1nb2: Difference between revisions

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New page: left|200px<br /><applet load="1nb2" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nb2, resolution 2.2Å" /> '''Crystal Structure of ...
 
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[[Image:1nb2.jpg|left|200px]]<br /><applet load="1nb2" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1nb2, resolution 2.2&Aring;" />
'''Crystal Structure of Nucleoside Diphosphate Kinase from Bacillus Halodenitrificans'''<br />


==Overview==
==Crystal Structure of Nucleoside Diphosphate Kinase from Bacillus Halodenitrificans==
We found that when grown under anaerobic conditions the moderate, halophile, gram-positive bacterium Bacillus halodenitrificans (ATCC 49067), synthesizes large amounts of a polypeptide complex that contains a heme, center capable of reversibly bind nitric oxide. This complex, when exposed, to air, dissociates and reassociates into two active components, a, Mn-containing superoxide dismutase (SOD) and a nucleoside diphosphate, kinase (BhNDK). The crystal structure of this latter enzyme has been, determined at 2.2A resolution using molecular replacement method, based on, the crystal structure of Drosophila melanogaster NDK. The model contains, 149 residues of a total 150 residues and 34 water molecules. BhNDK, consists of a four-stranded antiparallel beta-sheet, whose surfaces are, partially covered by six alpha-helices, and its overall and active site, structures are similar to those of homologous enzymes. However, the, hexameric packing of BhNDK shows that this enzyme is different from both, eukaryotic and gram-negative bacteria. The need for the bacterium to, presynthesize both SOD and NDK precursors which are activated during the, anaerobic-aerobic transition is discussed.
<StructureSection load='1nb2' size='340' side='right'caption='[[1nb2]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1nb2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Virgibacillus_halodenitrificans Virgibacillus halodenitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NB2 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]] 2.2&#8491;</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=1nb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nb2 OCA], [https://pdbe.org/1nb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nb2 RCSB], [https://www.ebi.ac.uk/pdbsum/1nb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nb2 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q7SIA9_VIRHA Q7SIA9_VIRHA] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.[HAMAP-Rule:MF_00451]
== 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/nb/1nb2_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=1nb2 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1NB2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Virgibacillus_halodenitrificans Virgibacillus halodenitrificans]. Active as [http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NB2 OCA].
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structure of a nucleoside diphosphate kinase from Bacillus halodenitrificans: coexpression of its activity with a Mn-superoxide dismutase., Chen CJ, Liu MY, Chang T, Chang WC, Wang BC, Le Gall J, J Struct Biol. 2003 May;142(2):247-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12713952 12713952]
[[Category: Large Structures]]
[[Category: Nucleoside-diphosphate kinase]]
[[Category: Single protein]]
[[Category: Virgibacillus halodenitrificans]]
[[Category: Virgibacillus halodenitrificans]]
[[Category: Chang, T.]]
[[Category: Chang T]]
[[Category: Chang, W.C.]]
[[Category: Chang W-C]]
[[Category: Chen, C.J.]]
[[Category: Chen C-J]]
[[Category: Gall, J.Le.]]
[[Category: Le Gall J]]
[[Category: Liu, M.Y.]]
[[Category: Liu M-Y]]
[[Category: Wang, B.C.]]
[[Category: Wang B-C]]
[[Category: bacillus halodenitrifians]]
[[Category: nucleoside diphosphate kinase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:52:23 2007''

Latest revision as of 16:27, 13 March 2024

Crystal Structure of Nucleoside Diphosphate Kinase from Bacillus HalodenitrificansCrystal Structure of Nucleoside Diphosphate Kinase from Bacillus Halodenitrificans

Structural highlights

1nb2 is a 1 chain structure with sequence from Virgibacillus halodenitrificans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q7SIA9_VIRHA Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.[HAMAP-Rule:MF_00451]

Evolutionary Conservation

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

See Also

1nb2, resolution 2.20Å

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