with 2',3-(RP)- cyclic-AMPS

Structural highlights

2yph is a 1 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CN37_MOUSE May participate in RNA metabolism in the myelinating cell, CNP is the third most abundant protein in central nervous system myelin.^[1]

Publication Abstract from PubMed

2H phosphoesterases catalyze reactions on nucleotide substrates and contain two conserved histidine residues in the active site. Very limited information is currently available on the details of the active site and substrate/product binding during the catalytic cycle of these enzymes. We performed a comprehensive X-ray crystallographic study of mouse 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase), a membrane-associated enzyme present at high levels in the tetrapod myelin sheath. We determined crystal structures of the CNPase phosphodiesterase domain complexed with substrate, product, and phosphorothioate analogues. The data provide detailed information on the CNPase reaction mechanism, including substrate binding mode and coordination of the nucleophilic water molecule. Linked to the reaction, an open/close motion of the beta5-alpha7 loop is observed. The role of the N terminus of helix alpha7 - unique for CNPase in the 2H family - during the reaction indicates that 2H phosphoesterases differ in their respective reaction mechanisms, despite the conserved catalytic residues. Furthermore, based on small-angle X-ray scattering, we present a model for the full-length enzyme, indicating the two domains of CNPase form an elongated molecule. Finally, based on our structural data and a comprehensive bioinformatics study, we discuss the conservation of CNPase in various organisms.

Crystallographic analysis of the reaction cycle of 2',3'-cyclic nucleotide 3'-phosphodiesterase, a unique member of the 2H phosphoesterase family.,Myllykoski M, Raasakka A, Lehtimaki M, Han H, Kursula I, Kursula P J Mol Biol. 2013 Jul 2. pii: S0022-2836(13)00391-4. doi:, 10.1016/j.jmb.2013.06.012. PMID:23831225^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Myllykoski M, Raasakka A, Han H, Kursula P. Myelin 2',3'-cyclic nucleotide 3'-phosphodiesterase: active-site ligand binding and molecular conformation. PLoS One. 2012;7(2):e32336. Epub 2012 Feb 29. PMID:22393399 doi:10.1371/journal.pone.0032336
↑ Myllykoski M, Raasakka A, Lehtimaki M, Han H, Kursula I, Kursula P. Crystallographic analysis of the reaction cycle of 2',3'-cyclic nucleotide 3'-phosphodiesterase, a unique member of the 2H phosphoesterase family. J Mol Biol. 2013 Jul 2. pii: S0022-2836(13)00391-4. doi:, 10.1016/j.jmb.2013.06.012. PMID:23831225 doi:10.1016/j.jmb.2013.06.012

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2yph"

@@ Line 1: / Line 1: @@
 ==Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation H230S, crystallized with 2',3-(RP)- cyclic-AMPS==
-<StructureSection load='2yph' size='340' side='right' caption='[[2yph]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='2yph' size='340' side='right'caption='[[2yph]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2yph]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YPH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2yph]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YPH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=QQY:[(3AR,4R,6R,6AR)-4-(6-AMINOPURIN-9-YL)-2-OXIDANYLIDENE-2-SULFANYL-3A,4,6,6A-TETRAHYDROFURO[3,4-D][1,3,2]DIOXAPHOSPHOL-6-YL]METHANOL'>QQY</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xmi|2xmi]], [[2y1p|2y1p]], [[2y3x|2y3x]], [[2ydb|2ydb]], [[2ydc|2ydc]], [[2ydd|2ydd]], [[2yoz|2yoz]], [[2yp0|2yp0]], [[2ype|2ype]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=QQY:[(3AR,4R,6R,6AR)-4-(6-AMINOPURIN-9-YL)-2-OXIDANYLIDENE-2-SULFANYL-3A,4,6,6A-TETRAHYDROFURO[3,4-D][1,3,2]DIOXAPHOSPHOL-6-YL]METHANOL'>QQY</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2',3'-cyclic-nucleotide_3'-phosphodiesterase 2',3'-cyclic-nucleotide 3'-phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.37 3.1.4.37] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2yph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yph OCA], [https://pdbe.org/2yph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yph RCSB], [https://www.ebi.ac.uk/pdbsum/2yph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yph ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yph OCA], [http://pdbe.org/2yph PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yph RCSB], [http://www.ebi.ac.uk/pdbsum/2yph PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yph ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CN37_MOUSE CN37_MOUSE]] May participate in RNA metabolism in the myelinating cell, CNP is the third most abundant protein in central nervous system myelin.<ref>PMID:22393399</ref>
+[https://www.uniprot.org/uniprot/CN37_MOUSE CN37_MOUSE] May participate in RNA metabolism in the myelinating cell, CNP is the third most abundant protein in central nervous system myelin.<ref>PMID:22393399</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 2yph" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 2',3'-cyclic-nucleotide 3'-phosphodiesterase]]
+[[Category: Large Structures]]
-[[Category: Lk3 transgenic mice]]
+[[Category: Mus musculus]]
-[[Category: Han, H]]
+[[Category: Han H]]
-[[Category: Kursula, P]]
+[[Category: Kursula P]]
-[[Category: Lehtimaki, M]]
+[[Category: Lehtimaki M]]
-[[Category: Myllykoski, M]]
+[[Category: Myllykoski M]]
-[[Category: Raasakka, A]]
+[[Category: Raasakka A]]
-[[Category: Hydrolase]]
-[[Category: Myelin]]
-[[Category: Nervous system]]

2yph

From Proteopedia

Current revision

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation H230S, crystallized with 2',3-(RP)- cyclic-AMPS

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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