2enb: Difference between revisions

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New page: left|200px<br /><applet load="2enb" size="450" color="white" frame="true" align="right" spinBox="true" caption="2enb, resolution 2.05Å" /> '''CRYSTAL STRUCTURES O...
 
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[[Image:2enb.gif|left|200px]]<br /><applet load="2enb" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2enb, resolution 2.05&Aring;" />
'''CRYSTAL STRUCTURES OF THE BINARY CA2+ AND PDTP COMPLEXES AND THE TERNARY COMPLEX OF THE ASP 21->GLU MUTANT OF STAPHYLOCOCCAL NUCLEASE. IMPLICATIONS FOR CATALYSIS AND LIGAND BINDING'''<br />


==Overview==
==CRYSTAL STRUCTURES OF THE BINARY CA2+ AND PDTP COMPLEXES AND THE TERNARY COMPLEX OF THE ASP 21->GLU MUTANT OF STAPHYLOCOCCAL NUCLEASE. IMPLICATIONS FOR CATALYSIS AND LIGAND BINDING==
The crystal structure of the Asp21--&gt;Glu mutant (D21E) of staphylococcal, nuclease (SNase) has been determined in three different complex forms. The, structure of the D21E ternary complex in which D21E is bound to both Ca2+, and the transition-state analogue, thymidine 3',5'-diphosphate (pdTp), was, determined to 1.95-A resolution. The structures of both binary complexes, D21E bound either to Ca2+ or pdTp, were determined to 2.15- and 2.05-A, resolution, respectively. In the ternary structure, we find a 1.5-A, movement of the Ca2+ in the active site, evidence of bidentate, coordination of Ca2+ by Glu21 and inner-sphere coordination of the Ca2+ by, Glu43. Comparison of the D21E binary structures with the ternary model, shows large movements of active site side chains expected to play a direct, role in catalysis. Glu43 moves in the binary nucleotide complex, whereas, Arg35 is oriented differently in the binary metal complex. From these, changes, we seek to explain the basis for the 1500-fold decrease in Vmax, of D21E relative to wild-type SNase (WT). Furthermore, we describe direct, structural evidence which explains the cooperativity of Ca2+ and pdTp, binding in the ternary complex relative to that of the binary complexes.
<StructureSection load='2enb' size='340' side='right'caption='[[2enb]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2enb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ENB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ENB 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]] 2.05&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</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=2enb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2enb OCA], [https://pdbe.org/2enb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2enb RCSB], [https://www.ebi.ac.uk/pdbsum/2enb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2enb ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
== 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/en/2enb_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=2enb ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2ENB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] with THP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2ENB OCA].
*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structures of the binary Ca2+ and pdTp complexes and the ternary complex of the Asp21--&gt;Glu mutant of staphylococcal nuclease. Implications for catalysis and ligand binding., Libson AM, Gittis AG, Lattman EE, Biochemistry. 1994 Jul 5;33(26):8007-16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8025105 8025105]
[[Category: Large Structures]]
[[Category: Micrococcal nuclease]]
[[Category: Single protein]]
[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
[[Category: Gittis, A.]]
[[Category: Gittis A]]
[[Category: Lattman, E.E.]]
[[Category: Lattman EE]]
[[Category: Libson, A.]]
[[Category: Libson A]]
[[Category: THP]]
[[Category: hydrolase(phosphoric diester)]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:05:06 2007''

Latest revision as of 12:19, 14 February 2024

CRYSTAL STRUCTURES OF THE BINARY CA2+ AND PDTP COMPLEXES AND THE TERNARY COMPLEX OF THE ASP 21->GLU MUTANT OF STAPHYLOCOCCAL NUCLEASE. IMPLICATIONS FOR CATALYSIS AND LIGAND BINDINGCRYSTAL STRUCTURES OF THE BINARY CA2+ AND PDTP COMPLEXES AND THE TERNARY COMPLEX OF THE ASP 21->GLU MUTANT OF STAPHYLOCOCCAL NUCLEASE. IMPLICATIONS FOR CATALYSIS AND LIGAND BINDING

Structural highlights

2enb is a 1 chain structure with sequence from Staphylococcus aureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.05Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NUC_STAAU Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2enb, resolution 2.05Å

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