1zm8: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
 
(9 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:1zm8.png|left|200px]]


<!--
==Apo Crystal structure of Nuclease A from Anabaena sp.==
The line below this paragraph, containing "STRUCTURE_1zm8", creates the "Structure Box" on the page.
<StructureSection load='1zm8' size='340' side='right'caption='[[1zm8]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1zm8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Anabaena_sp. Anabaena sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZM8 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_1zm8|  PDB=1zm8  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zm8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zm8 OCA], [https://pdbe.org/1zm8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zm8 RCSB], [https://www.ebi.ac.uk/pdbsum/1zm8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zm8 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NUCA_NOSS1 NUCA_NOSS1] Catalyzes the degradation of both RNA and DNA; has the potential to act as an endonuclease.
== 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/zm/1zm8_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=1zm8 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Nuclease A (NucA) is a nonspecific endonuclease from Anabaena sp. capable of degrading single- and double-stranded DNA and RNA in the presence of divalent metal ions. We have determined the structure of the delta(2-24),D121A mutant of NucA in the presence of Zn2+ and Mn2+ (PDB code 1ZM8). The mutations were introduced to remove the N-terminal signal peptide and to reduce the activity of the nonspecific nuclease, thereby reducing its toxicity to the Escherichia coli expression system. NucA contains a betabeta alpha metal finger motif and a hydrated Mn2+ ion at the active site. Unexpectedly, NucA was found to contain additional metal binding sites approximately 26 A apart from the catalytic metal binding site. A structural comparison between NucA and the closest analog for which structural data exist, the Serratia nuclease, indicates several interesting differences. First, NucA is a monomer rather than a dimer. Second, there is an unexpected structural homology between the N-terminal segments despite a poorly conserved sequence, which in Serratia includes a cysteine bridge thought to play a regulatory role. In addition, although a sequence alignment had suggested that NucA lacks a proposed catalytic residue corresponding to Arg57 in Serratia, the structure determined here indicates that Arg93 in NucA is positioned to fulfill this role. Based on comparison with DNA-bound nuclease structures of the betabeta alpha metal finger nuclease family and available mutational data on NucA, we propose that His124 acts as a catalytic base, and Arg93 participates in the catalysis possibly through stabilization of the transition state.


===Apo Crystal structure of Nuclease A from Anabaena sp.===
Structural insights into the mechanism of nuclease A, a betabeta alpha metal nuclease from Anabaena.,Ghosh M, Meiss G, Pingoud A, London RE, Pedersen LC J Biol Chem. 2005 Jul 29;280(30):27990-7. Epub 2005 May 15. PMID:15897201<ref>PMID:15897201</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<!--
</div>
The line below this paragraph, {{ABSTRACT_PUBMED_15897201}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1zm8" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15897201 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15897201}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Anabaena sp]]
1ZM8 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Anabaena_sp. Anabaena sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZM8 OCA].
[[Category: Large Structures]]
 
[[Category: Ghosh M]]
==Reference==
[[Category: London RE]]
<ref group="xtra">PMID:15897201</ref><references group="xtra"/>
[[Category: Meiss G]]
[[Category: Anabaena sp.]]
[[Category: Pedersen LC]]
[[Category: Ghosh, M.]]
[[Category: Pingoud A]]
[[Category: London, R E.]]
[[Category: Meiss, G.]]
[[Category: Pedersen, L C.]]
[[Category: Pingoud, A.]]
[[Category: Metal dependent]]
[[Category: Nuca]]
[[Category: Nuclease]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:47:04 2009''
Retrieved from "https://proteopedia.org/1zm8"