3l2b: Difference between revisions
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< | ==Crystal structure of the CBS and DRTGG domains of the regulatory region of Clostridium perfringens pyrophosphatase complexed with activator, diadenosine tetraphosphate== | ||
<StructureSection load='3l2b' size='340' side='right'caption='[[3l2b]], [[Resolution|resolution]] 2.27Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3l2b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens_str._13 Clostridium perfringens str. 13]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L2B FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.27Å</td></tr> | |||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene></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=3l2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l2b OCA], [https://pdbe.org/3l2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l2b RCSB], [https://www.ebi.ac.uk/pdbsum/3l2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l2b ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/IPYR_CLOPE IPYR_CLOPE] | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l2/3l2b_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3l2b ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Nucleotide-binding cystathionine beta-synthase (CBS) domains serve as regulatory units in numerous proteins distributed in all kingdoms of life. However, the underlying regulatory mechanisms remain to be established. Recently, we described a subfamily of CBS domain-containing pyrophosphatases (PPases) within family II PPases. Here, we express a novel CBS-PPase from Clostridium perfringens (CPE2055) and show that the enzyme is inhibited by AMP and activated by a novel effector, diadenosine 5',5-P1,P4-tetraphosphate (AP(4)A). The structures of the AMP and AP(4)A complexes of the regulatory region of C. perfringens PPase (cpCBS), comprising a pair of CBS domains interlinked by a DRTGG domain, were determined at 2.3 A resolution using X-ray crystallography. The structures obtained are the first structures of a DRTGG domain as part of a larger protein structure. The AMP complex contains two AMP molecules per cpCBS dimer, each bound to a single monomer, whereas in the activator-bound complex, one AP(4)A molecule bridges two monomers. In the nucleotide-bound structures, activator binding induces significant opening of the CBS domain interface, compared with the inhibitor complex. These results provide structural insight into the mechanism of CBS-PPase regulation by nucleotides. | |||
Crystal structures of the CBS and DRTGG domains of the regulatory region of Clostridiumperfringens pyrophosphatase complexed with the inhibitor, AMP, and activator, diadenosine tetraphosphate.,Tuominen H, Salminen A, Oksanen E, Jamsen J, Heikkila O, Lehtio L, Magretova NN, Goldman A, Baykov AA, Lahti R J Mol Biol. 2010 May 7;398(3):400-13. Epub 2010 Mar 19. PMID:20303981<ref>PMID:20303981</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3l2b" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Clostridium perfringens str. 13]] | ||
[[Category: Large Structures]] | |||
[[Category: Baykov AA]] | |||
== | [[Category: Goldman A]] | ||
< | [[Category: Heikkila O]] | ||
[[Category: Clostridium perfringens]] | [[Category: Jamsen J]] | ||
[[Category: | [[Category: Lahti R]] | ||
[[Category: Baykov | [[Category: Lehtio L]] | ||
[[Category: Goldman | [[Category: Magretova NN]] | ||
[[Category: Heikkila | [[Category: Oksanen E]] | ||
[[Category: Jamsen | [[Category: Salminen A]] | ||
[[Category: Lahti | [[Category: Tuominen H]] | ||
[[Category: Lehtio | |||
[[Category: Magretova | |||
[[Category: Oksanen | |||
[[Category: Salminen | |||
[[Category: Tuominen | |||
Latest revision as of 19:19, 1 November 2023
Crystal structure of the CBS and DRTGG domains of the regulatory region of Clostridium perfringens pyrophosphatase complexed with activator, diadenosine tetraphosphateCrystal structure of the CBS and DRTGG domains of the regulatory region of Clostridium perfringens pyrophosphatase complexed with activator, diadenosine tetraphosphate
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedNucleotide-binding cystathionine beta-synthase (CBS) domains serve as regulatory units in numerous proteins distributed in all kingdoms of life. However, the underlying regulatory mechanisms remain to be established. Recently, we described a subfamily of CBS domain-containing pyrophosphatases (PPases) within family II PPases. Here, we express a novel CBS-PPase from Clostridium perfringens (CPE2055) and show that the enzyme is inhibited by AMP and activated by a novel effector, diadenosine 5',5-P1,P4-tetraphosphate (AP(4)A). The structures of the AMP and AP(4)A complexes of the regulatory region of C. perfringens PPase (cpCBS), comprising a pair of CBS domains interlinked by a DRTGG domain, were determined at 2.3 A resolution using X-ray crystallography. The structures obtained are the first structures of a DRTGG domain as part of a larger protein structure. The AMP complex contains two AMP molecules per cpCBS dimer, each bound to a single monomer, whereas in the activator-bound complex, one AP(4)A molecule bridges two monomers. In the nucleotide-bound structures, activator binding induces significant opening of the CBS domain interface, compared with the inhibitor complex. These results provide structural insight into the mechanism of CBS-PPase regulation by nucleotides. Crystal structures of the CBS and DRTGG domains of the regulatory region of Clostridiumperfringens pyrophosphatase complexed with the inhibitor, AMP, and activator, diadenosine tetraphosphate.,Tuominen H, Salminen A, Oksanen E, Jamsen J, Heikkila O, Lehtio L, Magretova NN, Goldman A, Baykov AA, Lahti R J Mol Biol. 2010 May 7;398(3):400-13. Epub 2010 Mar 19. PMID:20303981[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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